In 1a05, motif occurs at the interface of the two duplicates.
In 1dgs, the motif is a circularly permuted reverse-ferredoxin core.


The motif in 1a05: motif occurs at the interface of the two duplicates.
The motif in 1j71: a core motif. Alternatively, this can be regarded as an interface motif because it uses corresponding elements from the two duplicates.


The motif in 1a05: motif occurs at the interface of the two duplicates. circularly permuted reverse-ferredoxin.


d1a2za_ hits d1nc3a_ (other superfamily) with Dali Z 13.3, and d2pth__ (othersuperfamily) hits d1nc3a_ with Z 9.5, thus d1a2za_ and d2pth__
are homologs (the Z score between these two is 7.6, less than 9). In addition, the superposition of 1a2z and 2pth has some details suggesting
homology between them. Compare d1a2za_ and d2pth__, one strand and one helix in the motif are insertions. So this is a hybrid motif.


The motif in 1a7j: comparing d1a7j__ and 1uj2 (same SCOP family), three strands and one helix in the motif in 1a7j are absent in 1uj2. So
this is a hybrid motif.


The motif in 1aa7 uses helices from the two different domains and the linker helix, and is an interface motif.
Although the first domain in 1aa7_A is also a 4-helix up-and-down bundle, this bundle cannot be homologous to the 4-helix
bundle in 1b68, because they are mirror images, i.e. superimpose helix 1 and 2 in 1b68 and 1aa7, helix 3 and 4 are on
different sides of the plane formed by helix 1 and 2.


The motif in 1aa7 uses helices from the two different domains and the linker helix, and is an interface motif.
Although the first domain in 1aa7_A is also a 4-helix up-and-down bundle, this bundle cannot be homologous to the 4-helix bundle in 1qkr,
because they are mirror images.
Note that in 1qkr paper, the authors mentioned that "five-helix bundles are uncommon,.." in page 606.


The motif in 1ac5: four strands are insertions to the Rossmann core, while one strand and the helix belong to the Rossmann core. Hybrid
motif, but the b-a-b connection in this motif is left-handed.


The motif in 1ac5: 2nd and 3rd helices are insertion, other elements belong to the Rossmann core. hybrid motif;
The motif in 1vk0: 1st strand and 1st helix are insertion, other elements belong to the RNaseH core. hybrid motif;
Basically, insertion in RNaseH is aligned to core elements in Rossmann, and insertion in Rossmann is aligned to core elements in RNaseH.


The motif in 1adj: comparing d1adja2 and d1bia_3 (different family same superfamily), the helix and the second strand are insertion. hybrid. the
inserted beta-strand is short.


The motif in 1aor: interface motif involving the two duplicates; crossed connection;


The motif in 1axn: the 3-helix bundle uses helix 5 in the 1st duplicate, helix 1 in the 2nd duplicate, and helix 2 in the 5th duplicate.
This is an interface motif at the interface of three duplicates and in any one duplicate, the arrangement of helix
1,2,5 is different than the arrangement in the interface motif.


In 1axn, the 3-helix bundle uses helix 5 in the 1st duplicate, helix 1 in the 2nd duplicate, and helix 2 in the
5th duplicate. This is an interface motif at the interface of three duplicates and in any one duplicate, the
arrangement of helix 1,2,5 is different than the arrangement in the interface motif.


The motif in 1b05: a hybrid motif, because a beta-hairpin is absent in the other duplicate and thus insertion.
The motif in 1lc0: although "Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" is a very variable fold, it is in SCOP a+b class and
does not have any resemblance to Rossmann-like structures. 1b05 is in a/b class and is Rossmann-like.
So these two motifs are analogs.


The babbb motif in 1b05: a hybrid motif, because a beta-hairpin is absent in the majority of homologs in this superfamily and therefore is an insertion. Other parts of the motif come from the core of this superfamily.
The babbb motif in 1nki: a core motif.
Thus, these two motifs are analogs.


The motif in 1b0p: hybrid, since the C-terminal beta-hairpin is absent in d1b0pa1, which is the other module on the same chain and in the same superfamily.


