LiteFold/InterPro · Datasets at Hugging Face

IPR012580

12,580

NUC153

Domain

8,338

false

This small domain is found in a novel nucleolar family [ ].

[ "GO:0005634" ]

[ "nucleus" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08159" ]

[ "NUC153" ]

[ 8338 ]

1

[]

0

[ "5wlc", "6ke6", "6lqp", "6lqq", "6lqr", "6lqu", "6lqv", "6rxu", "6rxv", "6rxx", "6rxz", "6zqb", "6zqc", "7ajt", "7d63", "7mq8", "7mq9", "9g33", "9n6v", "9n6w", "9n6x", "9n6y", "9n6z", "9n70", "9n72", "9n73" ]

26

[ "PUB00016366" ]

[ "15112237" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire." ]

[ 2004 ]

1

[]

0

null

[ "Eukaryota", "Solihabitans fulvus" ]

[ 8337, 1 ]

2

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 7, 2, 3, 3, 8, 7, 2, 5, 6, 2, 2, 12 ]

12

true

Domain

NUC153

4

IPR012582

12,582

DNA-dependent protein kinase catalytic subunit, CC3

DNAPKcs_CC3

Domain

2,150

false

This domain represents a region of the Circular Cradle segment (CC) from DNA-PKcs that covers the complete CC3 and part of CC4. This domain contains the Ku-binding site A and a the highly conserved region (HCR) II [ ]. DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joinin...

[ "GO:0006303", "GO:0005634" ]

[ "double-strand break repair via nonhomologous end joining", "nucleus" ]

[ "biological_process", "cellular_component" ]

2

[ "PFAM", "SMART" ]

[ "PF08163", "SM01344" ]

[ "DNAPKcs_CC3", "NUC194" ]

[ 2107, 2060 ]

2

[ "EC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "2.7.11.1", "R-DDI-5693571", "R-DDI-8866654", "R-GGA-351433", "R-GGA-353423", "R-HSA-1834949", "R-HSA-3270619", "R-HSA-5693571", "R-HSA-8866654", "R-MMU-5693571", "R-MMU-8866654" ]

[ "EC:2.7.11.1", "REACTOME:R-DDI-5693571", "REACTOME:R-DDI-8866654", "REACTOME:R-GGA-351433", "REACTOME:R-GGA-353423", "REACTOME:R-HSA-1834949", "REACTOME:R-HSA-3270619", "REACTOME:R-HSA-5693571", "REACTOME:R-HSA-8866654", "REACTOME:R-MMU-5693571", "REACTOME:R-MMU-8866654" ]

11

[ "5luq", "5w1r", "5y3r", "6zfp", "6zh2", "6zh4", "6zh6", "6zh8", "6zha", "6zhe", "7k0y", "7k10", "7k11", "7k17", "7k19", "7k1b", "7k1j", "7k1k", "7k1n", "7lt3", "7nfc", "7nfe", "7otm", "7otp", "7otv", "7otw", "7oty", "7sgl", "7su3", "7sud", "7tyr", "7z87"...

43

[ "PUB00098850", "PUB00098852", "PUB00098853", "PUB00098858" ]

[ "28840859", "28154079", "28652322", "33077952" ]

[ "Cryo-EM structure of human DNA-PK holoenzyme.", "DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.", "Cryo-EM structure of the DNA-PK holoenzyme.", "Dimers of DNA-PK create a stage for DNA double-strand break repair." ]

[ 2017, 2017, 2017, 2021 ]

4

[]

0

null

[ "Eukaryota" ]

[ 2150 ]

1

[ "Danio rerio", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 1, 1, 1, 5 ]

4

true

Domain

DNA-dependent protein kinase catalytic subunit, CC3

DNAPKcs_CC3

5

IPR012583

12,583

Pre-rRNA-processing protein RIX1, N-terminal

RIX1_N

Domain

3,428

false

Rix1 is a nucleoplasmic particle involved in rRNA processing/ribosome assembly [ , ]. It associates with two other proteins, Ipi1 and Ipi3, to form the RIX1 complex that allows Rea1 - the AAA ATPase - to associate with the 60S ribosomal subunit. More than 170 assembly factors are involved in the construction and matura...

[]

0

[ "PFAM" ]

[ "PF08167" ]

[ "RIX1" ]

[ 3428 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-HSA-6791226", "R-HSA-8849473", "R-MMU-6791226", "R-RNO-6791226", "R-SCE-6791226", "R-SPO-6791226" ]

[ "REACTOME:R-HSA-6791226", "REACTOME:R-HSA-8849473", "REACTOME:R-MMU-6791226", "REACTOME:R-RNO-6791226", "REACTOME:R-SCE-6791226", "REACTOME:R-SPO-6791226" ]

6

[ "6yle", "6ylh", "7uwf", "8fl2", "8fl3", "8fl4", "8ptw", "8pv4", "8pv6", "8pv8", "9dum", "9duo" ]

12

[ "PUB00073775", "PUB00073776", "PUB00073777" ]

[ "1511223", "12374754", "19737511" ]

[ "Fractionating language: different neural subsystems with different sensitive periods.", "60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm.", "The Rea1 tadpole loses its tail." ]

[ 1992, 2002, 2009 ]

3

[]

0

null

[ "Eukaryota" ]

[ 3428 ]

1

[ "Arabidopsis thaliana", "Danio rerio", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)", "Schizosaccharomyces pombe (st...

[ 7, 2, 11, 2, 1, 6, 4, 1, 1, 11 ]

10

true

Domain

Pre-rRNA-processing protein RIX1, N-terminal

RIX1_N

8

IPR012584

12,584

Nucleolar protein 11, N-terminal domain

NOL11_N

Domain

1,507

false

This entry covers a section of the β-propeller found at the N terminus of NOL11 [ ]. NOL11 is a nucleolar protein and a component of the human ribosomal small subunit (SSU) processome. It is required for the early stages of ribosome biogenesis in humans [ ]. It interacts with the C-terminal region of the known t-UTP/UT...

[ "GO:0005634" ]

[ "nucleus" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08168" ]

[ "NOL11_N" ]

[ 1507 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-BTA-6791226", "R-HSA-6790901", "R-HSA-6791226", "R-MMU-6791226" ]

[ "REACTOME:R-BTA-6791226", "REACTOME:R-HSA-6790901", "REACTOME:R-HSA-6791226", "REACTOME:R-MMU-6791226" ]

4

[ "7mq8", "7mq9", "7mqa" ]

3

[ "PUB00016366", "PUB00093458", "PUB00093459" ]

[ "15112237", "22916032", "25756904" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.", "NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing.", "The ribosome biogenesis factor Nol11 is required for optimal rDNA transc...

[ 2004, 2012, 2015 ]

3

[]

0

null

[ "Eukaryota" ]

[ 1507 ]

1

[ "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 1, 1, 3, 1, 3 ]

5

true

Domain

Nucleolar protein 11, N-terminal domain

NOL11_N

8

IPR012585

12,585

Anticodon nuclease activator Stp

Stp

Family

43

false

This family represents the anticodon nuclease activator protein Stp. Pre-existing host tRNAs are reprocessed during Bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5, by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA...

[ "GO:0004518", "GO:0050792" ]

[ "nuclease activity", "regulation of viral process" ]

[ "molecular_function", "biological_process" ]

2

[ "PFAM" ]

[ "PF08133" ]

[ "Nuclease_act" ]

[ 43 ]

1

[]

0

[]

0

[ "PUB00016404", "PUB00075346", "PUB00077554" ]

[ "3280805", "7791212", "14507369" ]

[ "Nucleotide and deduced amino acid sequence of stp: the bacteriophage T4 anticodon nuclease gene.", "Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems.", "Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite." ]

[ 1988, 1995, 2003 ]

3

[]

0

null

[ "Caudoviricetes" ]

[ 43 ]

1

[]

0

true

Family

Anticodon nuclease activator Stp

Stp

3

IPR012586

12,586

28S rRNA (cytosine-C(5))-methyltransferase repeat

NOP2_rpt

Repeat

110

false

This entry represents a characteristic repeat of 28S rRNA (cytosine-C(5))-methyltransferase (NOP2, also known as proliferating cell nuclear antigen p120), which is found in three copies [ ]. NOP2 is involved in ribosomal large subunit assembly [ , ]. It is an S-adenosyl-L-methionine-dependent methyltransferase that spe...

[]

0

[ "PFAM" ]

[ "PF08062" ]

[ "NOP2_rpt" ]

[ 110 ]

1

[ "REACTOME", "REACTOME" ]

[ "R-HSA-6790901", "R-HSA-8869496" ]

[ "REACTOME:R-HSA-6790901", "REACTOME:R-HSA-8869496" ]

2

[ "8fkt", "8fku", "8fkv", "8fkw", "8fkx", "8fky" ]

6

[ "PUB00016366", "PUB00097261", "PUB00154593" ]

[ "15112237", "24120868", "37410842" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.", "The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress.", "Principles of human pre-60<i>S</i> biogenesis." ]

[ 2004, 2013, 2023 ]

3

[]

0

null

[ "Eutheria", "Roseospira navarrensis" ]

[ 109, 1 ]

2

[ "Homo sapiens", "Mus musculus" ]

[ 1, 3 ]

2

true

Repeat

28S rRNA (cytosine-C(5))-methyltransferase repeat

NOP2_rpt

8

IPR012587

12,587

RNA helicase p68 repeat

P68_rpt

Repeat

838

false

This short region is found in two copies in RNA helicase p68 (DDX5), which is involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner [ ].

[]

0

[ "PFAM", "SMART" ]

[ "PF08061", "SM01414" ]

[ "P68HR", "P68HR" ]

[ 808, 838 ]

2

[ "EC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "3.6.4.13", "R-HSA-3899300", "R-HSA-72163", "R-HSA-9018519", "R-HSA-9682706", "R-HSA-9694686", "R-MMU-3899300", "R-MMU-72163", "R-MMU-9018519" ]

[ "EC:3.6.4.13", "REACTOME:R-HSA-3899300", "REACTOME:R-HSA-72163", "REACTOME:R-HSA-9018519", "REACTOME:R-HSA-9682706", "REACTOME:R-HSA-9694686", "REACTOME:R-MMU-3899300", "REACTOME:R-MMU-72163", "REACTOME:R-MMU-9018519" ]

9

[]

0

[ "PUB00078803" ]

[ "21343338" ]

[ "RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5' splice site." ]

[ 2011 ]

1

[]

0

null

[ "Bacteria", "Bilateria" ]

[ 3, 835 ]

2

[ "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 6, 8, 4 ]

3

true

Repeat

RNA helicase p68 repeat

P68_rpt

1

IPR012589

12,589

Plasma membrane ATPase proteolipid

Pmp1/Pmp2

Family

148

false

Pmp1 and its paralogue, Pmp2, are small single-spanning membrane proteins functioning as a regulatory subunit of the yeast plasma membrane H(+)-ATPase [ ]. Pmp1 forms a unique helix and exhibits a positively charged cytoplasmic domain that is able to specifically segregate phosphatidylserines (PSs) [ ].

[ "GO:0030234", "GO:0050790" ]

[ "enzyme regulator activity", "regulation of catalytic activity" ]

[ "molecular_function", "biological_process" ]

2

[ "PFAM" ]

[ "PF08114" ]

[ "PMP1_2" ]

[ 148 ]

1

[]

0

[]

0

[ "PUB00016522", "PUB00074621" ]

[ "8063750", "12427022" ]

[ "Two distinct genes encode small isoproteolipids affecting plasma membrane H(+)-ATPase activity of Saccharomyces cerevisiae.", "Deciphering the role of individual acyl chains in the interaction network between phosphatidylserines and a single-spanning membrane protein." ]

[ 1994, 2002 ]

2

[]

0

null

[ "Eukaryota", "Pseudomonadati" ]

[ 145, 3 ]

2

[ "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)" ]

[ 2 ]

1

true

Family

Plasma membrane ATPase proteolipid

Pmp1/Pmp2

8

IPR012590

12,590

POPLD domain

POPLD_dom

Domain

4,162

false

Ribonucleases P/MRP protein subunit POP1 is a subunit common to both ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends [ , ], and MRP ribonuclease complex, which cleaves pre-rRNA sequences [ ]. This domain is found towards the C-terminal of POP1 [ , ].

[]

0

[ "PFAM" ]

[ "PF08170" ]

[ "POPLD" ]

[ 4162 ]

1

[ "EC", "REACTOME" ]

[ "3.1.26.5", "R-HSA-6784531" ]

[ "EC:3.1.26.5", "REACTOME:R-HSA-6784531" ]

2

[ "6agb", "6ah3", "6ahr", "6ahu", "6w6v", "7c79", "7c7a" ]

7

[ "PUB00016366", "PUB00093445", "PUB00093446", "PUB00100391" ]

[ "15112237", "28115465", "30454648", "8918471" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.", "Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing.", "Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.", "hPop1: an autoantigenic protein subunit shared by ...

[ 2004, 2017, 2018, 1996 ]

4

[]

0

null

[ "Eukaryota" ]

[ 4162 ]

1

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 5, 1, 2, 2, 2, 2, 1, 3, 6, 1, 1, 7 ]

12

true

Domain

POPLD domain

POPLD_dom

6

IPR012591

12,591

PRO8NT domain

PRO8NT

Domain

4,904

false

The PRO8NT domain is found at the N terminus of pre-mRNA splicing factors of PRO8 family [ ]. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region [ ].

[ "GO:0000398" ]

[ "mRNA splicing, via spliceosome" ]

[ "biological_process" ]

1

[ "PFAM" ]

[ "PF08082" ]

[ "PRO8NT" ]

[ 4904 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-CEL-72163", "R-CEL-72165", "R-DDI-72163", "R-HSA-72163", "R-HSA-72165", "R-MMU-72163", "R-MMU-72165", "R-SPO-72163" ]

[ "REACTOME:R-CEL-72163", "REACTOME:R-CEL-72165", "REACTOME:R-DDI-72163", "REACTOME:R-HSA-72163", "REACTOME:R-HSA-72165", "REACTOME:R-MMU-72163", "REACTOME:R-MMU-72165", "REACTOME:R-SPO-72163" ]

8

[ "3jb9", "3jcm", "3jcr", "5gam", "5gan", "5gap", "5gm6", "5gmk", "5lj3", "5lj5", "5lqw", "5mps", "5mq0", "5mqf", "5nrl", "5o9z", "5wsg", "5xjc", "5y88", "5ylz", "5yzg", "5z56", "5z57", "5z58", "5zwm", "5zwo", "6ah0", "6ahd", "6bk8", "6exn", "6ff4", "6ff7"...

