Datasets:
DeepFoldProtein
/
malisam-dataset

Dataset card Data Studio Files
xet
Community
1
pair_id
stringlengths
30
30
group_id
stringlengths
14
14
set_name
stringclasses
1 value
seq1_id
stringlengths
22
22
seq2_id
stringlengths
22
22
seq1
stringlengths
48
145
seq2
stringlengths
46
302
ref_alignment
listlengths
35
95
percent_identity
float64
0
19.1
scop_labels
listlengths
0
0
meta
stringlengths
117
593
d1ps6a_d1f9za_:d1ps6a_-d1f9za_
d1ps6a_d1f9za_
malisam
d1ps6a_d1f9za_:d1ps6a_
d1ps6a_d1f9za_:d1f9za_
EFAALITGPVHKFTGHTEFFEERSQAKKVVMMLATERGVNITLGLPFIRTSVDHGT
MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELG
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13.333333
[]
{"notes": "In 1ps6, the motif occurs on the interface of the two duplicates. This is an interface motif.\n", "source_file": "d1ps6a_d1f9za_.manual.ali"}
d1qd1b1d1itwa_:d1qd1b1-d1itwa_
d1qd1b1d1itwa_
malisam
d1qd1b1d1itwa_:d1qd1b1
d1qd1b1d1itwa_:d1itwa_
PRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARK
SADSKSHVAHMDNGDFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGPDGKLHDTKAVIPD
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19.148936
[]
{"notes": "The motif in 1qd1: uses the last strand in ferredoxin and the C-terminal extensions, hybrid. Compare the two duplicates.\nThe motif in 1itw: Each duplicate in Isocitrate dehydrogenase has five strands, 1~5. The rudimant ICDH fold, or the large insertion as described in\nSCOP, 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\nsubunits.\n", "source_file": "d1qd1b1d1itwa_.manual.ali"}
d1qd1b1d1n62c2:d1qd1b1-d1n62c2
d1qd1b1d1n62c2
malisam
d1qd1b1d1n62c2:d1qd1b1
d1qd1b1d1n62c2:d1n62c2
PRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGATVAGARK
MIPGSFDYHRPKSIADAVALLTKLGEDARPLAGGHSLIPIMKTRLATPEHLVDLRDIGDLV
[ [ 6, 6 ], [ 7, 7 ], [ 8, 8 ], [ 9, 9 ], [ 10, 10 ], [ 11, 11 ], [ 21, 12 ], [ 22, 13 ], [ 23, 14 ], [ 24, 15 ], [ 25, 16 ], [ 26, 17 ], [ 27, 18 ], [ 28, 19 ], [ 29, 20 ], [ 30, 21 ], [ 31, 22 ], [ 32, 23 ], [ 33, 24 ], [ 39, 26 ], [ 40, 27 ], [ 41, 28 ], [ 42, 29 ], [ 43, 30 ], [ 44, 31 ], [ 54, 32 ], [ 55, 33 ], [ 56, 34 ], [ 57, 35 ], [ 58, 36 ], [ 59, 37 ], [ 60, 38 ], [ 61, 39 ], [ 62, 40 ], [ 90, 48 ], [ 91, 49 ], [ 92, 50 ], [ 93, 51 ], [ 94, 52 ], [ 95, 53 ], [ 96, 54 ], [ 97, 55 ] ]
14.285714
[]
{"notes": "The motif in 1qd1: uses the last strand in ferredoxin and the C-terminal extensions, hybrid. Compare the two duplicates.\nThe motif in 1n62: stand-along, core motif.\n", "source_file": "d1qd1b1d1n62c2.manual.ali"}
d1qh4a2d1ekga_:d1qh4a2-d1ekga_
d1qh4a2d1ekga_
malisam
d1qh4a2d1ekga_:d1qh4a2
d1qh4a2d1ekga_:d1ekga_
IRGFCLPPHCSRGERRAIEKLSVEALGSLGGDLKGKYYALRNMMARDWPDARGIWHNDNKTFLVWINEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKNY
LDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGK
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10.416667
[]
{"notes": "The motif in 1qh4: compare to d2lgsa2 (same superfamily), two strands are insertion; hybrid motif.\n", "source_file": "d1qh4a2d1ekga_.manual.ali"}