The motif in 1b3q: interface motif involving the two duplicates; crossed connection;
The motif in 1bia: a stand-along barrel by itself.


The motif in 1b62: compare d1b62a2 and d1amw__ (same superfamily), one strand and one helix is insertion. Hybrid motif. second helix too far away.
The core of this fold looks like a circularly permuted ferredoxin. The motif uses one edge strand of the ferredoxin core and the C-terminal extensions.


The motif in 1b6r: motif occurs at the interface of the ATP-grasp fold and Barrel-sandwich hybrid fold. interface motif;


The motif in 1b6r: motif occurs at the interface of the ATP-grasp fold and 'Barrel-sandwich hybrid' fold.
The motif in 1v97: stand-along, core motif.


The motif in 1ce8 uses one strand from the ATP-grasp core and two strands and one helix from C-terminal extension. Comparing d1ce8a6 with d1gsa_2
(different family same superfamily), the C-terminal extension is not present in d1gsa_2. So this is a hybrid motif. And it is analogous to real
dsRBD domains.


The motif in 1chm: one helix and one strand do not belong to the RNaseH core. The "Creatinase/prolidase N-terminal domain" superfamily has only two
proteins, and in the other protein (1n51) the inserted strand and helix are much deteriorated. Strictly speaking, this motif may not be a hybrid,
since it is present in all members in this superfamily.
However, since d1chma1 and d1g62a_ are drastically different structures, the motif in d1chma1 and the motif in d1g62a_ are very unlikely to be
homologs and are probably analogs.


The motif in 1cs1: Although each family in the PLP-dependent transferases superfamily has this motif, this is a hybrid, because PLP-dependent
transferases superfamily is homologous to some flavodoxin proteins. So this motif is a hybrid between the Rossmann-like core and the insertions, and
is therefore analogous to ancient folds like ferredoxin.


The motif in 1d7b: uses part of the Ig core and some inserted strands; hybrid motif. The most important feature in Ig fold is the
interlock composed of strands 2, 3, 5, 6 (if strands in a classic Ig are numbered from 1 to 7), like two scissors arranged mouth-to-mouth.
The motif in 1svb: the first domain in 1svb is almost all meander, so it cannot be homologous to Ig-like proteins.


The motif in 1dc1: compared to d1ckqa_ (same superfamiliy), two strands are insertion;
The motif in 1nf2: the inserted domain appears like a circular-permuted ferredoxin, and most of the elements in the motif come from this
ferredoxin-like part.


The motif in 1dc1: compared to d1ckqa_ (same superfamiliy), two strands are insertion;


The motif in 1dmz: compare to d1gxca_ (same family), the helix is the insertion. Can be analog to similar motifs in SCOP a+b class.


Comparing d1ds1a_ and d1e5sa_ (same superfamily, different family), one strand and one helix are insertions.
Thus the IF3-like motif in d1ds1a_ is a hybrid.


The motif in 1dzk: the last strand and the helix come from C-termianl extension, and the remaining part comes from the lipocalin core.
Hybrid motif.


The motif in 1dzt: comparing d1dzta_ and 2phla1 (different family same superfamily, since domain arrangement in 2phla1 is the same as subunit
arrangement in d1dzta_ and the curvature of the beta-sheets are very similar in these two proteins), the insertion is in different position relative to the core
structure. Hybrid motif.


The motif in 1e3p: the first two strands come from insertion, and the remaining part comes from the core. Hybrid motif.


The motif in 1e3p: first two strands come from insertion, third strand and first helix come from the core of the "Ribosomal
protein S5 domain 2-like" superfamily, last helix comes from C-terminal extension of another domain. hybrid motif.


The motif in 1ecf: compare d1ecfa2 (Class II glutamine amidotransferases) and d1pmab_ (Proteasome subunits), superimpose the two first strands,
and it seems that at least two strands in the reverse-ferredoxin motif in d1ecfa2 are insertions. hybrid motif.
The bottom line is that Ntn and reverse-ferredoxin are drastically different folds. So the reverse_ferredoxin motif in Ntn is analog to real
reverse_ferredoxin domains.