102

[ "PUB00016366", "PUB00044474" ]

[ "15112237", "16431982" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.", "Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome." ]

[ 2004, 2006 ]

2

[]

0

null

[ "Eukaryota" ]

[ 4904 ]

1

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 10, 1, 1, 2, 5, 3, 1, 5, 3, 1, 1, 21 ]

12

true

Domain

PRO8NT domain

PRO8NT

2

IPR012592

12,592

PROCN domain

PROCN

Domain

5,064

false

The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family [ ].

[ "GO:0000398" ]

[ "mRNA splicing, via spliceosome" ]

[ "biological_process" ]

1

[ "PFAM" ]

[ "PF08083" ]

[ "PROCN" ]

[ 5064 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-CEL-72163", "R-CEL-72165", "R-DDI-72163", "R-HSA-72163", "R-HSA-72165", "R-MMU-72163", "R-MMU-72165", "R-SPO-72163" ]

[ "REACTOME:R-CEL-72163", "REACTOME:R-CEL-72165", "REACTOME:R-DDI-72163", "REACTOME:R-HSA-72163", "REACTOME:R-HSA-72165", "REACTOME:R-MMU-72163", "REACTOME:R-MMU-72165", "REACTOME:R-SPO-72163" ]

8

[ "3jb9", "3jcm", "3jcr", "5gam", "5gan", "5gap", "5gm6", "5gmk", "5lj3", "5lj5", "5lqw", "5mps", "5mq0", "5mqf", "5nrl", "5o9z", "5wsg", "5xjc", "5y88", "5ylz", "5yzg", "5z56", "5z57", "5z58", "5zwm", "5zwo", "6ah0", "6ahd", "6bk8", "6exn", "6ff4", "6ff7"...

103

[ "PUB00016366" ]

[ "15112237" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire." ]

[ 2004 ]

1

[]

0

null

[ "Eukaryota" ]

[ 5064 ]

1

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 10, 1, 1, 2, 5, 3, 1, 6, 3, 1, 1, 30 ]

12

true

Domain

PROCN domain

PROCN

8

IPR012596

12,596

Bacteriophage T4, Y12G

Phage_T4_Y12G

Family

439

false

Proteins in this family are bacteriophage Y12G proteins. Gene Y12G encodes a 17.1kDa protein in Gp30-rIII intergenic region, which in T4 is a 75 amino acid basic peptide which has a C terminus rich in charged amino acids [ ][ ].

[]

0

[ "PFAM" ]

[ "PF08010" ]

[ "Phage_30_3" ]

[ 439 ]

1

[]

0

[]

0

[ "PUB00016570", "PUB00017073" ]

[ "8088550", "9272856" ]

[ "Cloning and expression of genes from the genomic region between genes cd and 30 of bacteriophage T4.", "A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within gene 30.3 by one position downstream." ]

[ 1994, 1997 ]

2

[]

0

null

[ "Bacteria", "Cylicocyclus nassatus", "Viruses", "marine sediment metagenome" ]

[ 76, 2, 357, 4 ]

4

[]

0

true

Family

Bacteriophage T4, Y12G

Phage_T4_Y12G

4

IPR012598

12,598

Plasmodium-MYXSPDY

Plasmod_MYXSPDY

Repeat

54

false

This repeat is found in hypothetical Plasmodium proteins.

[]

0

[ "PFAM" ]

[ "PF07981" ]

[ "Plasmod_MYXSPDY" ]

[ 54 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Plasmodium falciparum" ]

[ 3, 51 ]

2

[]

0

true

Repeat

Plasmodium-MYXSPDY

Plasmod_MYXSPDY

5

IPR012599

12,599

Peptidase C1A, propeptide

Propeptide_C1A

Domain

3,565

false

This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as in...

[ "GO:0004197", "GO:0050790" ]

[ "cysteine-type endopeptidase activity", "regulation of catalytic activity" ]

[ "molecular_function", "biological_process" ]

2

[ "PFAM" ]

[ "PF08127" ]

[ "Propeptide_C1" ]

[ 3565 ]

1

[ "EC", "GP", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACT...

[ "3.4.22.1", "GenProp1728", "R-BTA-1442490", "R-BTA-1679131", "R-BTA-2132295", "R-BTA-6798695", "R-HSA-1442490", "R-HSA-1679131", "R-HSA-2022090", "R-HSA-2132295", "R-HSA-6798695", "R-HSA-9766229", "R-MMU-1442490", "R-MMU-1679131", "R-MMU-2022090", "R-MMU-2132295", "R-MMU-6798695", ...

[ "EC:3.4.22.1", "GP:GenProp1728", "REACTOME:R-BTA-1442490", "REACTOME:R-BTA-1679131", "REACTOME:R-BTA-2132295", "REACTOME:R-BTA-6798695", "REACTOME:R-HSA-1442490", "REACTOME:R-HSA-1679131", "REACTOME:R-HSA-2022090", "REACTOME:R-HSA-2132295", "REACTOME:R-HSA-6798695", "REACTOME:R-HSA-9766229", ...

30

[ "1mir", "1pbh", "2pbh", "3pbh", "4i04" ]

5

[ "PUB00024019", "PUB00027359" ]

[ "7890671", "8740363" ]

[ "Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design.", "Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion." ]

[ 1995, 1996 ]

2

[]

0

null

[ "Eukaryota" ]

[ 3565 ]

1

[ "Arabidopsis thaliana", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Zea mays" ]

[ 14, 3, 1, 24, 3, 4, 5, 7 ]

8

true

Domain

Peptidase C1A, propeptide

Propeptide_C1A

7

IPR012600

12,600

Gingipain propeptide

Propeptide_C25

Domain

712

false

Gingipains are proteinases from Porphyromonas gingivalis, a major pathogen associated with chronic periodontitis. They belong to MEROPS peptidase family C25. There are three types: Arg-specific proteinases RgpA, and RgpB, and the Lys-specific proteinase Kgp. All three gingipain precursors contain a propeptide of around...

[ "GO:0004197" ]

[ "cysteine-type endopeptidase activity" ]

[ "molecular_function" ]

1

[ "PFAM" ]

[ "PF08126" ]

[ "Propeptide_C25" ]

[ 712 ]

1

[ "EC" ]

[ "3.4.22" ]

[ "EC:3.4.22" ]

1

[ "4ief", "5mun" ]

2

[ "PUB00075615" ]

[ "23762374" ]

[ "Propeptide-mediated inhibition of cognate gingipain proteinases." ]

[ 2013 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Chrysochromulina tobinii", "unclassified sequences" ]

[ 18, 602, 1, 91 ]

4

[]

0

true

Domain

Gingipain propeptide

Propeptide_C25

6

IPR012601

12,601

Spermatozal protamine type

Spermatozal_protamine_typ

Family

2

false

This entry consists of the spermatozal protamines. Spermatozal protamines play an important role in remodelling of the sperm chromatin during mammalian spermiogenesis. Nuclear elongation and chromatin condensation are concomitant with modifications in the basic protein complement associated with DNA. Somatic histones a...

[ "GO:0003677", "GO:0035092", "GO:0000228" ]

[ "DNA binding", "sperm DNA condensation", "nuclear chromosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "PFAM" ]

[ "PF08188" ]

[ "Protamine_3" ]

[ 2 ]

1

[]

0

[]

0

[ "PUB00016391" ]

[ "12672123" ]

[ "Expression of mammalian spermatozoal nucleoproteins." ]

[ 2003 ]

1

[]

0

null

[ "Hydrolagus colliei" ]

[ 2 ]

1

[]

0

true

Family

Spermatozal protamine type

Spermatozal_protamine_typ

1

IPR012602

12,602

PyrBI operon leader peptide

PyrBI_leader

Family

519

false

This family consists of the pyrBI operon leader peptides. The expression of the pyrBI operon, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase. is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism. In this mechanism, the concentration of...

[ "GO:0019856" ]

[ "pyrimidine nucleobase biosynthetic process" ]

[ "biological_process" ]

1

[ "PFAM", "PIRSF" ]

[ "PF08052", "PIRSF003249" ]

[ "PyrBI_leader", "PyrBI_leader" ]

[ 519, 302 ]

2

[]

0

[]

0

[ "PUB00016587" ]

[ "7517939" ]

[ "Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12." ]

[ 1994 ]

1

[]

0

null

[ "Gammaproteobacteria" ]

[ 519 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

PyrBI operon leader peptide

PyrBI_leader

4

IPR012603

12,603

ARID4A/B, PWWP domain

ARID4A/B_PWWP

Domain

2,907

false

This is the PWWD domain which is found N-terminal to the ARID/BRIGHT domain in proteins of the Retinoblastoma-binding protein 1 family [ , ]. Retinoblastoma-binding protein 1 (RBBP1, also known as (ARID4A) AT-rich interactive domain-containing protein 4A) and RBBP1-like 1 (RBBP1L1, also known as (ARID4B) AT-rich intera...

[]

0

[ "PFAM" ]

[ "PF08169" ]

[ "RBB1NT" ]

[ 2907 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-HSA-3214815", "R-HSA-427413", "R-HSA-9679191", "R-MMU-3214815", "R-RNO-3214815" ]

[ "REACTOME:R-HSA-3214815", "REACTOME:R-HSA-427413", "REACTOME:R-HSA-9679191", "REACTOME:R-MMU-3214815", "REACTOME:R-RNO-3214815" ]

5

[ "2yrv", "6l87", "7v8n" ]

3

[ "PUB00016366", "PUB00055474", "PUB00069483", "PUB00069484", "PUB00103212" ]

[ "15112237", "12724404", "23487765", "22693453", "34506790" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.", "Identification and characterization of three new components of the mSin3A corepressor complex.", "ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways.", "Allelic variation and d...

[ 2004, 2003, 2013, 2012, 2021 ]

5

[]

0

null

[ "Opisthokonta" ]

[ 2907 ]

1

[ "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 13, 1, 5, 6, 7 ]

5

true

Domain

ARID4A/B, PWWP domain

ARID4A/B_PWWP

3

IPR012604

12,604

RBM1CTR

Domain

1,476

false

This region is found in RBM1-like RNA binding hnRNPs [ ].

[]

0

[ "PFAM" ]

[ "PF08081" ]

[ "RBM1CTR" ]

[ 1476 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-HSA-72163", "R-HSA-72203", "R-HSA-9013418", "R-HSA-9013422", "R-HSA-9696264", "R-HSA-9696270", "R-HSA-9696273", "R-MMU-72163", "R-MMU-72203", "R-MMU-9013418", "R-MMU-9013422", "R-MMU-9696264", "R-MMU-9696270", "R-MMU-9696273", "R-RNO-72163", "R-RNO-72203", "R-RNO-9013418", "R-RN...

[ "REACTOME:R-HSA-72163", "REACTOME:R-HSA-72203", "REACTOME:R-HSA-9013418", "REACTOME:R-HSA-9013422", "REACTOME:R-HSA-9696264", "REACTOME:R-HSA-9696270", "REACTOME:R-HSA-9696273", "REACTOME:R-MMU-72163", "REACTOME:R-MMU-72203", "REACTOME:R-MMU-9013418", "REACTOME:R-MMU-9013422", "REACTOME:R-MMU-...

21

[]

0

[ "PUB00016366" ]

[ "15112237" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire." ]

[ 2004 ]

1

[]

0

null

[ "Bilateria" ]

[ 1476 ]

1

[ "Danio rerio", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 4, 22, 6, 14 ]

4

true

Domain

RBM1CTR

4

IPR012605

12,605

RepA1 leader peptide Tap

RepA1_leader_peptide_Tap

Family

376

false

This entry represents of the RepA1 leader peptide known as Tap found in IncFII plasmids. The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to t...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF08048", "TIGR03475" ]

[ "RepA1_leader", "tap_IncFII_lead" ]

[ 376, 370 ]

2

[]

0

[]

0

[ "PUB00016461", "PUB00042990" ]

[ "1447133", "1378398" ]

[ "Expression of the repA1 gene of IncFII plasmid NR1 is translationally coupled to expression of an overlapping leader peptide.", "Replication control of plasmid R1: RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation." ]

[ 1992, 1992 ]

2

[]

0

null

[ "Bacteria" ]

[ 376 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

RepA1 leader peptide Tap

RepA1_leader_peptide_Tap

4

IPR012606

12,606

Small ribosomal subunit protein uS15, N-terminal

Ribosomal_uS15_N

Domain

6,611

false

This domain is found at the N terminus of ribosomal uS15 proteins. Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in ac...

[ "GO:0003735", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "translation", "ribosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "PFAM", "SMART" ]

[ "PF08069", "SM01386" ]

[ "Ribosomal_S13_N", "Ribosomal_S13_N" ]

[ 6603, 6535 ]

2

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-156827", "R-BTA-1799339", "R-BTA-6791226", "R-BTA-72649", "R-BTA-72689", "R-BTA-72695", "R-BTA-72702", "R-BTA-72706", "R-BTA-975956", "R-BTA-975957", "R-CEL-156827", "R-CEL-1799339", "R-CEL-72649", "R-CEL-72689", "R-CEL-72695", "R-CEL-72702", "R-CEL-72706", "R-CEL-975956", ...

[ "REACTOME:R-BTA-156827", "REACTOME:R-BTA-1799339", "REACTOME:R-BTA-6791226", "REACTOME:R-BTA-72649", "REACTOME:R-BTA-72689", "REACTOME:R-BTA-72695", "REACTOME:R-BTA-72702", "REACTOME:R-BTA-72706", "REACTOME:R-BTA-975956", "REACTOME:R-BTA-975957", "REACTOME:R-CEL-156827", "REACTOME:R-CEL-179933...

100

[ "3j6x", "3j6y", "3j77", "3j78", "3j7a", "3j7p", "3j7r", "3j80", "3j81", "3jag", "3jah", "3jai", "3jaj", "3jam", "3jan", "3jap", "3jbn", "3jbo", "3jbp", "4bts", "4d5l", "4d61", "4kzx", "4kzy", "4kzz", "4u3m", "4u3n", "4u3u", "4u4n", "4u4o", "4u4q", "4u4r"...