d1qnia1d1k4za_:d1qnia1-d1k4za_
d1qnia1d1k4za_
malisam
d1qnia1d1k4za_:d1qnia1
d1qnia1d1k4za_:d1k4za_
VTLESDNKVIRDGNKVRVYMTSVAPQYGMTDFKVKEGDEVTVYITNLDMVEDVCHALHMEMVGRMLVEAA
MPPRKELVGNKWFIENYENETESLVIDANKDESIFIGKCSQVLVQIKGKVNAISLSETESCSVVLDSSISGMDVIKSNKFGIQVNHSLPQISIDKSDGGNIYLSKESLNTEIYTSCSTAINVNLPIGEDDDYVEFPIPEQMKHSFADGKFKSAVFEH
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7.5
[]
{"notes": "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 \nhybrid. Basically, 1qni is a greek-key structure and is fundamentally different from the real beta-helix structures like 1k4z. So the motifs in\n1qni and 1k4z are analogs.\n", "source_file": "d1qnia1d1k4za_.manual.ali"}
d1qo0d_d1hjp_1:d1qo0d_-d1hjp_1
d1qo0d_d1hjp_1
malisam
d1qo0d_d1hjp_1:d1qo0d_
d1qo0d_d1hjp_1:d1hjp_1
EYESPAVLSQIIELECSANSLLGSLRELQPLDAHRVLPVLVSARRISEEMA
DAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL
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5.555556
[]
{"notes": "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,\nand 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\nleft-handed 3-helix bundles.\n", "source_file": "d1qo0d_d1hjp_1.manual.ali"}
d1qysa_d1i7b.1:d1qysa_-d1i7b.1
d1qysa_d1i7b.1
malisam
d1qysa_d1i7b.1:d1qysa_
d1qysa_d1i7b.1:d1i7b.1
DIQVQVNIDDNGKNFDYTYTVTTESELQKVLNELMDYIKKQGAKRVRISITARTKKEAEKFAAILIKVFAELGYNDINVTFDGDTVTVEGQL
AHFFEGTEKLLEVWFSRQQPKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNFMKPSHQGYPHRNFQEEIEFLNAIFPNGAGYCMGRMNSDCWYLYTLDFPE
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9.210526
[]
{"notes": "Top7 is a de novo designed protein, and thus is analog to the natural protein 1i7b. Top7 paper mentioned that\nthere is no significant BLAST hit when Top7 sequence is used as query to search nr database.\n", "source_file": "d1qysa_d1i7b.1.manual.ali"}
d1r2ja2d1ecmb_:d1r2ja2-d1ecmb_
d1r2ja2d1ecmb_
malisam
d1r2ja2d1ecmb_:d1r2ja2
d1r2ja2d1ecmb_:d1ecmb_
GLGLGSRENGEFTAHVGSLCSSLRSVMTSQGMAAWTVQRLGLAGSGASLPMLVAASLAYGRKSVAWGCVGILRACRTAAVAHARTR
PLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLITLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKIN
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5.970149
[]
{"notes": "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\nall-alpha domain. The N-terminal all-alpha domain is basically a superhelix arrangement while the C-terminal Bromodomain-like domain is a\nup-and-down arrangement. So these are TWO domains instead of one big all-alpha domain. Therefore, the query motif is an interface motif using\nelements from both domains.\n", "source_file": "d1r2ja2d1ecmb_.manual.ali"}
d1rwha2d1n67a2:d1rwha2-d1n67a2
d1rwha2d1n67a2
malisam
d1rwha2d1n67a2:d1rwha2
d1rwha2d1n67a2:d1n67a2
EGQWGAAVPADEWSGATALGEVAAVGQHLVGPGRTGLTARKSWFVSGDVTVCLGADISTASGAKVEGNKYSVIRNDATAQSVEFKTAKTTAATFWKPGMAGDLGASGPACVVFSRHGNELSLAVSEPTQKAAG