Comparing the two duplicates in 1efd, the motif results from some deletions in the Rossmann-like structure. Strictly speaking, this is not a hybrid motif.
However, since eIF1-like fold is drastically different than Rossmann structures, the motif in 1efd and the motif in 1d1r are analogs.


Comparing the two duplicates in 1efd, the motif results from some deletions in the Rossmann-like structure. Strictly speaking, this is not a hybrid motif.
However, since d1r0va3 (and its homolog d1w7aa4) is drastically different than Rossmann structures, the motif in 1efd and the motif in 1r0v are analogs.


In 1eg3, helix 1 and 4 in the first EF domain and helix 1 and 2 in the second EF domain form a right-handed superhelix, which is an interface motif.


The motif in 1ert: comparing d1ert__ and d1h75a_ (same family, different protein), one strand and one helix are insertion. hybrid.


The motif in 1fbx:  3-helix bundle uses a N-terminal inserted helix and the two core helices in the T-fold, so this is a hybrid motif. I
kept the loop with the one-turn helix to make the topology up-and-down. Actually, this motif is more like a 4-helix bundle.


The motif in 1fy2: part of the motif comes from the permuted flavodoxin core, part comes from C-terminal insertion. The insertion looks different in
different family, e.g. d1gpma2. So this is a hybrid motif and is analog to the thioredoxin core motif.


The motif in 1g99: compared to d1ig8a1 (same superfamily), two strands are insertion to the RNaseH core. hybrid motif.
The motif in 1gqy: although it looks like a dsRBD, the helix belongs to the Rossmann core because without it, half of the Rossmann sheet is
not covered. So this motif cannot be dsRBD and thus has nothing to do with RNaseH domains (RNaseH is thought to originated from dsRBD).


The motif in 1g99: compared to d1ig8a1 (same superfamily), two strands are insertion to the RNaseH core. hybrid motif.
The motif in 1izn is the dimerization domain.


comparing d1gc5a_ & d1rkd__ (other family, but sure homolog to d1gc5a_, since they are very similar, including an inserted domain). The insertion
that forms part of the DCoH motif is absent in d1rkd__. So the motif in d1gc5a_ is a hybrid.


The motif in 1gx3: compare d1gx3a_ with classic cysteine proteinase papain d1ppn__ (same superfamily), half of the barrel in 1gx3 is
absent in 1ppn. So this is a hybrid motif and is analog to true barrels in all-beta class. Note that the cysteine proteinase superfamily is
very diverged in structures.


The motif in 1gx3: compare d1gx3a_ with classic cysteine proteinase papain d1ppn__ (same superfamily), half of the barrel in 1gx3 is absent in
1ppn. So this is a hybrid motif and is analog to true barrels in all-beta class. Note that the cysteine proteinase superfamily is very
diverged in structures.


1gxj (Smc hinge domain) appears to have two duplicates. Each duplicate has three strands linked by two helices. The two duplicates swap the
helix between strand 1 and strand 2. So, although the SCOP fold "Smc hinge domain" only has one protein, I think its core is different from 1p5d,
which is apparently a mini-Rossmann. Thus these two motifs are analogs.


The motif in 1h0h: hybrid, see the "structural drift" paper.


The motif in 1h5w: 4-helix bundle uses corresponding parts from two monomers, so it is an interface motif.


The motif in 1h6d: compared to d1lc0a2 (same superfamily), two strands are insertion. Hybrid. See d1drw_2 for the consensus of this fold as described
in SCOP.


In 1hbn_B, the 4-helix bundle uses two helices from the ferredoxin core and two inserted helices. This is a hybrid motif.


The motif in 1hi9 comes from two insertions and a Rossmann helix. Hybrid motif.


The motif in 1hrd: first helix is from the Rossmann core, the other two helices are from C-terminal extension. So this is a hybrid motif.


From the 1htj paper, the last three helices (helix 10-12) are an integral extension of the RGS fold with many hydrophobic interactions.
The last three helices are absent in other RGS, so they are insertions. The 3-helix motif in 1htj is a hybrid, using 1 helix from the
insertion and 2 helices from the RGS core.