635

[ "PUB00007068", "PUB00007069", "PUB00007070", "PUB00016366" ]

[ "11297922", "11290319", "11114498", "15112237" ]

[ "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal proteins.", "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire." ]

[ 2001, 2001, 2000, 2004 ]

4

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 933, 3, 5629, 46 ]

4

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 5, 1, 1, 2, 3, 4, 1, 8, 17, 1, 1, 15 ]

12

true

Domain

Small ribosomal subunit protein uS15, N-terminal

Ribosomal_uS15_N

4

IPR012607

12,607

Ribosome hibernation factor SRA

SRA-like

Family

631

false

This family represents the stationary-phase-induced ribosome-associated protein SRA also known as protein D. This protein was originally thought to be a ribosomal protein [ ]. More recently it was shown that this is a bona fide ribosome hibernation factor that together with the factors Rmf, Hpf and RaiA is bound to the...

[ "GO:0006412" ]

[ "translation" ]

[ "biological_process" ]

1

[ "NCBIFAM", "PFAM" ]

[ "NF007473", "PF08136" ]

[ "PRK10057.1", "SRA_like" ]

[ 629, 609 ]

2

[]

0

[]

0

[ "PUB00016523", "PUB00104534", "PUB00151185" ]

[ "11168583", "11292794", "36834540" ]

[ "Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli.", "Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase.", "Ribosome Protein Composition Mediates Translation during the <i>Escherichia coli</i> Stationary Phase...

[ 2000, 2001, 2023 ]

3

[]

0

null

[ "Escherichia phage vB_EcoS Sa179lw", "Gammaproteobacteria" ]

[ 1, 630 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Ribosome hibernation factor SRA

SRA-like

1

IPR012608

12,608

Sex peptide

Sex_peptide

Family

29

false

This family consists of Sex Peptides (SP) that are found in Drosophila. On mating, Drosophila females decreases her remating rate and increases her egg-laying rate due, in part, to the transfer of SP from the male to the female. SP are found in seminal fluids transferred from the male to the female during mating. The m...

[ "GO:0005179", "GO:0046008", "GO:0005576" ]

[ "hormone activity", "regulation of female receptivity, post-mating", "extracellular region" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "PFAM" ]

[ "PF08138" ]

[ "Sex_peptide" ]

[ 29 ]

1

[]

0

[ "2laq" ]

1

[ "PUB00016438" ]

[ "12913117" ]

[ "Sex peptide and the sperm effect in Drosophila melanogaster." ]

[ 2003 ]

1

[]

0

null

[ "Sophophora" ]

[ 29 ]

1

[ "Drosophila melanogaster" ]

[ 6 ]

1

true

Family

Sex peptide

Sex_peptide

5

IPR012609

12,609

Sporulation stage V, protein M

Spore_V_M

Family

944

false

This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber of the sporangium during the process of sporulation in B. subtilis. SpoVM forms an amphipathic α-helix and is recruited to the...

[]

0

[ "NCBIFAM", "PFAM" ]

[ "NF033436", "PF08183" ]

[ "SpoVM_broad", "SpoV" ]

[ 909, 846 ]

2

[]

0

[ "2mvh", "2mvj" ]

2

[ "PUB00016502", "PUB00105103", "PUB00105104" ]

[ "12562810", "19265022", "25625300" ]

[ "Subcellular localization of a small sporulation protein in Bacillus subtilis.", "Geometric cue for protein localization in a bacterium.", "Modeling curvature-dependent subcellular localization of the small sporulation protein SpoVM in Bacillus subtilis." ]

[ 2003, 2009, 2015 ]

3

[]

0

null

[ "Bacillota", "Trypanosomatidae", "bioreactor metagenome" ]

[ 913, 30, 1 ]

3

[]

0

true

Family

Sporulation stage V, protein M

Spore_V_M

3

IPR012610

12,610

Small acid-soluble spore protein, SspH

SASP_SspH

Family

2,197

false

This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor fo...

[ "GO:0030436", "GO:0042601" ]

[ "asexual sporulation", "endospore-forming forespore" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "PFAM", "NCBIFAM" ]

[ "MF_00667", "PF08141", "TIGR02861" ]

[ "SspH", "SspH", "SASP_H" ]

[ 1741, 2197, 1897 ]

3

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00016477" ]

[ "10333516" ]

[ "Regulation of four genes encoding small, acid-soluble spore proteins in Bacillus subtilis." ]

[ 1999 ]

1

[]

0

null

[ "Bacteria", "Phytophthora kernoviae 00238/432", "ecological metagenomes" ]

[ 2188, 1, 8 ]

3

[]

0

true

Family

Small acid-soluble spore protein, SspH

SASP_SspH

5

IPR012611

12,611

Small acid-soluble spore protein, SspK

SASP_SspK

Family

638

false

This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspK gene is monocistronic and transcription is primarily by the RNA ...

[ "GO:0030436", "GO:0042601" ]

[ "asexual sporulation", "endospore-forming forespore" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "PFAM", "NCBIFAM" ]

[ "MF_01504", "PF08176", "TIGR03091" ]

[ "SspK", "SspK", "SASP_sspK" ]

[ 532, 638, 496 ]

3

[]

0

[]

0

[ "PUB00016550" ]

[ "10806362" ]

[ "Analysis of the regulation and function of five genes encoding small, acid-soluble spore proteins of Bacillus subtilis." ]

[ 2000 ]

1

[]

0

null

[ "Bacillales" ]

[ 638 ]

1

[]

0

true

Family

Small acid-soluble spore protein, SspK

SASP_SspK

4

IPR012612

12,612

Small acid-soluble spore protein, SspN

SASP_SspN

Family

558

false

This family consists of the small acid-soluble spore protein (SASP) N type (sspN). SspN is a 48 residues protein that is expressed only in the forespore compartment of sporulating Bacillus subtilis. The sspN gene is recognised equally by both sigma-G and sigma-F. The role of SspN is still not well-defined [ ].

[ "GO:0030436", "GO:0042601" ]

[ "asexual sporulation", "endospore-forming forespore" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "NCBIFAM", "PFAM" ]

[ "MF_01505", "NF006904", "PF08177" ]

[ "SspN", "PRK09398.1", "SspN" ]

[ 450, 520, 558 ]

3

[]

0

[]

0

[ "PUB00016477" ]

[ "10333516" ]

[ "Regulation of four genes encoding small, acid-soluble spore proteins in Bacillus subtilis." ]

[ 1999 ]

1

[]

0

null

[ "Bacillales" ]

[ 558 ]

1

[]

0

true

Family

Small acid-soluble spore protein, SspN

SASP_SspN

6

IPR012613

12,613

Small acid-soluble spore protein, SspO

SASP_SspO

Family

616

false

This family consists of the small acid-soluble spore proteins (SASP) O type (sspO). SspO (originally cotK) are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspO is the first gene in a likely operon with sspP and transcription of...

[ "GO:0030436", "GO:0042601" ]

[ "asexual sporulation", "endospore-forming forespore" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "PFAM", "NCBIFAM" ]

[ "MF_00665", "PF08175", "TIGR02864" ]

[ "SspO", "SspO", "spore_sspO" ]

[ 401, 614, 614 ]

3

[]

0

[]

0

[ "PUB00016550" ]

[ "10806362" ]

[ "Analysis of the regulation and function of five genes encoding small, acid-soluble spore proteins of Bacillus subtilis." ]

[ 2000 ]

1

[]

0

null

[ "Bacillota" ]

[ 616 ]

1

[]

0

true

Family

Small acid-soluble spore protein, SspO

SASP_SspO

4

IPR012614

12,614

Small acid-soluble spore protein, SspP

SASP_SspP

Family

972

false

This family consists of the small acid-soluble spore proteins (SASP) P type (sspP). sspP is expressed only in the forespore compartment of the sporulating cell. sspP is also expressed under sigma-G control from the same promoter as sspO. Mutations deleting sspP causes no discernible effect on sporulation, spore propert...

[ "GO:0030435" ]

[ "sporulation resulting in formation of a cellular spore" ]

[ "biological_process" ]

1

[ "HAMAP", "PFAM" ]

[ "MF_00666", "PF08179" ]

[ "SspP", "SspP" ]

[ 408, 972 ]

2

[]

0

[]

0

[ "PUB00016550" ]

[ "10806362" ]

[ "Analysis of the regulation and function of five genes encoding small, acid-soluble spore proteins of Bacillus subtilis." ]

[ 2000 ]

1

[]

0

null

[ "Bacillota" ]

[ 972 ]

1

[]

0

true

Family

Small acid-soluble spore protein, SspP

SASP_SspP

7

IPR012615

12,615

Trematode Eggshell Synthesis

TES

Family

248

false

Proteins in this family have been identified in a number of distantly related species of trematodes. This protein is crucial for eggshell synthesis in trematodes [ ].

[]

0

[ "PFAM" ]

[ "PF08034" ]

[ "TES" ]

[ 248 ]

1

[]

0

[]

0

[ "PUB00062148" ]

[ "9279584" ]

[ "A novel cDNA clone of Schistosoma japonicum encoding the 34,000 Dalton eggshell precursor protein." ]

[ 1997 ]

1

[]

0

null

[ "Digenea" ]

[ 248 ]

1

[]

0

true

Family

Trematode Eggshell Synthesis

TES

1

IPR012616

12,616

CDP-alcohol phosphatidyltransferase, C-terminal

CDP-OH_P_trans_C

Domain

2,160

false

This domain is found on CDP-alcohol phosphatidyltransferases. These enzymes catalyse the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond.

[]

0

[ "PFAM" ]

[ "PF08009" ]

[ "CDP-OH_P_tran_2" ]

[ 2160 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 2142, 4, 14 ]

3

[]

0

true

Domain

CDP-alcohol phosphatidyltransferase, C-terminal

CDP-OH_P_trans_C

7

IPR012617

12,617

Apoptosis-antagonizing transcription factor, C-terminal

AATF_C

Domain

4,172

false

This C-terminal domain is found in apoptosis-antagonizing transcription factor (AATF) proteins [ ]. This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription.

[ "GO:0005634" ]

[ "nucleus" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08164" ]

[ "TRAUB" ]

[ 4172 ]

1

[ "REACTOME" ]

[ "R-HSA-193648" ]

[ "REACTOME:R-HSA-193648" ]

1

[ "6lqp", "6lqq", "6lqr", "6lqu", "6lqv", "6rxu", "6rxv", "6rxx", "6rxz", "6zqb", "6zqc", "7ajt", "7d63", "7mq8", "7mq9", "7suk", "9g33", "9n6v", "9n6w", "9n6x", "9n6y", "9n6z", "9n70", "9n72", "9n73" ]

25

[ "PUB00016366" ]

[ "15112237" ]

[ "Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire." ]

[ 2004 ]

1

[]

0

null

[ "Eukaryota" ]

[ 4172 ]

1

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 7, 1, 6, 1, 8, 2, 1, 2, 10, 1, 1, 13 ]

12

true

Domain

Apoptosis-antagonizing transcription factor, C-terminal

AATF_C

2

IPR012618

12,618

Tetracycline resistance leader peptide, TetL

Tet-R_leader_TetL

Family

35

false

The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can revers...

[ "GO:0046677" ]

[ "response to antibiotic" ]

[ "biological_process" ]

1

[ "NCBIFAM", "PFAM" ]

[ "NF033685", "PF08050" ]

[ "Tet_leader_L", "Tet_res_leader" ]

[ 34, 35 ]

2

[]

0

[]

0

[ "PUB00001751", "PUB00035982", "PUB00035983", "PUB00035984", "PUB00035985", "PUB00035990", "PUB00105242" ]

[ "2996983", "16887689", "15837373", "1423217", "15944459", "9988470", "11807047" ]

[ "Nucleotide sequence of the tetracycline resistance gene of pTHT15, a thermophilic Bacillus plasmid: comparison with staphylococcal TcR controls.", "Acquired tetracycline and/or macrolide-lincosamides-streptogramin resistance in anaerobes.", "Update on acquired tetracycline resistance genes.", "Bacterial resi...

[ 1985, 2003, 2005, 1992, 2005, 1998, 2002 ]

7

[]

0

null

[ "Bacteria" ]

[ 35 ]

1

[]

0

true

Family

Tetracycline resistance leader peptide, TetL

Tet-R_leader_TetL

4

IPR012620

12,620

Tryptophanese operon leader peptide

Trp_operon_leader_peptide

Family

213

false

This entry defines the apparent leader peptides of tryptophanase operons in Escherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae, and related species. It has been suggested that these peptides act in cis to alter the behaviour of the translating ribosome [ ]. The tryptophanese (tna) opero...

[ "GO:0031554", "GO:0031556" ]

[ "regulation of termination of DNA-templated transcription", "transcriptional attenuation by ribosome" ]

[ "biological_process", "biological_process" ]

2

[ "PFAM", "NCBIFAM" ]

[ "PF08053", "TIGR02616" ]

[ "Tna_leader", "tnaC_leader" ]

[ 87, 212 ]

2

[ "GP" ]

[ "GenProp0456" ]

[ "GP:GenProp0456" ]

1

[ "4uy8", "5m6s", "6i0y", "7o19", "7o1a", "7o1c", "7oiz", "7oj0" ]

8

[ "PUB00016514", "PUB00020755" ]

[ "14563884", "9045840" ]

[ "A transcriptional pause synchronizes translation with transcription in the tryptophanase operon leader region.", "Regulation of the Escherichia coli tna operon: nascent leader peptide control at the tnaC stop codon." ]

[ 2003, 1997 ]

2

[]

0

null

[ "Bacteria" ]

[ 213 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tryptophanese operon leader peptide

Trp_operon_leader_peptide

2

IPR012621

12,621

Mitochondrial import receptor subunit TOM7

Tom7

Family

2,512

false

This family consists of mitochondrial import receptor subunit TOM7. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membr...