EKYGKFYNLSIKGTIDQIDKTNNTYRQTIYVNPSGDNVIAPVLTGNLKPNTDSNALIDQQNTSIKVYKVDNAADLSESYFVNPENFEDVTNSVNITFPNPNQYKVEFNTPDDQITTPYIVVVNGHIDPNSKGDLALRSTLYGYNSNIIWRSMSWDNEVAFNNGSGSGDGIDKPVVPEQPDEPGEIEPIPEK
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4.225352
[]
{"notes": "The motif in 1rwh: This protein has two all-beta domains: Hyaluronate lyase-like (H) and Supersandwich (S). All proteins containing H have\nS, 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.\nThe motif in 1n67: uses immunoglobulin core elements as well as a C-terminal extension, hybrid.\n", "source_file": "d1rwha2d1n67a2.manual.ali"}
d1slca_d1sq9a_:d1slca_-d1sq9a_
d1slca_d1sq9a_
malisam
d1slca_d1sq9a_:d1slca_
d1slca_d1sq9a_:d1sq9a_
AADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLE
GEFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEEDILAVDEHGDSLAEPGVFDVKFLKKGWRSGMGADLNESLCCVCLDRSIRWFREAG
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11.267606
[]
{"notes": "The motif in 1slc: it uses strands 3456789. Although it is not a hybrid motif because all these seven strands are present in other\nhomologs of this family, this structure appears to be Ig-like: switch the positions of the very first and very last strands, then the very\nfirst 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.\nThe motif in 1sq9: uses core elements in the propeller.\n", "source_file": "d1slca_d1sq9a_.manual.ali"}
d1smta_d1b7ta4:d1smta_-d1b7ta4
d1smta_d1b7ta4
malisam
d1smta_d1b7ta4:d1smta_
d1smta_d1b7ta4:d1b7ta4
IAPEVAQSLAEFFAVLADPNRLRLLSLLARSEQLQDHHIVALYQNALDHLQECIAPEVAQSLAEFFAVLADPNRLRLLSLLARSEQLQDHHIVALYQNALDHLQE
DDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNITGWLEKNKDPINENVVALLGASKEPLVAELFKA
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13.461538
[]
{"notes": "The motif in 1smt: it comes from a dimer interface, so it is an interface motif. \nAs long as the DALI hits are not DNA/RNA-binding 3-helix bundle, they can be used as analogs to the interface motif.\n", "source_file": "d1smta_d1b7ta4.manual.ali"}
d1st6a2d1jqna_:d1st6a2-d1jqna_
d1st6a2d1jqna_
malisam
d1st6a2d1jqna_:d1st6a2
d1st6a2d1jqna_:d1jqna_
THQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWTANKTTVEGIQATVKSARELTPQVVSAARILLRNPGNQAAYEHFETMKNQWIDNVEKMTGLVDEAI
NPNVTADITRHVLLLSRWKATDLFLKDIQVLVSELSMVEATPELLALVGEEGAAEPYRYLMKNLRSRLMATQAWLEARLKGEELPKPEGLLTQNEELWEPLYACYQSLQACGMGIIANGDLLDTLRRVKCFGVPLV
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9.473684
[]
{"notes": "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\nbundle, 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\nanything in this fold as analog to the hybrid motif, since it may bear homologous part to the interface motif. 1jqn is in \"TIM\nbeta/alpha-barrel\" fold.\n", "source_file": "d1st6a2d1jqna_.manual.ali"}
d1st6a8d1gvna_:d1st6a8-d1gvna_
d1st6a8d1gvna_
malisam
d1st6a8d1gvna_:d1st6a8
d1st6a8d1gvna_:d1gvna_
PPPPEEKDEEFPEQKAGEAINQPMMMAARQLHDEARKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPWY
VTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVNLLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNKEKV
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8.333333
[]
{"notes": "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\nis a hybrid motif with one inserted helix and two core helices.\n", "source_file": "d1st6a8d1gvna_.manual.ali"}
d1st6a8d1r5id_:d1st6a8-d1r5id_
d1st6a8d1r5id_
malisam
d1st6a8d1r5id_:d1st6a8
d1st6a8d1r5id_:d1r5id_
PPPPEEKDEEFPEQKAGEAINQPMMMAARQLHDEARKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPWY
MKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNF
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7.352941
[]
{"notes": "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\nis a hybrid motif with one inserted helix and two core helices.\n", "source_file": "d1st6a8d1r5id_.manual.ali"}
d1tv8a_d1nbwb_:d1tv8a_-d1nbwb_
d1tv8a_d1nbwb_
malisam
d1tv8a_d1nbwb_:d1tv8a_
d1tv8a_d1nbwb_:d1nbwb_
IRDLRLSVTDRCNFRCDYCMPKEVFGDDFVFLPKNELLTFDEMARIAKVYAELGVTRARLSSDGKFYGCLFATVDGFNVKAFIRSGVTDEELKEQFKALWQIRDD
PPGVRLFYDPRGHHAGAINELCWGLEEQGVPCQTITYDGGGDAAALGALAARSSPLRVGIGLSASGEIALTHAQLPADAPLATGHVTDSDDQLRTLGANAGQLVKVLPLSERN
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13.846154
[]
{"notes": "The motif in 1tv8: a hybrid motif in an opened TIM-barrel.\n1nbw has basically a mini-Rossmann core.\n", "source_file": "d1tv8a_d1nbwb_.manual.ali"}
d1tv8a_d1t3ea3:d1tv8a_-d1t3ea3
d1tv8a_d1t3ea3
malisam
d1tv8a_d1t3ea3:d1tv8a_
d1tv8a_d1t3ea3:d1t3ea3
LNVKVNVVIQKGINDDQIIPMLEYFKDKHIEIRFIEFMDVGNDNGWDFSKVVTKDEMLTMIEQHFEIDPVEPKYFGEVAKYYRHKDNGVQFGLITSVSQS
PVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPR
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8.333333
[]
{"notes": "The motif in 1tv8: a hybrid motif in an opened TIM-barrel.\n1t3e is basically Rossmann-like.\n", "source_file": "d1tv8a_d1t3ea3.manual.ali"}
d1ukfa_d1gsa_2:d1ukfa_-d1gsa_2
d1ukfa_d1gsa_2
malisam
d1ukfa_d1gsa_2:d1ukfa_
d1ukfa_d1gsa_2:d1gsa_2
GFSLRREPKTVHASGGSAQLGQTVAHDVAQSGRKHLLSLRFANVQGHAIACSCEGSQFKLFDPNLGEFQSSRSAAPQLIKGLIDHYNSLNYDVACVNEFRVSV
NEKLFTAWFSDLTPETLVTRNKAQLKAFWEKHSDIILKPLDGMGGASIFRVKEGDPNLGVIAETLTEHGTRYCMAQNYLPAIKD
[ [ 6, 14 ], [ 7, 15 ], [ 8, 16 ], [ 9, 17 ], [ 10, 18 ], [ 11, 19 ], [ 19, 20 ], [ 20, 21 ], [ 21, 22 ], [ 22, 23 ], [ 23, 24 ], [ 24, 25 ], [ 25, 26 ], [ 26, 27 ], [ 27, 28 ], [ 28, 29 ], [ 29, 30 ], [ 30, 31 ], [ 32, 32 ], [ 33, 33 ], [ 34, 34 ], [ 35, 35 ], [ 36, 36 ], [ 37, 37 ], [ 38, 38 ], [ 39, 39 ], [ 40, 40 ], [ 45, 45 ], [ 46, 46 ], [ 47, 47 ], [ 48, 48 ], [ 49, 49 ], [ 50, 50 ], [ 51, 51 ], [ 52, 52 ], [ 57, 53 ], [ 58, 54 ], [ 76, 55 ], [ 77, 56 ], [ 78, 57 ], [ 79, 58 ], [ 80, 59 ], [ 81, 60 ], [ 82, 61 ], [ 83, 62 ], [ 84, 63 ], [ 85, 64 ], [ 86, 65 ], [ 87, 66 ], [ 92, 69 ], [ 93, 70 ], [ 94, 71 ], [ 95, 72 ], [ 96, 73 ], [ 97, 74 ], [ 98, 75 ], [ 99, 76 ], [ 100, 77 ], [ 101, 78 ], [ 102, 79 ] ]
3.333333
[]
{"notes": "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. \nThis cysteine proteinase superfamily is very diverged in structures.\n", "source_file": "d1ukfa_d1gsa_2.manual.ali"}