From the 1htj paper, the last three helices (helix 10-12) are an integral extension of the RGS fold with many hydrophobic interactions.
These three helices are absent in other RGS, so they are insertions. The 4-helix motif is a hybrid, using 2 helices from the RGS core and
2 helices from the insertion.


The motif in 1i9e: two strands don't belong to the Ig core; hybrid motif.
Although 1mzk is also Ig-like (the first strand in Ig fold is the 5th strand in 1mzk, according to SCOP's 11 strands numbering), the motif
in 1i9e and the motif in 1mzk can not be homologs: if strands in Ig fold is counted from 1 to 7, all other strands are labeled as i
(insertion), the motif in 1i9e is 34ii56 while the motif in 1mzk is iii127. So no homologous elements are superimposed.


The motif in 1i9e: two strands don't belong to the Ig core; hybrid motif.


The motif in 1iho: comparing d1ihoa_ with d1coza_ (different family same superfamily, note the split between the first and the fourth strands). The
insertion is one strand and one helix, which is absent in d1coza_.
The motif in 1ep7: one strand and one helix are N-terminal extension to the thioredoxin fold. hybrid motif.


The motif in 1is8: the helix is not in the T-fold core, compared to 1r51 or 1b66 (same superfamily). hybrid motif.


In 1izn, the 4-helix bundle uses corresponding parts in the two chains. interface motif. Note that the two chains are not identical, but they are in the same superfamily in SCOP.
In 1gkz, the 4-helix bundle is the core motif of that domain.


In 1izn, the 4-helix bundle uses corresponding parts in the two chains. interface motif. Note that the two chains are not identical, but they are in
the same superfamily in SCOP.
In 1kek, the 4-helix bundle is an individual subdomain inserted in the Rossmann structure.


In 1izn, the 4-helix bundle uses corresponding parts in the two chains. interface motif. Note that the two chains are not identical, but they are in the same superfamily in SCOP.
In 2gsc, the 4-helix bundle is an individual domain by itself.


The motif in 1j22: From the paper for 1j22, in Fig. 2, d1j22a_ have similar catalytic residues as Hjc (d1gefa_). Thus,  d1j22a_ IS
an endonuclease superfamily member. Therefore, one strand and one helix in the motif are insertion. In other families, the insertion adopts
different conformations, e.g. d1ckqa_. So this hybrid motif is analogous to thioredoxin.


Comparing d1jdbc2 with d1gg9a1 and d1g2ia_, they are homologs (same SCOP superfamily but different family). Note the angle of the helix after strand
4. The motif in 1jdb is a hybrid because two strands in it do not belong to the flavodoxin core.


The motif in 1jnw: hybrid motif; compare to 1i0r, the core is a barrel;


The motif in 1k2f: uses part of the Ig core and the inserted strand; hybrid motif. The most important feature in Ig fold is the interlock
composed of strands 2, 3, 5, 6 (if strands in a classic Ig is numbered from 1 to 7), like two scissors arranged mouth-to-mouth.
The motif in 1svb: the first domain in 1svb is almost all meander, so it cannot be homologous to Ig-like proteins.


The motif in 1k9k: 4-helix bundle comes from a dimer interface, so it is an interface motif.


The motif in 1knz: 4-helix bundle uses corresponding parts from the two monomers, so it is an interface motif.


The motif in 1l6r: two strands are insertions; hybrid motif in a Rossmann structure.
In 1ir6: comparing d1ir6a_ and d1k20a_ (same superfamily), domain 2 in these two homologs are not exactly the same. Anyway,
domain 2 does not have a Rossmann-like structure. So the motif in 1l6r and the motif in 1ir6 are analogs.


The motif in 1l6r: two strands are insertions; hybrid motif in a Rossmann structure.
The motif in 1nrv: core motif in SH2 fold.


The motif in 1lci: the first helix is a N-terminal extension, the second one is present in the other duplicate, the third one is a
Rossmann helix. So this is a hybrid motif, but needs circular permutation to make it into a common topology.


1lq7 is an artificial protein, so it is analog to the natural protein 1gqe.