[ "GO:0030150", "GO:0005742" ]

[ "protein import into mitochondrial matrix", "mitochondrial outer membrane translocase complex" ]

[ "biological_process", "cellular_component" ]

2

[ "PFAM" ]

[ "PF08038" ]

[ "Tom7" ]

[ 2512 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-BTA-5205685", "R-HSA-1268020", "R-HSA-5205685", "R-MMU-5205685", "R-SSC-5205685" ]

[ "REACTOME:R-BTA-5205685", "REACTOME:R-HSA-1268020", "REACTOME:R-HSA-5205685", "REACTOME:R-MMU-5205685", "REACTOME:R-SSC-5205685" ]

5

[ "6jnf", "6ucu", "6ucv", "7ck6", "7cp9", "7vby", "7vc4", "7vd2", "7vdd", "8b4i", "8hco", "8w5j", "8w5k", "8xdn", "8xkw", "8xkx", "8xky", "8xva", "9eih", "9eii", "9eij", "9etm", "9i6b", "9i7p", "9i7s", "9i7t", "9j99", "9jxv" ]

28

[ "PUB00016558" ]

[ "9642296" ]

[ "Unique composition of the preprotein translocase of the outer mitochondrial membrane from plants." ]

[ 1998 ]

1

[]

0

null

[ "Eukaryota" ]

[ 2512 ]

1

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 6, 1, 1, 1, 3, 1, 1, 6, 1, 1, 1, 4 ]

12

true

Family

Mitochondrial import receptor subunit TOM7

Tom7

9

IPR012622

12,622

Potassium channel toxin gamma/Ergtoxin

Ergtoxin

Family

35

false

The Ergtoxin (ErgTx) family is a class of peptides from scorpion venom that specifically block ERG (ether-a-go-go-related gene) K+ channels of the nerve, heart and endocrine cells [ , , ].

[ "GO:0019870", "GO:0005576" ]

[ "potassium channel inhibitor activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM", "PROSITE" ]

[ "PF08086", "PS60026" ]

[ "Toxin_17", "ERGTX" ]

[ 35, 35 ]

2

[ "PROSITEDOC" ]

[ "PDOC60026" ]

[ "PROSITEDOC:PDOC60026" ]

1

[ "1ne5", "1px9" ]

2

[ "PUB00029028", "PUB00033819", "PUB00033820" ]

[ "12650941", "11023354", "12459475" ]

[ "Solution structure of CnErg1 (Ergtoxin), a HERG specific scorpion toxin.", "Disulfide bridges of ergtoxin, a member of a new sub-family of peptide blockers of the ether-a-go-go-related K+ channel.", "A large number of novel Ergtoxin-like genes and ERG K+-channels blocking peptides from scorpions of the genus C...

[ 2003, 2000, 2002 ]

3

[]

0

null

[ "Centruroides" ]

[ 35 ]

1

[]

0

true

Family

Potassium channel toxin gamma/Ergtoxin

Ergtoxin

7

IPR012624

12,624

Conotoxin I-superfamily

Toxin_19

Family

27

false

This family consists of the I-superfamily of conotoxins. This is a new class of peptides in the venom of some Conus species. These toxins are characterised by four disulphide bridges and inhibit of modify ion channels of nerve cells. The I-superfamily conotoxins is found in five or six major clades of cone snails and c...

[]

0

[ "PFAM" ]

[ "PF08088" ]

[ "Toxin_19" ]

[ 27 ]

1

[]

0

[ "2jry", "2jtu", "2p4l" ]

3

[ "PUB00016427" ]

[ "15450929" ]

[ "Novel conopeptides of the I-superfamily occur in several clades of cone snails." ]

[ 2004 ]

1

[]

0

null

[ "Protostomia" ]

[ 27 ]

1

[ "Drosophila melanogaster" ]

[ 2 ]

1

true

Family

Conotoxin I-superfamily

Toxin_19

2

IPR012625

12,625

Huwentoxin-II-like

Hwtx-2-like

Family

142

false

This entry mainly consists of the huwentoxin-II (HWTX-II) family of toxins secreted by spiders. These toxins are found in venom that secreted from the bird spider Selenocosmia huwena Wang. The HWTX-II adopts a novel scaffold different from the ICK motif that is found in other huwentoxins. HWTX-II consists of 37 amino a...

[ "GO:0090729", "GO:0005576" ]

[ "toxin activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM", "PROSITE" ]

[ "PF08089", "PS60022" ]

[ "Toxin_20", "HWTX_2" ]

[ 141, 102 ]

2

[ "PROSITEDOC" ]

[ "PDOC60022" ]

[ "PROSITEDOC:PDOC60022" ]

1

[ "1i25", "2kgh" ]

2

[ "PUB00016370" ]

[ "15066414" ]

[ "An overview of peptide toxins from the venom of the Chinese bird spider Selenocosmia huwena Wang [=Ornithoctonus huwena (Wang)]." ]

[ 2004 ]

1

[]

0

null

[ "Araneae" ]

[ 142 ]

1

[]

0

true

Family

Huwentoxin-II-like

Hwtx-2-like

9

IPR012626

12,626

Spider insecticidal peptide

Spider_insecticidal_peptide

Family

12

false

This family consists of insecticidal peptides isolated from venom of spiders of Aptostichus schlingeri (Trap-door spider) and Calisoga sp. Nine insecticidal peptides were isolated from the venom of the A. schlinger spider and seven of these toxins cause flaccid paralysis to insect larvae within 10 min of injection. How...

[ "GO:0005576" ]

[ "extracellular region" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08091" ]

[ "Toxin_21" ]

[ 12 ]

1

[]

0

[ "2m36" ]

1

[ "PUB00016363", "PUB00075632" ]

[ "1440641", "23473802" ]

[ "Identification of insecticidal peptides from venom of the trap-door spider, Aptostichus schlingeri (Ctenizidae).", "The insecticidal neurotoxin Aps III is an atypical knottin peptide that potently blocks insect voltage-gated sodium channels." ]

[ 1992, 2013 ]

2

[]

0

null

[ "Bacteria", "Opisthokonta" ]

[ 3, 9 ]

2

[]

0

true

Family

Spider insecticidal peptide

Spider_insecticidal_peptide

7

IPR012628

12,628

Magi 5 toxic peptide

Toxin_23

Family

30

false

This family consists of toxic peptides (Magi 5) found in the venom of the Hexathelidae spider. Magi 5 is the first spider toxin with binding affinity to site 4 of a mammalian sodium channel and the toxin has an insecticidal effect on larvae, causing paralysis when injected into the larvae. This entry also includes some...

[ "GO:0019871", "GO:0005576" ]

[ "sodium channel inhibitor activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM" ]

[ "PF08093" ]

[ "Toxin_23" ]

[ 30 ]

1

[]

0

[ "1g9p", "1hp3", "2gx1" ]

3

[]

0

[]

0

null

[ "Opisthokonta", "Rhodanobacter denitrificans" ]

[ 29, 1 ]

2

[]

0

true

Family

Magi 5 toxic peptide

Toxin_23

5

IPR012629

12,629

Conotoxin TVIIAGS

Conotoxin_TVIIAGS

Family

3

false

This family consists of conotoxins isolated from the venom of cone snail Conus tulipa and Conus geographus. Conotoxin TVIIA, isolated from Conus tulipa displays little sequence homology with other well-characterised pharmacological classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geo...

[ "GO:0019871", "GO:0005576" ]

[ "sodium channel inhibitor activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM" ]

[ "PF08094" ]

[ "Toxin_24" ]

[ 3 ]

1

[]

0

[ "1ag7", "1eyo" ]

2

[ "PUB00016551" ]

[ "10903496" ]

[ "Conotoxin TVIIA, a novel peptide from the venom of Conus tulipa 1. Isolation, characterization and chemical synthesis." ]

[ 2000 ]

1

[]

0

null

[ "Gastridium" ]

[ 3 ]

1

[]

0

true

Family

Conotoxin TVIIAGS

Conotoxin_TVIIAGS

6

IPR012631

12,631

Conotoxin T-superfamily

Toxin_26

Family

2

false

This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding typ...

[ "GO:0005576" ]

[ "extracellular region" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08097" ]

[ "Toxin_26" ]

[ 2 ]

1

[]

0

[]

0

[ "PUB00016378" ]

[ "10521453" ]

[ "The T-superfamily of conotoxins." ]

[ 1999 ]

1

[]

0

null

[ "Conus aulicus" ]

[ 2 ]

1

[]

0

true

Family

Conotoxin T-superfamily

Toxin_26

3

IPR012632

12,632

Scorpion calcine

Scorpion_calcine

Family

93

false

Toxins of the scorpion calcine family bind directly to ryanodine receptors (RyRs), intracellular channel targets of the endoplasmic reticulum, and induce long lasting channel openings in a mode of smaller conductance. They have the ability to translocate into cells by crossing the plasma membrane [ , , ]. Toxins of sco...

[ "GO:0019855", "GO:0005576" ]

[ "calcium channel inhibitor activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM", "PROSITE" ]

[ "PF08099", "PS60028" ]

[ "Toxin_27", "SCORPION_CALCINE" ]

[ 15, 92 ]

2

[ "PROSITEDOC" ]

[ "PDOC60028" ]

[ "PROSITEDOC:PDOC60028" ]

1

[ "1c6w", "1ie6", "2kql", "8dtb", "8duj" ]

5

[ "PUB00016414", "PUB00033810", "PUB00033811", "PUB00033812", "PUB00033813" ]

[ "10861934", "10075681", "10713267", "15653689", "12429019" ]

[ "A new fold in the scorpion toxin family, associated with an activity on a ryanodine-sensitive calcium channel.", "Activation of ryanodine receptors by imperatoxin A and a peptide segment of the II-III loop of the dihydropyridine receptor.", "Chemical synthesis and characterization of maurocalcine, a scorpion t...

[ 2000, 1999, 2000, 2005, 2003 ]

5

[]

0

null

[ "Bacteria", "Eukaryota" ]

[ 18, 75 ]

2

[]

0

true

Family

Scorpion calcine

Scorpion_calcine

8

IPR012633

12,633

SFI toxin

Toxin_28

Family

10

false

This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels an...

[ "GO:0005576" ]

[ "extracellular region" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08115" ]

[ "Toxin_28" ]

[ 10 ]

1

[]

0

[ "2mf3" ]

1

[]

0

[]

0

null

[ "Segestria florentina" ]

[ 10 ]

1

[]

0

true

Family

SFI toxin

Toxin_28

6

IPR012634

12,634

PhTx neurotoxin

Toxin_29

Family

6

false

This family consists of PhTx insecticidal neurotoxins that are found in the venom of Phoneutria nigriventer (Brazilian armed spider). The venom of the P. nigrivente contains numerous neurotoxic polypeptides of 30-140 amino acids, which exert a range of biological effects. While some of these neurotoxins are lethal to m...

[ "GO:0005576" ]

[ "extracellular region" ]

[ "cellular_component" ]

1

[ "PFAM" ]

[ "PF08116" ]

[ "Toxin_29" ]

[ 6 ]

1

[]

0

[]

0

[ "PUB00016488" ]

[ "10978749" ]

[ "Purification and amino acid sequence of a highly insecticidal toxin from the venom of the brazilian spider Phoneutria nigriventer which inhibits NMDA-evoked currents in rat hippocampal neurones." ]

[ 2001 ]

1

[]

0

null

[ "Ctenidae" ]

[ 6 ]

1

[]

0

true

Family

PhTx neurotoxin

Toxin_29

3

IPR012635

12,635

Parabutoxin

Family

3

false

This entry represents proteins that are acidic alpha-KTx short chain scorpion toxins. These toxins are named parabutoxins, that binds and inhibit voltage-sensitive potassium channels and inhibit the vertebrate potassium channel Kv1.1 with low affinity. Furthermore, they lack the crucial pore-plugging lysine. In additio...

[ "GO:0019870", "GO:0005576" ]

[ "potassium channel inhibitor activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM" ]

[ "PF08119" ]

[ "Toxin_31" ]

[ 3 ]

1

[]

0

[]

0

[ "PUB00016529" ]

[ "14561751" ]

[ "A subfamily of acidic alpha-K(+) toxins." ]

[ 2004 ]

1

[]

0

null

[ "Parabuthus" ]

[ 3 ]

1

[]

0

true

Family

Parabutoxin

2

IPR012637

12,637

Waglerin

Toxin_33

Family

2

false

This family consists of the lethal peptides (waglerins) that are found in the venom of Trimeresurus wagleri (Wagler's pit viper) (Tropidolaemus wagleri). Waglerins are 22-24 residue lethal peptides and are competitive antagonist of the muscle nicotinic receptor (nAChR). Waglerin-1 possesses a distinctive selectivity fo...

[ "GO:0030550", "GO:0005576" ]

[ "acetylcholine receptor inhibitor activity", "extracellular region" ]

[ "molecular_function", "cellular_component" ]

2

[ "PFAM" ]

[ "PF08121" ]

[ "Toxin_33" ]

[ 2 ]

1

[]

0

[]

0

[ "PUB00016545" ]

[ "8533138" ]

[ "Structure-function studies of waglerin I, a lethal peptide from the venom of Wagler's pit viper, Trimeresurus wagleri." ]

[ 1995 ]

1

[]

0

null

[ "Tropidolaemus wagleri" ]

[ 2 ]

1

[]

0

true

Family

Waglerin

Toxin_33

8

IPR012638

12,638

Tryptophan leader peptide

Trp_leader1

Family

246

false

This family consists of tryptophan (trp) leader peptides from Streptomyces spp [ ]. Tryptophan accumulation is the principal event resulting in down regulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either...

[]

0

[ "PFAM" ]

[ "PF08055" ]

[ "Trp_leader1" ]

[ 246 ]

1

[]

0

[]

0

[ "PUB00016401", "PUB00086672" ]

[ "15262409", "9695930" ]

[ "The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis.", "Regulation of an anthranilate synthase gene in Streptomyces venezuelae by a trp attenuator." ]

[ 2004, 1998 ]

2

[]

0

null

[ "Actinomycetes" ]

[ 246 ]

1

[]

0

true

Family

Tryptophan leader peptide

Trp_leader1

9

IPR012640

12,640

Membrane lipoprotein, lipid attachment site

Membr_lipoprot_lipid_attach_CS

Conserved_site

3,080

false

In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [ , ]. This li...