d1uoua1d1fs1b1:d1uoua1-d1fs1b1
d1uoua1d1fs1b1
malisam
d1uoua1d1fs1b1:d1uoua1
d1uoua1d1fs1b1:d1fs1b1
SAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGL
DPVPLPNVNAAILKKVIQWCTHHKDDPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFN
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6.896552
[]
{"notes": "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\ncrossover helix of the Rossmann domain. So it is a hybrid motif.\n", "source_file": "d1uoua1d1fs1b1.manual.ali"}
d1ur3m_d1k87a1:d1ur3m_-d1k87a1
d1ur3m_d1k87a1
malisam
d1ur3m_d1k87a1:d1ur3m_
d1ur3m_d1k87a1:d1k87a1
GRLFNDDYFQPLRDELAVVAEELNAGSIEQVVNAWVLRLPSSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDV
QKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISNGNRSPSLFVNAATWGLLFTGNEASLSRSLNRIIGKSGEPLIRKGVDMAMRLMGEQFVT
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8.77193
[]
{"notes": "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.\n", "source_file": "d1ur3m_d1k87a1.manual.ali"}
d1uw1a_d1q9ua_:d1uw1a_-d1q9ua_
d1uw1a_d1q9ua_
malisam
d1uw1a_d1q9ua_:d1uw1a_
d1uw1a_d1q9ua_:d1q9ua_
DDKKTNWLKRIYRVRPCVKCKVAPRNWKVKNKHLRIYNMCKTCFNNSIDIGDDTYHGHDDWLMYADS
MFHYTVDVSTGMNETIERLEESLKQEGFGVLWQFSVTEKLQEKGLDFSTPMVILEVCNPQEAARVLNENLLVGYFLPCKLVVYQENGTTKIGMPKPTMLVGMMNDPALKEIAADIEKRLAACLDRCR
[ [ 2, 10 ], [ 3, 11 ], [ 4, 12 ], [ 5, 13 ], [ 6, 14 ], [ 7, 15 ], [ 8, 16 ], [ 9, 17 ], [ 10, 18 ], [ 11, 19 ], [ 12, 20 ], [ 13, 21 ], [ 14, 22 ], [ 15, 23 ], [ 20, 26 ], [ 21, 27 ], [ 22, 28 ], [ 23, 29 ], [ 24, 30 ], [ 25, 31 ], [ 26, 32 ], [ 27, 33 ], [ 28, 34 ], [ 29, 35 ], [ 30, 36 ], [ 31, 49 ], [ 32, 50 ], [ 33, 51 ], [ 34, 52 ], [ 35, 53 ], [ 36, 54 ], [ 37, 55 ], [ 55, 76 ], [ 56, 77 ], [ 57, 78 ], [ 58, 79 ], [ 59, 80 ], [ 60, 81 ], [ 61, 82 ] ]
2.564103
[]
{"notes": "1uw1 is an artificial protein, so it is analogous to the natural protein 1q9u.\n", "source_file": "d1uw1a_d1q9ua_.manual.ali"}
d1uyra1d1vkka_:d1uyra1-d1vkka_
d1uyra1d1vkka_
malisam
d1uyra1d1vkka_:d1uyra1
d1uyra1d1vkka_:d1vkka_
DVKLTDDFFISNELIEDENGELTEVEREPGANAIGMVAFKITVKTPEYPRGRQFVVVANDITFKIGSFGPQEDEFFNKVTEYARKRGIPRIYLAANSGARDDLAGVEKIVEWMSYVPAKRNMP
VVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLELPERQPRFVVYSYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAELTKVFEIRTTDDLTETWLKEKLAFFR
[ [ 7, 22 ], [ 8, 23 ], [ 9, 24 ], [ 10, 25 ], [ 11, 26 ], [ 12, 27 ], [ 13, 28 ], [ 14, 29 ], [ 15, 30 ], [ 16, 31 ], [ 17, 32 ], [ 18, 34 ], [ 19, 35 ], [ 20, 36 ], [ 21, 37 ], [ 22, 38 ], [ 23, 39 ], [ 24, 40 ], [ 34, 59 ], [ 35, 60 ], [ 36, 61 ], [ 37, 62 ], [ 38, 63 ], [ 39, 64 ], [ 40, 65 ], [ 41, 66 ], [ 42, 67 ], [ 43, 68 ], [ 44, 69 ], [ 45, 70 ], [ 49, 77 ], [ 50, 78 ], [ 51, 79 ], [ 52, 80 ], [ 53, 81 ], [ 54, 82 ], [ 55, 83 ], [ 56, 84 ], [ 57, 85 ], [ 58, 86 ], [ 59, 87 ], [ 60, 88 ], [ 61, 89 ], [ 62, 90 ], [ 63, 91 ], [ 68, 92 ], [ 69, 93 ], [ 70, 94 ], [ 71, 95 ], [ 72, 96 ], [ 73, 97 ], [ 74, 98 ], [ 75, 99 ], [ 76, 100 ], [ 77, 101 ], [ 78, 102 ], [ 79, 103 ], [ 80, 104 ], [ 81, 105 ], [ 82, 106 ], [ 83, 107 ], [ 84, 108 ], [ 85, 109 ], [ 86, 110 ], [ 87, 111 ], [ 88, 113 ], [ 89, 114 ], [ 90, 115 ], [ 91, 116 ], [ 92, 117 ], [ 93, 118 ], [ 94, 119 ], [ 101, 124 ], [ 102, 125 ], [ 103, 126 ], [ 104, 127 ], [ 105, 128 ], [ 106, 129 ], [ 107, 130 ], [ 108, 131 ], [ 109, 132 ], [ 110, 133 ], [ 111, 134 ], [ 112, 135 ], [ 113, 136 ] ]