The motif in 1lwd: the 4-helix bundle uses the first and the last helices in the core structure, the other two helices come from
C-terminal extension. So this is a hybrid motif, but the topology is down-down-up-down.


The motif in 1m9n: occurs in the interface of the two duplicates.


The motif in 1miw: compare 1miw to d1fa0a4 (different family, same superfamily), a C-terminal beta-hairpin is insertion.
The motif in 1gyf: core motif.


The motif in 1mk5: it uses corresponding core elements in two monomers and is an interface motif.
The motif in 1efu: it uses corresponding core elements in two duplicates and is an interface motif.
The two motifs are analogous because 1mk5 is a barrel but 1efu is a a+b structure.


The motif in 1mw5: barrel formed by two monomers, interface motif.


In 1n00, the 4-helix bundle uses the first two helices in the 2nd duplicate and the first two helices in the 4th duplicate.
It occurs in the interface between two duplicates. Therefore, it is an interface motif.


The motif in 1n7v: The helix is a deteriorated blade in the propeller. This is a hybrid motif and can be analog to similar motifs in
SCOP a+b class.


The motif in 1nf2: compare 1nf2 with 1l6r (same family), the inserted subdomain is a circularly permuted ferredoxin in 1l6r. So the motif in 1nf2 is a hybrid.
The motif in 1ptm: occurs at the interface of the two duplicates, hybrid.


In 1nkt, the 3-helix bundle uses one helix in the N-terminal extra all-alpha subdomain, one helix before the first strand in the
Rossmann-like fold (this helix can be considered as part of the Rossmann fold), and one helix after the P-loop. This is a hybrid motif, but
the topology is up-down-down. So we make a circular permutation.


The motif in 1o02: hybrid; uses N-terminal extension and the 2nd and 3rd strands in the Rossmann core.
The motif in 1ihn: there is only one structure in this SCOP fold. No homologs to compare with. But this fold is very different from Rossmann fold.
So these two motifs are analogs.


The motif in 1o17: compare to d2tpt_2 (same family); two strands are insertions; hybrid motif resulted from a helix-to-strand transition in a Rossmann structure.
In 1ir6, comparing d1ir6a_ and d1k20a_ (same superfamily), domain 2 in these two homologs are not exactly the same. Anyway, domain 2 does
not have a Rossmann-like structure. So the motif in 1o17 and the motif in 1ir6 are analogs.


The motif in 1o17: compare to d2tpt_2 (same family); two strands are insertions; hybrid motif resulted from a helix-to-strand transition in a Rossmann structure.
The motif in 1jyr: core motif in SH2 fold.


The motif in 1ogq: compare d1ogqa_ to d1g9ua_ (same superfamily), one strand is insertion. hybrid motif.
The bottom line is that Leucine-rich repeat and KH domain are drastically different structures. So similar motifs come from them are analogs.


The motif in 1ogs: first two strands come from N-terminal extension, helix belongs to TIM-barrel, last two strands are insertion to TIM-barrel.
Hybrid.


The motif in 1ogs: first two strands come from N-terminal extension, helix belongs to TIM-barrel, last two strands are insertion to TIM-barrel. Hybrid.


1uw1 is an artificial protein and can be used as analog to natural proteins.


The motif is composed of two alpha-hairpins. In 1okr, the C-terminal extension has three helices and is probably a duplicated DNA/RNA-binding 3-helix bundle, only adapted to dimerization.
The motif uses two helices from each chain and is an interface motif. In 1m98, the motif covers two entire duplicates and thus is not an interface motif.
So the alpha-hairpins in 1okr and 1m98 are probably analogs.


The motif in 1okr: comes from two monomers, interface motif.


The motif in 1omo: interface motif uses elements from the two dimerization domains;
The motif in 1i7b: interface motif uses elements from the two duplicates;
Since the dimerization domain in 1omo and the duplicate in 1i7b are so different and so unlikely to evolutionarily related, these two motifs are analogs.


The motif in 1ovm: compared with d1dhs__ (same superfamily, same cofactor-binding mode), a helix-to-strand transition generated the motif.
The motif in 1914: core motif, comparing the two homologous domains (SRP9 and SRP14).
Strictly speaking, the motif in 1ovm is not a hybrid motif. However, since 1ovm is a Rossmann-like structure while 1914 is apparently not, these two
motifs are analogs.