[]

0

[ "PFAM" ]

[ "PF08139" ]

[ "LPAM_1" ]

[ 3080 ]

1

[]

0

[]

0

[ "PUB00002367", "PUB00004947", "PUB00016431" ]

[ "2202727", "3253732", "11309113" ]

[ "Lipoproteins in bacteria.", "Distinctive properties of signal sequences from bacterial lipoproteins.", "Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines." ]

[ 1990, 1988, 2001 ]

3

[]

0

null

[ "Archaea", "Bacteria", "Pancrustacea", "Viruses", "metagenomes", "plasmids" ]

[ 2, 2889, 2, 146, 39, 2 ]

6

[]

0

true

Conserved_site

Membrane lipoprotein, lipid attachment site

Membr_lipoprot_lipid_attach_CS

4

IPR012641

12,641

Cysteine rich domain, Polydnavirus

Polydnavirus_Cys-rich

Domain

37

false

This entry represents a cysteine rich motif found in a group of proteins from Polydnavirus [ ]. Some proteins have multiple copies of this domain.

[]

0

[ "PFAM" ]

[ "PF08008" ]

[ "Viral_cys_rich" ]

[ 37 ]

1

[]

0

[ "1xi7", "1xj1" ]

2

[ "PUB00016505" ]

[ "11724552" ]

[ "Solution structure of the carboxyl-terminal cysteine-rich domain of the VHv1.1 polydnaviral gene product: comparison with other cystine knot structural folds." ]

[ 2001 ]

1

[]

0

null

[ "Endopterygota", "Polydnaviriformidae" ]

[ 7, 30 ]

2

[]

0

true

Domain

Cysteine rich domain, Polydnavirus

Polydnavirus_Cys-rich

7

IPR012642

12,642

Transcription regulator Wos2-domain

Tscrpt_reg_Wos2-domain

Domain

2,871

false

Proteins containing the Wos2 domain are involved in the regulation of the cell cycle [ ] and are Myb-related transcriptional activators.

[ "GO:0006355" ]

[ "regulation of DNA-templated transcription" ]

[ "biological_process" ]

1

[ "PFAM" ]

[ "PF07988" ]

[ "LMSTEN" ]

[ 2871 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-HSA-5601884", "R-HSA-8939236", "R-HSA-9018519", "R-HSA-9616222", "R-HSA-983231", "R-HSA-9834899" ]

[ "REACTOME:R-HSA-5601884", "REACTOME:R-HSA-8939236", "REACTOME:R-HSA-9018519", "REACTOME:R-HSA-9616222", "REACTOME:R-HSA-983231", "REACTOME:R-HSA-9834899" ]

6

[ "1sb0", "2agh", "5svh", "6dmx", "6dnq" ]

5

[ "PUB00016394" ]

[ "10581266" ]

[ "The identification of Wos2, a p23 homologue that interacts with Wee1 and Cdc2 in the mitotic control of fission yeasts." ]

[ 1999 ]

1

[]

0

null

[ "Alpharetrovirus", "Vertebrata" ]

[ 4, 2867 ]

2

[ "Danio rerio", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 6, 32, 13, 9 ]

4

true

Domain

Transcription regulator Wos2-domain

Tscrpt_reg_Wos2-domain

4

IPR012643

12,643

Wound-inducible basic

Wound_ind

Family

275

false

This family consists of the wound-inducible basic proteins from plants. The metabolic activities of plants are dramatically altered upon mechanical injury or pathogen attack. A large number of proteins accumulates at wound or infection sites, such as the wound-inducible basic proteins. These proteins are small, 47 amin...

[]

0

[ "PFAM", "PANTHER" ]

[ "PF08186", "PTHR36752" ]

[ "Wound_ind", "" ]

[ 274, 244 ]

2

[]

0

[]

0

[ "PUB00016560" ]

[ "8310075" ]

[ "Isolation and characterization of a cDNA clone encoding a small wound-inducible protein from Phaseolus vulgaris." ]

[ 1993 ]

1

[]

0

null

[ "Eukaryota" ]

[ 275 ]

1

[ "Arabidopsis thaliana", "Oryza sativa subsp. japonica", "Zea mays" ]

[ 2, 3, 1 ]

3

true

Family

Wound-inducible basic

Wound_ind

2

IPR012644

12,644

Conserved hypothetical protein CHP02300, FYDLN acid

CHP02300_FYDLN_acid

Family

3,049

false

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this fa...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09538", "TIGR02300" ]

[ "FYDLN_acid", "FYDLN_acid" ]

[ 3042, 2663 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 2999, 14, 36 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02300, FYDLN acid

CHP02300_FYDLN_acid

3

IPR012645

12,645

Conserved hypothetical protein CHP02301

CHP02301

Family

1,204

false

Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus (Caulobacter vibrioides), and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulphide bond. The function...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09539", "TIGR02301" ]

[ "DUF2385", "" ]

[ 1204, 1203 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 1196, 8 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP02301

CHP02301

7

IPR012646

12,646

RNA ligase, DRB0094

RNA_ligase_DRB0094

Family

673

false

RNA repair, though not as well characterised as DNA repair, is an important component of many biological systems. These include the kinteoplastid RNA-editing process and the defence of Bacteriophage T4 against tRNA damage caused by host nucleases. RNA ligase is an essential enzyme in the process of RNA repair [ ]. It i...

[]

0

[ "NCBIFAM" ]

[ "TIGR02306" ]

[ "RNA_lig_DRB0094" ]

[ 673 ]

1

[]

0

[ "5cot", "5cou", "5cov", "6vt0", "6vt1", "6vt3", "6vt4", "6vt5", "6vt6", "6vt8", "6vt9", "6vtb", "6vtd", "6vte", "6vtf", "6vtg" ]

16

[ "PUB00017748", "PUB00035972" ]

[ "15333634", "14992715" ]

[ "An RNA ligase from Deinococcus radiodurans.", "RNA ligase; picking up the pieces." ]

[ 2004, 2004 ]

2

[]

0

null

[ "Bacteria", "Eukaryota", "Viruses", "marine sediment metagenome" ]

[ 526, 56, 85, 6 ]

4

[]

0

true

Family

RNA ligase, DRB0094

RNA_ligase_DRB0094

1

IPR012647

12,647

RNA ligase, Rnl2

RNA_lig_RNL2

Family

465

false

Members of this family ligate (seal breaks in) RNA. Members so far include phage [ ] proteins that can counteract a host defence of cleavage of specific tRNA molecules and trypanosome ligases involved in RNA editing [ ].

[ "GO:0003972", "GO:0005524", "GO:0016874" ]

[ "RNA ligase (ATP) activity", "ATP binding", "ligase activity" ]

[ "molecular_function", "molecular_function", "molecular_function" ]

3

[ "NCBIFAM" ]

[ "TIGR02307" ]

[ "RNA_lig_RNL2" ]

[ 465 ]

1

[ "EC" ]

[ "6.5.1.3" ]

[ "EC:6.5.1.3" ]

1

[ "1s68", "1xdn", "2hvq", "2hvr", "2hvs" ]

5

[ "PUB00095678", "PUB00095680" ]

[ "24158792", "11134327" ]

[ "Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3'-OH base mispairs and damaged base lesions.", "Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex." ]

[ 2013, 2001 ]

2

[]

[ "IPR044263" ]

0

1

0

[ "Eukaryota", "Pseudomonadati", "Viruses" ]

[ 100, 80, 285 ]

3

[]

0

true

Family

RNA ligase, Rnl2

RNA_lig_RNL2

8

IPR012648

12,648

T4 RNA ligase 1

Rnl1

Family

356

false

Members of this family are phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage [ ]. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. The structure of...

[ "GO:0003972" ]

[ "RNA ligase (ATP) activity" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM" ]

[ "MF_04149", "TIGR02308" ]

[ "RNALIG_T4", "RNA_lig_T4_1" ]

[ 317, 356 ]

2

[]

0

[ "2c5u", "5tt6", "9do4" ]

3

[ "PUB00077072", "PUB00094221" ]

[ "2444436", "17068206" ]

[ "Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA.", "Structure-guided mutational analysis of T4 RNA ligase 1." ]

[ 1987, 2006 ]

2

[]

0

null

[ "Bacteria", "Orbiliaceae", "Viruses", "ecological metagenomes" ]

[ 3, 11, 339, 3 ]

4

[]

0

true

Family

T4 RNA ligase 1

Rnl1

3

IPR012649

12,649

Phosphonopyruvate hydrolase

PPH

Family

178

false

This family consists of phosphonopyruvate hydrolase (PPH), an enzyme closely related to phosphoenolpyruvate phosphomutase. It cleaves the direct C-P bond of phosphonopyruvate. The characterised example is from Variovorax sp. Pal2 [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR02321" ]

[ "Pphn_pyruv_hyd" ]

[ 178 ]

1

[]

0

[ "2dua", "2hjp", "2hrw" ]

3

[ "PUB00016671" ]

[ "12697757" ]

[ "Protein kinase A signaling pathway regulates transcriptional activity of SAF-1 by unmasking its DNA-binding domains." ]

[ 2003 ]

1

[]

0

null

[ "Bacteria", "freshwater metagenome", "leotiomyceta" ]

[ 141, 1, 36 ]

3

[]

0

true

Family

Phosphonopyruvate hydrolase

PPH

7

IPR012650

12,650

Conserved hypothetical protein CHP02328

CHP02328

Family

814

false

Members of this family are found in a small number of taxonomically well-separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the firmicutes. The function of this protein is unknown.

[]

0

[ "NCBIFAM" ]

[ "TIGR02328" ]

[ "" ]

[ 814 ]

1

[]

0

[]

0

[]

0

[ "IPR004260" ]

[]

1

0

1

[ "Bacteria", "bioreactor metagenome" ]

[ 813, 1 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP02328

CHP02328

3

IPR012651

12,651

Thiamine transporter ThiT

Thia_Transptr_ThiT

Family

3,111

false

Members of this protein family have been assigned as thiamine transporters by a phylogenomic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine tran...

[ "GO:0015234", "GO:0015888", "GO:0005886" ]

[ "thiamine transmembrane transporter activity", "thiamine transport", "plasma membrane" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "PFAM", "NCBIFAM" ]

[ "PF09515", "TIGR02357" ]

[ "Thia_YuaJ", "ECF_ThiT_YuaJ" ]

[ 3111, 2529 ]

2

[ "GP" ]

[ "GenProp1094" ]

[ "GP:GenProp1094" ]

1

[ "3rlb", "4mes", "4mhw", "4muu", "4n4d", "4pop", "4pov", "4tkr" ]

8

[ "PUB00055602", "PUB00055603" ]

[ "20218726", "20497229" ]

[ "Biochemical characterization of ThiT from Lactococcus lactis: a thiamin transporter with picomolar substrate binding affinity.", "Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions." ]

[ 2010, 2011 ]

2

[]

0

null

[ "Bacteria", "Candidatus Methanofastidiosum methylothiophilum", "unclassified sequences" ]

[ 3074, 4, 33 ]

3

[]

0

true

Family

Thiamine transporter ThiT

Thia_Transptr_ThiT

2

IPR012652

12,652

Energy coupling factor transporter S component ThiW

ThiW

Family

1,988

false

Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved, to a structural element called THI found in the untranslated upstrea...

[]

0

[ "PFAM", "PIRSF", "NCBIFAM" ]

[ "PF09512", "PIRSF024534", "TIGR02359" ]

[ "ThiW", "ThiW", "thiW" ]

[ 1988, 1915, 1959 ]

3

[ "GP" ]

[ "GenProp1094" ]

[ "GP:GenProp1094" ]

1

[]

0

[ "PUB00017761" ]

[ "12376536" ]

[ "Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms." ]

[ 2002 ]

1

[]

0

null

[ "Archaea", "Bacteria", "unclassified sequences" ]

[ 43, 1913, 32 ]

3

[]

0

true

Family

Energy coupling factor transporter S component ThiW

ThiW

5

IPR012653

12,653

Dimethylamine methyltransferase MtbB

Dimeth_MeTrfase_MtbB

Family

250

false

This family consists of dimethylamine methyltransferase MtbB, mainly from the genus Methanosarcina. It is found in three nearly identical copies in each of Methanosarcina acetivorans, Methanosarcina barkeri, and Methanosarcina mazei. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrro...

[ "GO:0008168", "GO:0015948" ]

[ "methyltransferase activity", "methanogenesis" ]

[ "molecular_function", "biological_process" ]

2

[ "PFAM", "NCBIFAM" ]

[ "PF09505", "TIGR02368" ]

[ "Dimeth_Pyl", "dimeth_PyL" ]

[ 250, 135 ]

2

[ "EC", "METACYC" ]

[ "2.1.1.249", "PWY-5248" ]

[ "EC:2.1.1.249", "METACYC:PWY-5248" ]

2

[]

0

[ "PUB00016082", "PUB00075715" ]

[ "10852929", "16096277" ]

[ "Reconstitution of dimethylamine:coenzyme M methyl transfer with a discrete corrinoid protein and two methyltransferases purified from Methanosarcina barkeri.", "The residue mass of L-pyrrolysine in three distinct methylamine methyltransferases." ]

[ 2000, 2005 ]

2

[]

0

null

[ "Bacteria", "Methanobacteriati", "ecological metagenomes" ]

[ 62, 171, 17 ]

3

[]

0

true

Family

Dimethylamine methyltransferase MtbB

Dimeth_MeTrfase_MtbB

5

IPR012654

12,654

Conserved hypothetical protein CHP02391

CHP02391

Domain

1,727

false

This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09509", "TIGR02391" ]

[ "Hypoth_Ymh", "hypoth_ymh" ]

[ 1727, 1209 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Acyrthosiphon pisum", "Archaea", "Bacteria", "Streptococcus phage IPP34", "unclassified sequences" ]

[ 1, 45, 1643, 1, 37 ]

5

[]

0

true

Domain

Conserved hypothetical protein CHP02391

CHP02391

6

IPR012655

12,655

Uncharacterised protein YrzI

YrzI

Family

1,318

false

Members of this family are very small proteins, about 47 residues each. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09501", "TIGR02413" ]

[ "Bac_small_YrzI", "Bac_small_yrzI" ]

[ 1318, 922 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacillota", "Reticulomyxa filosa" ]

[ 1317, 1 ]

2

[]

0

true

Family

Uncharacterised protein YrzI

YrzI

3

IPR012656

12,656

Conserved hypothetical protein CHP02421, QEGLA

CHP02421_QEGLA

Family

1,865

false

Members of this family include a possible metal-binding motif HEXXXH and, nearby, a perfectly conserved motif QEGLA. All members belong to the proteobacteria, including Agrobacterium tumefaciens and several species of Vibrio and Pseudomonas, and are found in only one copy per chromosome (Vibrio vulnificus, with two chr...

[]

0

[ "NCBIFAM" ]

[ "TIGR02421" ]

[ "QEGLA" ]

[ 1865 ]

1

[]

0

[]

0

[]

0

[ "IPR012548" ]

[]

1

0

1

[ "Bacteria", "Chaetothyriales", "marine sediment metagenome" ]

[ 1860, 2, 3 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02421, QEGLA

CHP02421_QEGLA

5

IPR012657

12,657

23S rRNA-intervening sequence protein

23S_rRNA-intervening_sequence

Family

17,328

false

This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes [ , , ]. It folds into an anti-parallel four-helix bundle and forms homopentamers [ ].

[]

0

[ "PFAM", "PIRSF", "PANTHER", "NCBIFAM", "CDD" ]

[ "PF05635", "PIRSF035652", "PTHR38471", "TIGR02436", "cd16377" ]

[ "23S_rRNA_IVP", "CHP02436", "", "", "23S_rRNA_IVP_like" ]

[ 16440, 4259, 15426, 17325, 9657 ]

5

[]

0

[ "2gsc", "2rld" ]

2

[ "PUB00011556", "PUB00020253", "PUB00036068", "PUB00066743" ]

[ "8341711", "7751314", "16948161", "17644584" ]

[ "Intervening sequence with conserved open reading frame in eubacterial 23S rRNA genes.", "Characterization of the 23S and 5S rRNA genes of Coxiella burnetii and identification of an intervening sequence within the 23S rRNA gene.", "Crystal structure of the conserved hypothetical cytosolic protein Xcc0516 from X...

[ 1993, 1995, 2006, 2007 ]

4

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "unclassified sequences" ]

[ 17, 16946, 7, 7, 351 ]

5

[]

0

true

Family

23S rRNA-intervening sequence protein

23S_rRNA-intervening_sequence

9

IPR012658

12,658

Uncharacterized protein YheV

YheV

Family

3,343

false

Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminal and a probable metal-binding motif CPXCX(18)CXXC, including the uncharacterised protein YheV from E. coli. Members are found in various proteobacteria.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09526", "TIGR02443" ]

[ "DUF2387", "" ]

[ 3343, 3178 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Symbiodinium pilosum", "metagenomes" ]

[ 3331, 1, 11 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Uncharacterized protein YheV

YheV

5

IPR012659

12,659

Conserved hypothetical protein CHP02444

CHP02444

Family

2,586

false

Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09523", "TIGR02444" ]

[ "DUF2390", "" ]

[ 2586, 2423 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 2556, 4, 26 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02444

CHP02444

1

IPR012660

12,660

Thioesterase, putative

YiiD_C

Domain

4,046

false

This entry consists of a broadly distributed uncharacterised domain found often as a standalone protein. The member from is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an N-terminal acetyltransferase domain ( ). The function of these proteins are...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09500", "TIGR02447" ]

[ "YiiD_C", "yiiD_Cterm" ]

[ 4046, 3756 ]

2

[ "EC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC"...

[ "2.3.1.-", "PWY-3602", "PWY-361", "PWY-4801", "PWY-4922", "PWY-5048", "PWY-5139", "PWY-5268", "PWY-5284", "PWY-5292", "PWY-5307", "PWY-5313", "PWY-5317", "PWY-5318", "PWY-5353", "PWY-5400", "PWY-5473", "PWY-5475", "PWY-5477", "PWY-5660", "PWY-5679", "PWY-5710", "PWY-5794"...

[ "EC:2.3.1.-", "METACYC:PWY-3602", "METACYC:PWY-361", "METACYC:PWY-4801", "METACYC:PWY-4922", "METACYC:PWY-5048", "METACYC:PWY-5139", "METACYC:PWY-5268", "METACYC:PWY-5284", "METACYC:PWY-5292", "METACYC:PWY-5307", "METACYC:PWY-5313", "METACYC:PWY-5317", "METACYC:PWY-5318", "METACYC:PWY-53...

219

[ "1t82", "3lmb", "8ayv" ]

3

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "Thermoplasmatota", "ecological metagenomes" ]

[ 4007, 18, 2, 19 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Domain

Thioesterase, putative

YiiD_C

8

IPR012661

12,661

Conserved hypothetical protein CHP02448

CHP02448

Family

3,861

false

This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1, and also in Pseudomonas putida (strain KT2440), four in Pseudomonas syringae pv. tomato str. DC3000, and single members in several other Proteobacteria...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09498", "TIGR02448" ]

[ "DUF2388", "" ]

[ 3861, 3620 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Eukaryota", "Pseudomonadati", "marine sediment metagenome" ]

[ 5, 3853, 3 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02448

CHP02448

4

IPR012663

12,663

Conserved hypothetical protein CHP02450, tryptophan-rich

CHP02450_Tryp

Family

1,717

false

Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all sp...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09493", "TIGR02450" ]

[ "DUF2389", "" ]

[ 1717, 1638 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 1625, 83, 9 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02450, tryptophan-rich

CHP02450_Tryp

4

IPR012664

12,664

Conserved hypothetical protein CHP02452

CHP02452

Family

5,530

false

Members of this uncharacterised protein family are found in Streptomyces, Anabaena sp. (strain PCC 7120), Clostridium acetobutylicum, Lactobacillus johnsonii NCC 533, Deinococcus radiodurans, and Pirellula sp. for a broad but sparse phylogenetic distribution that at least suggests lateral gene transfer.

[]

0

[ "PIRSF", "NCBIFAM" ]

[ "PIRSF014899", "TIGR02452" ]

[ "UCP014899", "" ]

[ 2342, 5508 ]

2

[]

0

[ "3sig", "3sih", "3sii", "3sij", "5zda", "5zdb", "5zdc", "5zdd", "5zde", "5zdf", "5zdg" ]

11

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "Viruses", "metagenomes" ]

[ 2052, 3414, 43, 21 ]

4

[ "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)" ]

[ 1 ]

1

true

Family

Conserved hypothetical protein CHP02452

CHP02452

8

IPR012665

12,665

Trehalose synthase

Trehalose_synth

Family

903

false

Trehalose synthase catalyzes a one-step conversion of maltose to trehalose [ ]. This is an alternative to the OtsAB and TreYZ pathways. This family includes a characterised example from Pseudomonas stutzeri and other very closely related sequences from other Pseudomonads. Not all functionally equivalent sequences may b...

[]

0

[ "NCBIFAM" ]

[ "TIGR02455" ]

[ "TreS_stutzeri" ]

[ 903 ]

1

[]

0

[]

0

[ "PUB00027647" ]

[ "12626396" ]

[ "New insights on trehalose: a multifunctional molecule." ]

[ 2003 ]

1

[]

0

null

[ "Bacteria", "plant metagenome" ]

[ 898, 5 ]

2

[]

0

true

Family

Trehalose synthase

Trehalose_synth

7

IPR012666

12,666

Cobalt transporter subunit CbtA, putative

CbtA_put

Family

4,834

false

This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems [ ]. Evidence for this assignment includes 1) prediction of five transmembrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream pro...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09490", "TIGR02458" ]

[ "CbtA", "CbtA" ]

[ 4834, 1639 ]

2

[]

0

[]

0

[ "PUB00015657" ]

[ "12869542" ]

[ "Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes." ]

[ 2003 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 233, 4545, 10, 46 ]

4

[]

0

true

Family

Cobalt transporter subunit CbtA, putative

CbtA_put

3

IPR012667

12,667

Cobalt transporter subunit CbtB, putative

CbtB_put

Family

4,541

false

This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems [ ]. Evidence for this assignment includes 1) prediction of a single transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2)...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09489", "TIGR02459" ]

[ "CbtB", "CbtB" ]

[ 4541, 1317 ]

2

[]

0

[]

0

[ "PUB00015657" ]

[ "12869542" ]

[ "Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes." ]

[ 2003 ]

1

[]

0

null

[ "Archaea", "Bacteria", "unclassified sequences" ]

[ 228, 4257, 56 ]

3

[]

0

true

Family

Cobalt transporter subunit CbtB, putative

CbtB_put

3

IPR012668

12,668

Conserved hypothetical protein CHP02466

CHP02466

Family

3,256

false

This family consists of uncharacterised proteins predominantly found in tailed bacteriophages and proteobacterial prophages.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF13759", "TIGR02466" ]

[ "2OG-FeII_Oxy_5", "" ]

[ 3256, 1552 ]

2

[]

0

[ "2rg4", "3bvc" ]

2

[]

0

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "metagenomes" ]

[ 9, 2394, 264, 395, 194 ]

5

[]

0

true

Family

Conserved hypothetical protein CHP02466

CHP02466

3

IPR012669

12,669

Pectic acid lyase

Pectate_lyase

Family

1,924

false

Members of this family are isozymes of pectate lyase ( ), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09492", "TIGR02474" ]

[ "Pec_lyase", "pec_lyase" ]

[ 1924, 1455 ]

2

[]

0

[ "1gxm", "1gxn", "1gxo", "1r76" ]

4

[]

0

[]

0

null

[ "Bacteria", "Candidatus Iainarchaeum sp.", "Eukaryota", "unclassified sequences" ]

[ 1895, 1, 6, 22 ]

4

[]

0

true

Family

Pectic acid lyase

Pectate_lyase

6

IPR012670

12,670

Type III secretion system, YscI/HrpB

T3SS_YscI/HrpB

Family

1,128

false

This entry consists of bacterial type III secretion system proteins which share a conserved C-terminal domain. These proteins are designated YscI (Yop proteins translocation protein I) in Yersinia and HrpB (hypersensitivity response and pathogenicity protein B) in plant pathogens such as Pseudomonas syringae. This entr...

[ "GO:0030254" ]

[ "protein secretion by the type III secretion system" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02497" ]

[ "yscI_hrpB_dom" ]

[ 1128 ]

1

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[ "PUB00095090" ]

[ "25614137" ]

[ "PscI is a type III secretion needle anchoring protein with in vitro polymerization capacities." ]

[ 2015 ]

1

[]

0

null

[ "Bacteria", "bioreactor metagenome" ]

[ 1127, 1 ]

2

[]

0

true

Family

Type III secretion system, YscI/HrpB

T3SS_YscI/HrpB

2

IPR012671

12,671

Type III export protein PscE/YscE

T3SS_PscE/YscE

Family

837

false

Members of this family are found exclusively in type III secretion apparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis [ , , ]. This is a small protein (about 70 amino acids) known as YscE in Y. pestis, SsaE of Salmonella spp., PscE of...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF08988", "TIGR02501" ]

[ "T3SS_needle_E", "type_III_yscE" ]

[ 835, 680 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "1zw0", "2p58", "2q1k", "2uwj", "3ph0", "7y6b", "7y6c" ]

7

[ "PUB00020581", "PUB00039043", "PUB00048615", "PUB00106879", "PUB00106882" ]

[ "1860816", "16195558", "18281060", "35861543", "20494986" ]

[ "Analysis of virC, an operon involved in the secretion of Yop proteins by Yersinia enterocolitica.", "Crystal structure of the Yersinia type III secretion protein YscE.", "Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone...

[ 1991, 2005, 2008, 2022, 2010 ]

5

[]

0

null

[ "Bacteria", "Herpotrichiellaceae", "invertebrate metagenome" ]

[ 833, 3, 1 ]

3

[]

0

true

Family

Type III export protein PscE/YscE

T3SS_PscE/YscE

7

IPR012672

12,672

Type III secretion system YscX

T3SS_YscX

Family

297

false

Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09474", "TIGR02502" ]

[ "Type_III_YscX", "type_III_YscX" ]

[ 297, 130 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "7qih", "7qii", "7qij", "8ara", "8arb", "8arc" ]

6

[ "PUB00017092" ]

[ "9882687" ]

[ "Identification of SycN, YscX, and YscY, three new elements of the Yersinia yop virulon." ]

[ 1999 ]

1

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 295, 2 ]

2

[]

0

true

Family

Type III secretion system YscX

T3SS_YscX

7

IPR012673

12,673

Type III secretion system chaperone SycN

T3SS_SynN

Family

221

false

Members of this protein family are part of the machinery of bacterial type III secretion in a number of bacteria that target animal cells. In the well-studied system from Yersinia, a complex of this protein (SycN) and YscB acts as a chaperone for the export of YopN [ , ]. YopN then acts to control effector protein secr...

[ "GO:0009306" ]

[ "protein secretion" ]

[ "biological_process" ]

1

[ "PFAM", "NCBIFAM", "CDD" ]

[ "PF21665", "TIGR02503", "cd17031" ]

[ "Type_III_SycN", "type_III_SycN", "T3SC_IA_SycN-like" ]

[ 204, 162, 176 ]

3

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "1xkp" ]

1

[ "PUB00011919", "PUB00016605", "PUB00017092", "PUB00020751", "PUB00046883", "PUB00069641", "PUB00140539", "PUB00140540", "PUB00140541", "PUB00140542", "PUB00140543" ]

[ "11849537", "10094626", "9882687", "15701523", "15502305", "23355975", "2160939", "16091038", "9371466", "14527656", "11514512" ]

[ "Functional analysis of the enteropathogenic Escherichia coli type III secretion system chaperone CesT identifies domains that mediate substrate interactions.", "A complex composed of SycN and YscB functions as a specific chaperone for YopN in Yersinia pestis.", "Identification of SycN, YscX, and YscY, three ne...

[ 2002, 1998, 1999, 2005, 2004, 2013, 1990, 2005, 1997, 2003, 2001 ]

11

[]

0

null

[ "Bacteria", "invertebrate metagenome" ]

[ 220, 1 ]

2

[]

0

true

Family

Type III secretion system chaperone SycN

T3SS_SynN

1

IPR012674

12,674

Calycin

Homologous_superfamily

85,466

false

Calycins form a large protein superfamily that share similar β-barrel structures. Calycins can be divided into families that include lipocalins, fatty acid binding proteins, triabin, and thrombin inhibitor [ ]. Of these families, the lipocalin family ( ) is the largest and functionally the most diverse. Lipocalins are ...