The motif in 1p5g: comparing the three duplicates, the first two strands are insertion. Hybrid motif. Since the three domains apparently have a
mini-Rossman core, this motif can be used as analog to a+b motifs.


Compare 1pdz to d1bqg_1 (other family), the anti-parallel strand is the insertion. The motif in 1pdz comes from a TIM-barrel-like structure.
The motif in 1b66 comes from a a+b sandwich. They are analogs.


Compare 1pdz to d1bqg_1 (other family), the anti-parallel strand is the insertion. The motif in 1pdz comes from a TIM-barrel-like structure.
The motif in 1iru_M comes from Ntn-like a+b sandwich. They are analogs.


The motif in 1pie: two helices come from the "Ribosomal protein S5 domain 2-like" core and the third helix comes from C-terminal
extension. hybrid motif.


1pqs is a cloning artefact. It should be a ubiquitin fold.


In 1ps6, the motif occurs on the interface of the two duplicates. This is an interface motif.


The motif in 1qd1: uses the last strand in ferredoxin and the C-terminal extensions, hybrid. Compare the two duplicates.
The motif in 1itw: Each duplicate in Isocitrate dehydrogenase has five strands, 1~5. The rudimant ICDH fold, or the large insertion as described in
SCOP, uses strands 5, 1, 3. So this is a core motif. Note that the dimerization strands are after strand 5 in both the complete and the rudiment ICDH
subunits.


The motif in 1qd1: uses the last strand in ferredoxin and the C-terminal extensions, hybrid. Compare the two duplicates.
The motif in 1n62: stand-along, core motif.


The motif in 1qh4: compare to d2lgsa2 (same superfamily), two strands are insertion; hybrid motif.


The motif in 1qni: compared to 2cbp (same superfamily), the first strand in 1qni is an insertion. So this right-handed beta-helix in 1qni is a
hybrid. Basically, 1qni is a greek-key structure and is fundamentally different from the real beta-helix structures like 1k4z. So the motifs in
1qni and 1k4z are analogs.


In 1qo0, the motif uses one helix from the flavodoxin core in the first monomer, one helix from the N-terminal extension from the second monomer,
and one helix from the flavodoxin core in the second monomer. This is an interface as well as hybrid motif and is analogous to real RuvA C-like
left-handed 3-helix bundles.


Top7 is a de novo designed protein, and thus is analog to the natural protein 1i7b. Top7 paper mentioned that
there is no significant BLAST hit when Top7 sequence is used as query to search nr database.


The motif in 1r2j: the 3-helix bundle uses one helix from the C_terminal Bromodomain-like domain and two helices from the N-terminal
all-alpha domain. The N-terminal all-alpha domain is basically a superhelix arrangement while the C-terminal Bromodomain-like domain is a
up-and-down arrangement. So these are TWO domains instead of one big all-alpha domain. Therefore, the query motif is an interface motif using
elements from both domains.


The motif in 1rwh: This protein has two all-beta domains: Hyaluronate lyase-like (H) and Supersandwich (S). All proteins containing H have
S, but not vice versa. Since H and S are two separate domains, this motif is an interface motif, using some strands in H and some in S.
The motif in 1n67: uses immunoglobulin core elements as well as a C-terminal extension, hybrid.


The motif in 1slc: it uses strands 3456789. Although it is not a hybrid motif because all these seven strands are present in other
homologs of this family, this structure appears to be Ig-like: switch the positions of the very first and very last strands, then the very
first strand is strand 1 in Ig fold, there are two strands inserted after strand 4 in Ig and two strands inserted after strand 5 in Ig.
The motif in 1sq9: uses core elements in the propeller.


The motif in 1smt: it comes from a dimer interface, so it is an interface motif.
As long as the DALI hits are not DNA/RNA-binding 3-helix bundle, they can be used as analogs to the interface motif.