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:2.40.128.20", "SSF50814" ]

[ "", "" ]

[ 83819, 79222 ]

2

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-163560", "R-BTA-189483", "R-BTA-2162123", "R-BTA-400206", "R-BTA-5362517", "R-BTA-5365859", "R-BTA-6798695", "R-BTA-9707564", "R-CEL-159418", "R-CEL-163560", "R-CEL-189483", "R-CEL-2453902", "R-CEL-5362517", "R-CEL-5365859", "R-CEL-6798695", "R-CEL-975634", "R-DRE-163560", "...

[ "REACTOME:R-BTA-163560", "REACTOME:R-BTA-189483", "REACTOME:R-BTA-2162123", "REACTOME:R-BTA-400206", "REACTOME:R-BTA-5362517", "REACTOME:R-BTA-5365859", "REACTOME:R-BTA-6798695", "REACTOME:R-BTA-9707564", "REACTOME:R-CEL-159418", "REACTOME:R-CEL-163560", "REACTOME:R-CEL-189483", "REACTOME:R-CE...

91

[ "1a18", "1a2d", "1a3y", "1a57", "1ab0", "1acd", "1adl", "1ael", "1alb", "1aqb", "1avg", "1b0o", "1b4m", "1b56", "1b8e", "1bbp", "1beb", "1bj7", "1blr", "1bm5", "1brp", "1brq", "1bso", "1bsq", "1bsy", "1bwy", "1cbi", "1cbq", "1cbr", "1cbs", "1cj5", "1crb"...

1,506

[ "PUB00014136", "PUB00014138", "PUB00014139", "PUB00014140", "PUB00014141", "PUB00015733" ]

[ "11058743", "11058763", "11058769", "11058756", "12432930", "12909634" ]

[ "The lipocalin protein family: structural and sequence overview.", "Major urinary proteins, alpha(2U)-globulins and aphrodisin.", "Immunocalins: a lipocalin subfamily that modulates immune and inflammatory responses.", "The core lipocalin, bovine beta-lactoglobulin.", "Lipocalin-type and hematopoietic prost...

[ 2000, 2000, 2000, 2000, 2002, 2003 ]

6

[]

0

null

[ "Bacteria", "Eukaryota", "Stenosarchaea group", "Viruses", "unclassified sequences" ]

[ 27936, 57153, 15, 55, 307 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Zea mays" ]

[ 42, 38, 55, 29, 2, 118, 139, 31, 192, 34 ]

10

true

Homologous_superfamily

Calycin

8

IPR012676

12,676

TGS-like

Homologous_superfamily

104,464

false

The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine 3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) [ ]. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organ...

[]

0

[ "SSF" ]

[ "SSF81271" ]

[ "" ]

[ 104464 ]

1

[ "EC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", ...

[ "6.1.1.3", "R-BTA-114608", "R-BTA-9629569", "R-CEL-114608", "R-DDI-9629569", "R-DME-114608", "R-DME-9629569", "R-DRE-114608", "R-GGA-114608", "R-HSA-114608", "R-HSA-379716", "R-HSA-379726", "R-HSA-5368286", "R-HSA-5389840", "R-HSA-5419276", "R-HSA-9629569", "R-HSA-9937383", "R-MMU-...

[ "EC:6.1.1.3", "REACTOME:R-BTA-114608", "REACTOME:R-BTA-9629569", "REACTOME:R-CEL-114608", "REACTOME:R-DDI-9629569", "REACTOME:R-DME-114608", "REACTOME:R-DME-9629569", "REACTOME:R-DRE-114608", "REACTOME:R-GGA-114608", "REACTOME:R-HSA-114608", "REACTOME:R-HSA-379716", "REACTOME:R-HSA-379726", ...

26

[ "1jal", "1ni3", "1nyq", "1nyr", "1qf6", "1tje", "1tke", "1tkg", "1tky", "1wwt", "1wxq", "2dby", "2dwq", "2eki", "2kmm", "2ohf", "3hvz", "3j7y", "3j9m", "4a9a", "4ce4", "4v1a", "5aj4", "5ee0", "5ee1", "5ee3", "5ee9", "5iqr", "5kps", "5kpv", "5kpw", "5kpx"...

131

[ "PUB00007363", "PUB00016351" ]

[ "10447505", "12837776" ]

[ "Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.", "Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid." ]

[ 1999, 2003 ]

2

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "unclassified sequences" ]

[ 2561, 76659, 23656, 12, 1576 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 36, 6, 9, 10, 4, 23, 23, 4, 14, 33, 5, 5, 60 ]

13

true

Homologous_superfamily

TGS-like

9

IPR012677

12,677

Nucleotide-binding alpha-beta plait domain superfamily

Nucleotide-bd_a/b_plait_sf

Homologous_superfamily

858,830

false

This superfamily represents nucleotide-binding domains with an α-β plait structure, which consists of either a ferredoxin-like (β-α-β)2 fold, such as that found in RNA-binding domains of various ribonucleoproteins or in viral DNA-binding domains [ , ]; or a β-(α)-β-α-β(2) fold, such as that found in the ribosomal prote...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:3.30.70.330" ]

[ "" ]

[ 858830 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-111367", "R-BTA-112382", "R-BTA-113418", "R-BTA-156827", "R-BTA-159227", "R-BTA-159230", "R-BTA-159231", "R-BTA-159236", "R-BTA-429947", "R-BTA-450408", "R-BTA-674695", "R-BTA-6796648", "R-BTA-6803529", "R-BTA-6807505", "R-BTA-72086", "R-BTA-72163", "R-BTA-72165", "R-BTA-721...

[ "REACTOME:R-BTA-111367", "REACTOME:R-BTA-112382", "REACTOME:R-BTA-113418", "REACTOME:R-BTA-156827", "REACTOME:R-BTA-159227", "REACTOME:R-BTA-159230", "REACTOME:R-BTA-159231", "REACTOME:R-BTA-159236", "REACTOME:R-BTA-429947", "REACTOME:R-BTA-450408", "REACTOME:R-BTA-674695", "REACTOME:R-BTA-679...

601

[ "1a7g", "1a9n", "1aud", "1b7f", "1by9", "1cvj", "1d8z", "1d9a", "1dbd", "1dhm", "1drz", "1dz5", "1f9f", "1ffk", "1fht", "1fj7", "1fjc", "1fje", "1fnx", "1fo1", "1ft8", "1fxl", "1g2e", "1h2t", "1h2u", "1h2v", "1h6k", "1ha1", "1hd0", "1hd1", "1hl6", "1iqt"...

3,008

[ "PUB00007413", "PUB00016352", "PUB00016354" ]

[ "7553871", "15231733", "9159935" ]

[ "Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein EBNA 1.", "U2AF homology motifs: protein recognition in the RRM world.", "Evolution of the large-subunit ribosomal RNA binding site for protein L23/25." ]

[ 1995, 2004, 1997 ]

3

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "unclassified sequences" ]

[ 1796, 62483, 790394, 2979, 1178 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 1475, 197, 1569, 532, 3, 1410, 987, 81, 933, 1186, 62, 81, 2551 ]

13

true

Homologous_superfamily

Nucleotide-binding alpha-beta plait domain superfamily

Nucleotide-bd_a/b_plait_sf

7

IPR012678

12,678

Ribosomal protein uL23/eL15/eS24 core domain superfamily

Ribosomal_uL23/eL15/eS24_sf

Homologous_superfamily

65,677

false

Ribosomal proteins uL23, eL15 and eS24 share a common core domain consisting of a β-(α)-β-α-β(2) structure folded into three layers, α/β/α, where the β-sheets are antiparallel. Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome ...

[ "GO:0003735", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "translation", "ribosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "SSF" ]

[ "SSF54189" ]

[ "" ]

[ 65677 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-156827", "R-BTA-1799339", "R-BTA-6791226", "R-BTA-72649", "R-BTA-72689", "R-BTA-72695", "R-BTA-72702", "R-BTA-72706", "R-BTA-975956", "R-BTA-975957", "R-CEL-156827", "R-CEL-1799339", "R-CEL-5389840", "R-CEL-5419276", "R-CEL-72689", "R-CEL-72706", "R-CEL-975956", "R-CEL-97595...

[ "REACTOME:R-BTA-156827", "REACTOME:R-BTA-1799339", "REACTOME:R-BTA-6791226", "REACTOME:R-BTA-72649", "REACTOME:R-BTA-72689", "REACTOME:R-BTA-72695", "REACTOME:R-BTA-72702", "REACTOME:R-BTA-72706", "REACTOME:R-BTA-975956", "REACTOME:R-BTA-975957", "REACTOME:R-CEL-156827", "REACTOME:R-CEL-179933...

104

[ "1ffk", "1jj2", "1k73", "1k8a", "1k9m", "1kc8", "1kd1", "1kqs", "1m1k", "1m90", "1ml5", "1n88", "1n8r", "1nji", "1nkw", "1nwx", "1nwy", "1q7y", "1q81", "1q82", "1q86", "1qvf", "1qvg", "1s72", "1sm1", "1vq4", "1vq5", "1vq6", "1vq7", "1vq8", "1vq9", "1vqk"...

2,208

[ "PUB00007068", "PUB00007069", "PUB00007070" ]

[ "11297922", "11290319", "11114498" ]

[ "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal proteins." ]

[ 2001, 2001, 2000 ]

3

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 2747, 23358, 39016, 556 ]

4

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 29, 5, 8, 9, 1, 33, 20, 4, 30, 45, 6, 7, 105 ]

13

true

Homologous_superfamily

Ribosomal protein uL23/eL15/eS24 core domain superfamily

Ribosomal_uL23/eL15/eS24_sf

5

IPR012681

12,681

Nucleobase cation symporter-1, NCS1

NCS1

Family

5,939

false

The Nucleobase Cation Symporter-1 (NCS1) family are H+/Na+ symporters specific for the uptake of purines, pyrimidines and related metabolites (http://www.tcdb.org/search/result.php?tc=2.A.39). This entry consists of bacterial and yeast transporters of the NCS1 family. Members of this family possess twelve putative tran...

[ "GO:0022857", "GO:0055085", "GO:0016020" ]

[ "transmembrane transporter activity", "transmembrane transport", "membrane" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR00800" ]

[ "ncs1" ]

[ 5939 ]

1

[ "GP", "GP" ]

[ "GenProp0686", "GenProp0687" ]

[ "GP:GenProp0686", "GP:GenProp0687" ]

2

[]

0

[]

0

[ "IPR045225" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "hydrothermal vent metagenome" ]

[ 2451, 3485, 3 ]

3

[ "Escherichia coli (strain K12)", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)", "Schizosaccharomyces pombe (strain 972 / ATCC 24843)" ]

[ 1, 1, 10, 2 ]

4

true

Family

Nucleobase cation symporter-1, NCS1

NCS1

7

IPR012683

12,683

Conserved hypothetical protein CHP02302, transmembrane

CHP02302_TM

Family

2,724

false

Members of this family are found predominantly in the alphaproteobacteria and bacteroidetes. Each has 2-3 predicted transmembrane helices near the N terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum conta...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF13779", "TIGR02302" ]

[ "DUF4175", "aProt_lowcomp" ]

[ 2724, 1638 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified sequences", "uncultured marine thaumarchaeote KM3_45_G08" ]

[ 2692, 6, 25, 1 ]

4

[]

0

true

Family

Conserved hypothetical protein CHP02302, transmembrane

CHP02302_TM

9

IPR012685

12,685

Conserved hypothetical protein CHP02304, F390 synthetase-related

CHP02304_F390_synth-rel

Family

1,140

false

Members of this family form a distinct clade within a larger family of proteins that also includes coenzyme F390 synthetase, an enzyme known in Methanobacterium thermoautotrophicum and a few other methanogenic archaea. The enzyme adenylates coenzyme F420 to F390, a reversible process, during oxygen stress. Other inform...

[]

0

[ "NCBIFAM" ]

[ "TIGR02304" ]

[ "aden_form_hyp" ]

[ 1140 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Promethearchaeati", "ecological metagenomes" ]

[ 1135, 3, 2 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02304, F390 synthetase-related

CHP02304_F390_synth-rel

4

IPR012687

12,687

4-HPA 3-monooxygenase large component, Deinococcus-type

HpaB_Deino-type

Family

1,013

false

This entry represents the monooxygenase found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence, although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist...

[ "GO:0016712", "GO:0050660", "GO:0010124" ]

[ "oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", "flavin adenine dinucleotide binding", "phenylacetate catabolic process" ]

[ "molecular_function", "molecular_function", "biological_process" ]

3

[ "NCBIFAM" ]

[ "TIGR02309" ]

[ "HpaB-1" ]

[ 1013 ]

1

[ "EC", "GP", "METACYC", "METACYC" ]

[ "1.14.14.9", "GenProp0231", "PWY-7398", "PWY-7431" ]

[ "EC:1.14.14.9", "GP:GenProp0231", "METACYC:PWY-7398", "METACYC:PWY-7431" ]

4

[ "2yyg", "2yyi", "2yyj", "2yyk", "2yyl", "2yym", "9lft" ]

7

[]

0

[ "IPR004925" ]

[]

1

0

1

[ "Bacteria", "Candidatus Sysuiplasma superficiale", "Geodia barretti", "ecological metagenomes" ]

[ 981, 1, 8, 23 ]

4

[]

0

true

Family

4-HPA 3-monooxygenase large component, Deinococcus-type

HpaB_Deino-type

4

IPR012688

12,688

4-hydroxyphenylacetate 3-monooxygenase oxygenase component, gammaproteobacteria

HpaB_gammaproteobact

Family

868

false

4-hydroxyphenylacetate (4HPA) 3-monooxygenase consists of two components, a large component, HpaB, which is an oxygenase, and a small component, HpaC, which is a reductase. 4-HPA 3-monooxygenase is NADH-dependent and uses FAD as the redox chromophore. HpaB utilises FADH2 supplied by HpaC to catalyse the hydroxylation o...

[ "GO:0016712", "GO:0050660", "GO:0010124" ]

[ "oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", "flavin adenine dinucleotide binding", "phenylacetate catabolic process" ]

[ "molecular_function", "molecular_function", "biological_process" ]

3

[ "NCBIFAM" ]

[ "TIGR02310" ]

[ "HpaB-2" ]

[ 868 ]

1

[ "EC", "GP", "METACYC", "METACYC" ]

[ "1.14.14.9", "GenProp0231", "PWY-7398", "PWY-7431" ]

[ "EC:1.14.14.9", "GP:GenProp0231", "METACYC:PWY-7398", "METACYC:PWY-7431" ]

4

[ "6b1b", "6eb0", "6qyh", "6qyi", "9bke" ]

5

[ "PUB00016840", "PUB00050164" ]

[ "10653707", "17804419" ]

[ "Characterization of 4-hydroxyphenylacetate 3-hydroxylase (HpaB) of Escherichia coli as a reduced flavin adenine dinucleotide-utilizing monooxygenase.", "Crystal structure of the oxygenase component (HpaB) of the 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8." ]

[ 2000, 2007 ]

2

[ "IPR024677" ]

[]

1

0

1

[ "Pseudomonadota" ]

[ 868 ]

1

[]

0

true

Family

4-hydroxyphenylacetate 3-monooxygenase oxygenase component, gammaproteobacteria

HpaB_gammaproteobact

8

IPR012689

12,689

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

HpaI

Family

2,561

false

This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde [ ]. The gene for this enzyme is generally found adjacent to other genes for this pathway [ ].

[ "GO:0010124" ]

[ "phenylacetate catabolic process" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02311" ]

[ "HpaI" ]

[ 2561 ]

1

[ "EC", "GP" ]

[ "4.1.2.52", "GenProp0231" ]

[ "EC:4.1.2.52", "GP:GenProp0231" ]

2

[ "2v5j", "2v5k", "4b5s", "4b5t", "4b5u", "4b5v", "4b5w", "4b5x", "7et8", "7et9", "7eta", "7etb", "7etc", "7etd", "7ete", "7etf", "7etg", "7eth", "7eti", "7v8t" ]

20

[ "PUB00055089", "PUB00055090" ]

[ "15996099", "20364820" ]

[ "Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI.", "Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling." ]

[ 2005, 2010 ]

2

[]

[ "IPR023701" ]

0

1

0

[ "Bacteria", "Papaver nudicaule", "unclassified sequences" ]

[ 2552, 1, 8 ]

3

[]

0

true

Family

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

HpaI

1

IPR012690

12,690

2-oxo-hept-4-ene-1,7-dioic acid hydratase

HpcG

Family

3,242

false

This entry represents the enzyme which hydrates the double bond of 2-oxo-hepta-4-ene-1,7-dioic acid to form 4-hydroxy-2-oxo-heptane-1,7-dioic acid in the catabolism of 4-hydroxyphenylacetic acid. The gene for this enzyme is generally found adjacent to other genes of this pathway [ , ].

[ "GO:0018817", "GO:0009056" ]

[ "2-oxo-hept-3-ene-1,7-dioate hydratase activity", "catabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02312" ]

[ "HpaH" ]

[ 3242 ]

1

[ "GP" ]

[ "GenProp0231" ]

[ "GP:GenProp0231" ]

1

[ "2eb4", "2eb5", "2eb6" ]

3

[ "PUB00043972", "PUB00082333" ]

[ "17559873", "17012798" ]

[ "Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli.", "Expression, purification and crystallization of 2-oxo-hept-4-ene-1,7-dioate hydratase (HpcG) from Escherichia coli C." ]

[ 2007, 2006 ]

2

[]

0

null

[ "Bacteria", "unclassified sequences" ]

[ 3233, 9 ]

2

[]

0

true

Family

2-oxo-hept-4-ene-1,7-dioic acid hydratase

HpcG

8

IPR012691

12,691

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase variant

HpaI_NOT_DapA

Family

309

false

This entry represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate...

[ "GO:0008840", "GO:0019877", "GO:0005737" ]

[ "4-hydroxy-tetrahydrodipicolinate synthase activity", "diaminopimelate biosynthetic process", "cytoplasm" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR02313" ]

[ "HpaI-NOT-DapA" ]

[ 309 ]

1

[ "GP" ]

[ "GenProp0231" ]

[ "GP:GenProp0231" ]

1

[]

0

[]

0

[ "IPR005263" ]

[]

1

0

1

[ "Bacteria" ]

[ 309 ]

1

[]

0

true

Family

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase variant

HpaI_NOT_DapA

9

IPR012692

12,692

ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria

ABC_MetN_proteobac

Family

2,014

false

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found o...

[ "GO:0005524", "GO:0033232", "GO:0048473", "GO:0009276" ]

[ "ATP binding", "ABC-type D-methionine transporter activity", "D-methionine transmembrane transport", "Gram-negative-bacterium-type cell wall" ]

[ "molecular_function", "molecular_function", "biological_process", "cellular_component" ]

4

[ "NCBIFAM" ]

[ "TIGR02314" ]

[ "ABC_MetN" ]

[ 2014 ]

1

[ "EC" ]

[ "7.4.2.11" ]

[ "EC:7.4.2.11" ]

1

[ "3dhw", "3tui", "3tuj", "3tuz", "6cvl" ]

5

[ "PUB00004290", "PUB00014769", "PUB00017894", "PUB00017895", "PUB00017896", "PUB00017897", "PUB00017898", "PUB00017899", "PUB00025109", "PUB00026406", "PUB00043654" ]

[ "9872322", "9873074", "11421269", "1282354", "9640644", "11988180", "11470432", "11402022", "11080142", "11532960", "11421270" ]

[ "Crystal structure of the ATP-binding subunit of an ABC transporter.", "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.", "ABC transporters: physiology, structure and mechanism--an overview.", "ABC transporters: from microorgani...

[ 1998, 1999, 2001, 1992, 1998, 2002, 2001, 2001, 2000, 2001, 2001 ]

11

[]

0

null

[ "Bacteria", "Ecdysozoa" ]

[ 2011, 3 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria

ABC_MetN_proteobac

5

IPR012693

12,693

ABC transporter, phosphonate import, PhnC

ABC_transpr_PhnC

Family

8,819

false

The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [ ]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [ , ]. More than 50 subfamil...

[ "GO:0005524", "GO:0015416", "GO:0015716", "GO:0016020" ]

[ "ATP binding", "ABC-type phosphonate transporter activity", "organic phosphonate transport", "membrane" ]

[ "molecular_function", "molecular_function", "biological_process", "cellular_component" ]

4

[ "NCBIFAM", "CDD" ]

[ "TIGR02315", "cd03256" ]

[ "ABC_phnC", "ABC_PhnC_transporter" ]

[ 8260, 8771 ]

2

[ "EC", "GP", "GP", "PROSITEDOC" ]

[ "7.3.2.2", "GenProp0232", "GenProp0236", "PDOC51237" ]

[ "EC:7.3.2.2", "GP:GenProp0232", "GP:GenProp0236", "PROSITEDOC:PDOC51237" ]

4

[]

0

[ "PUB00014769", "PUB00017894", "PUB00033214", "PUB00043019", "PUB00043654", "PUB00070841", "PUB00080858", "PUB00080859", "PUB00080860" ]

[ "9873074", "11421269", "11952414", "8335257", "11421270", "9791102", "1368181", "8755882", "1846145" ]

[ "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.", "ABC transporters: physiology, structure and mechanism--an overview.", "Phosphonates and their degradation by microorganisms.", "Evidence for a fourteen-gene, phnC to phnP locus...

[ 1999, 2001, 2002, 1993, 2001, 1998, 1992, 1996, 1991 ]

9

[]

0

null

[ "Bacteria", "Eukaryota", "Methanobacteriota", "Siphoviridae sp. ct86u1", "unclassified sequences" ]

[ 8433, 9, 295, 1, 81 ]

5

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

ABC transporter, phosphonate import, PhnC

ABC_transpr_PhnC

6

IPR012694

12,694

Propionate--CoA ligase

Propion_PrpE

Family

2,221

false

This family contains one of three readily separable clades of proteins in the group of acetate and propionate--CoA ligases. Characterised members of this family act on propionate [ ]. From propionyl-CoA, there is a cyclic degradation pathway: it is ligated by PrpC to the TCA cycle intermediate oxaloacetate, acted upon ...

[ "GO:0050218", "GO:0019629" ]

[ "propionate-CoA ligase activity", "propionate catabolic process, 2-methylcitrate cycle" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02316" ]

[ "propion_prpE" ]

[ 2221 ]

1

[ "GP" ]

[ "GenProp1687" ]

[ "GP:GenProp1687" ]

1

[]

0

[ "PUB00066984" ]

[ "10411265" ]

[ "The prpE gene of Salmonella typhimurium LT2 encodes propionyl-CoA synthetase." ]

[ 1999 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "Sym plasmid", "metagenomes" ]

[ 2204, 4, 1, 12 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Propionate--CoA ligase

Propion_PrpE

3

IPR012695

12,695

2-methylisocitrate lyase

PrpB

Family

7,692

false

Propionate is the second most abundant low molecular mass carbon source found in soil, being generated by the degradation of several amino acids, fementation of crabohydrates and the oxidation of odd-chain fatty acids. Many different organisms are capable of metabolising propionate and several distinct pathways for uti...

[ "GO:0046421", "GO:0019629" ]

[ "methylisocitrate lyase activity", "propionate catabolic process, 2-methylcitrate cycle" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01939", "TIGR02317" ]

[ "PrpB", "prpB" ]

[ 4967, 7691 ]

2

[ "EC", "GP", "GP", "METACYC" ]

[ "4.1.3.30", "GenProp0240", "GenProp1687", "PWY-5747" ]

[ "EC:4.1.3.30", "GP:GenProp0240", "GP:GenProp1687", "METACYC:PWY-5747" ]

4

[ "1mum", "1o5q", "1oqf", "1ujq", "1xg3", "1xg4", "3eoo", "4iqd", "4iqe", "6t4v", "6t5m", "9hgk", "9hgo", "9hgq", "9hhs", "9hhy", "9hra" ]

17

[ "PUB00022299", "PUB00027466", "PUB00033216" ]

[ "14575713", "12706720", "9325432" ]

[ "Crystal structure of Salmonella typhimurium 2-methylisocitrate lyase (PrpB) and its complex with pyruvate and Mg(2+).", "Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.", "Propionate oxidation in Escherichia coli: evidence for operatio...

[ 2003, 2003, 1997 ]

3

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 99, 7476, 29, 88 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

2-methylisocitrate lyase

PrpB

1

IPR012696

12,696

Phosphonate metabolism PhnM

PhnM

Family

5,572

false

This family refers to Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase (also known as RPnTP diphosphatase or PhnM). PhnM is associated with phosphonate utilization in a number of bacterial species. It catalyzes the hydrolysis of alpha-D-ribose 1-methylphosphonate triphosphate (RPnTP) to form alpha-D-ribo...

[ "GO:0019700" ]

[ "organic phosphonate catabolic process" ]

[ "biological_process" ]

1

[ "NCBIFAM", "PIRSF", "NCBIFAM", "CDD" ]

[ "NF011987", "PIRSF038971", "TIGR02318", "cd01306" ]

[ "PRK15446.2-3", "PhnM", "phosphono_phnM", "PhnM" ]

[ 4654, 5486, 4083, 2733 ]

4

[ "GP", "GP", "GP" ]

[ "GenProp0232", "GenProp1381", "GenProp1630" ]

[ "GP:GenProp0232", "GP:GenProp1381", "GP:GenProp1630" ]

3

[]

0

[ "PUB00033214", "PUB00079189" ]

[ "11952414", "22089136" ]

[ "Phosphonates and their degradation by microorganisms.", "Intermediates in the transformation of phosphonates to phosphate by bacteria." ]

[ 2002, 2011 ]

2

[]

0

null

[ "Bacteria", "Methanobacteriota", "Symbiodiniaceae", "metagenomes" ]

[ 5492, 63, 2, 15 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Phosphonate metabolism PhnM

PhnM

1

IPR012697

12,697

Carboxyvinyl-carboxyphosphonate phosphorylmutase

CPEP_Pphonmut

Family

14

false

This family consists of carboxyvinyl-carboxyphosphonate phosphorylmutase (CPEP phosphonomutase), an unusual enzyme involved in the biosynthesis of the antibiotic bialaphos. So far, it is known only in that pathway and only in Streptomyces hygroscopicus. Some related proteins annotated as being functionally equivalent a...

[]

0

[ "NCBIFAM" ]

[ "TIGR02319" ]

[ "CPEP_Pphonmut" ]

[ 14 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Actinomycetes" ]

[ 14 ]

1

[]

0

true

Family

Carboxyvinyl-carboxyphosphonate phosphorylmutase

CPEP_Pphonmut

4

IPR012699

12,699

Ribose 1,5-bisphosphate phosphokinase PhnN

PhnN

Family

3,792

false

Many bacteria can use organophosphonates as a source of phosphate by cleaving the carbon-phosphorus bond with a multi-enzyme pathway collectively called carbon-phosphorus lyase. PhnN is part of this pathway and catalyses the phosphorylation of ribose 1,5-bisphosphate to 5-phospho-D-ribosyl alpha-1-diphosphate (PRPP) [ ...

[ "GO:0033863", "GO:0006015" ]

[ "ribose 1,5-bisphosphate phosphokinase activity", "5-phosphoribose 1-diphosphate biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00836", "TIGR02322" ]

[ "PhnN", "phosphon_PhnN" ]

[ 3621, 3761 ]

2

[ "EC", "GP", "GP", "METACYC", "METACYC" ]

[ "2.7.4.23", "GenProp0232", "GenProp1630", "PWY-7805", "PWY-7807" ]

[ "EC:2.7.4.23", "GP:GenProp0232", "GP:GenProp1630", "METACYC:PWY-7805", "METACYC:PWY-7807" ]

5

[]

0

[ "PUB00056812", "PUB00056813" ]

[ "12700258", "19733071" ]

[ "Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.", "A fluorescent substrate for carbon-phosphorus lyase: towards the pathway for organophosphonate metabolism in bacteria." ]

[ 2003, 2009 ]

2

[]

0

null

[ "Bacteria", "Cyprideis torosa", "metagenomes" ]

[ 3781, 1, 10 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Ribose 1,5-bisphosphate phosphokinase PhnN

PhnN

4