The motif in 1st6: the 4-helix bundle uses corresponding parts in two duplicates. This is an interface motif. Each duplicate is also a 4-helix
bundle, but is mirror image to the interface motif. 1st6 is in the Four-helical up-and-down bundle fold in SCOP. So I cannot use
anything in this fold as analog to the hybrid motif, since it may bear homologous part to the interface motif. 1jqn is in "TIM
beta/alpha-barrel" fold.


The motif in 1st6: comparing the 8 duplicates, we know that the helix before the last duplicate is an insertion. So the three helix bundle
is a hybrid motif with one inserted helix and two core helices.


The motif in 1tv8: a hybrid motif in an opened TIM-barrel.
1nbw has basically a mini-Rossmann core.


The motif in 1tv8: a hybrid motif in an opened TIM-barrel.
1t3e is basically Rossmann-like.


The motif in 1ukf: compare d1qmya_ and 1ukf, the two helices in the reverse-ferredoxin motif in 1ukf are absent in d1qmya_. So this is a hybrid motif.
This cysteine proteinase superfamily is very diverged in structures.


The motif in 1uou: it uses two helices in the N-terminal all-alpha domain, one insertion helix in the Rossmann-like domain, and the
crossover helix of the Rossmann domain. So it is a hybrid motif.


The motif in 1ur3: helix 1 and 4 are insertions while helix 2 and 3 are TIM barrel helices. So this is a hybrid motif.


1uw1 is an artificial protein, so it is analogous to the natural protein 1q9u.


Compare 1uyr and d1tyfa_ (different SCOP family, same superfamily), A N-terminal beta-hairpin is insertion. So the motif in 1uyr is a hybrid.


Compare 1uyr and d1tyfa_ (different SCOP family, same superfamily), A N-terminal beta-hairpin is insertion. So the motif in 1uyr is a hybrid.
The motif in 1a79 uses core elements from the endonuclease fold.


Compare d1vaoa2 and d2mbr_1 (same superfamily, the other domain is the same), one strand and one helix are insertion. Hybrid motif in 1vao.


The motif in 1vk3: if 1vk3 is considered to be an elaborated ferredoxin, one helix and two strands in the motif are insertions. Hybrid motif.
The motif in 1lbu: comparing with 1vhh, which lacks the last strand in the motif, this hedgehog/DD-peptidase fold has a circularly permuted
ferredoxin core. So the motif in 1lbu is a hybrid with the last strand being insertion.


The motif in 1vk3: if 1vk3 is considered to be an elaborated ferredoxin, one helix and two strands in the motif are insertions. Hybrid motif.
The motif in 1w2i: the last strand does not belong to the ferredoxin core.
These two motifs are analogs. In the superposition, the first ferredoxin strand in 1vk3 will be aligned to the first ferredoxin strand in
1w2i. But that is OK, since they are aligned back-to-back, i.e. the helix-packing face in one strand is aligned to the
non-helix-packing face in the other strand.


The motif in 2cst: Although each family in the PLP-dependent transferases superfamily has this motif, this is a hybrid, because PLP-dependent
transferases superfamily is homologous to some flavodoxin proteins. So this motif is a hybrid between the Rossmann-like core and the insertions, and
is therefore analogous to ancient folds like KH.


The motif in 2gaw: one strand is insertion, compared to d1pmab_ (d2gaw.1 is circularly permuted). This motif can be analog to motifs in
SCOP all beta class, like NusG.


The ubiquitin motif in 2one is a hybrid consisting of the first TIM strand, an inserted antiparallel strand, and a reversed helix.
It is analogous to real ubiquibin-like core motifs like the one in 1hz6.


The motif in 3pmg: comparing the three duplicates, the C-terminal beta hairpin in the first duplicate is an addition. Hybrid motif. These
three duplicates apparently have a mini-Rossmann core.
The motif in 1e8c: compare 1e8c_A with d1gg4a3 (same family), it appears that the antiparallel strand in 1e8c_A is originally a helix or loop
connecting the two parallel strands. Anyway, this can be regarded as a core motif.


The motif in 6mht: methyltransferase is homologous to Rossmann-like proteins, so the anti-parallel strand is an insertion. So the motif is
analogous to IF3-like.