4.705882
[]
{"notes": "Compare 1uyr and d1tyfa_ (different SCOP family, same superfamily), A N-terminal beta-hairpin is insertion. So the motif in 1uyr is a hybrid.\n", "source_file": "d1uyra1d1vkka_.manual.ali"}
d1uyrb1d1a79a1:d1uyrb1-d1a79a1
d1uyrb1d1a79a1
malisam
d1uyrb1d1a79a1:d1uyrb1
d1uyrb1d1a79a1:d1a79a1
ATPYPVKEWLQPKRYKAHLMGTTYVYDFPELFRQASSSQWKNFSADVKLTDDFFISNELIEDENGELTEVEREPGANAIGMVAFKITVKTPEYPRGRQFVVVANDITFKIGSFGPQEDEFFNKVTEYARKRGIPRIYLAANSGAR
ERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP
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11.594203
[]
{"notes": "Compare 1uyr and d1tyfa_ (different SCOP family, same superfamily), A N-terminal beta-hairpin is insertion. So the motif in 1uyr is a hybrid.\nThe motif in 1a79 uses core elements from the endonuclease fold.\n", "source_file": "d1uyrb1d1a79a1.manual.ali"}
d1vaoa2d1no5a_:d1vaoa2-d1no5a_
d1vaoa2d1no5a_
malisam
d1vaoa2d1no5a_:d1vaoa2
d1vaoa2d1no5a_:d1no5a_
EFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISASAIVAPRNVADVQSIVGLANKFSFGSVVLDM
QLDIKSEELAIVKTILQQLVPDYTVWAFGSRVKGKAKKYSDLDLAIISEEPLDFLARDRLKEAFSESDLPWRVDLLDWATTSEDFREIIRKVYVVIQEKE
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10.526316
[]
{"notes": "Compare d1vaoa2 and d2mbr_1 (same superfamily, the other domain is the same), one strand and one helix are insertion. Hybrid motif in 1vao.\n", "source_file": "d1vaoa2d1no5a_.manual.ali"}
d1vk3a3d1lbu_2:d1vk3a3-d1lbu_2
d1vk3a3d1lbu_2
malisam
d1vk3a3d1lbu_2:d1vk3a3
d1vk3a3d1lbu_2:d1lbu_2
KASRPGQVIVIFGGATGRDGAGGVLSATSELVAKGNLGAIVHLDRVPLRLFGDVVAEVIEEPVYRVMYR
GHAADLGAGSQGFCALAQAARNHGFTEILGPGYPGHNDHTHVAGGDGRFWSAPSCGI
[ [ 3, 0 ], [ 4, 1 ], [ 5, 2 ], [ 6, 3 ], [ 7, 4 ], [ 8, 5 ], [ 9, 6 ], [ 10, 7 ], [ 11, 8 ], [ 12, 9 ], [ 22, 10 ], [ 23, 11 ], [ 24, 12 ], [ 25, 13 ], [ 26, 14 ], [ 27, 15 ], [ 28, 16 ], [ 29, 17 ], [ 30, 18 ], [ 31, 19 ], [ 32, 20 ], [ 33, 21 ], [ 34, 22 ], [ 35, 23 ], [ 36, 24 ], [ 37, 26 ], [ 38, 27 ], [ 39, 28 ], [ 40, 29 ], [ 41, 30 ], [ 54, 38 ], [ 55, 39 ], [ 56, 40 ], [ 57, 41 ], [ 58, 42 ], [ 59, 43 ], [ 60, 46 ], [ 61, 47 ], [ 62, 48 ], [ 63, 49 ], [ 64, 50 ], [ 65, 51 ] ]
4.761905
[]
{"notes": "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.\nThe motif in 1lbu: comparing with 1vhh, which lacks the last strand in the motif, this hedgehog/DD-peptidase fold has a circularly permuted\nferredoxin core. So the motif in 1lbu is a hybrid with the last strand being insertion.\n", "source_file": "d1vk3a3d1lbu_2.manual.ali"}
d1vk3a3d1w2ia_:d1vk3a3-d1w2ia_
d1vk3a3d1w2ia_
malisam
d1vk3a3d1w2ia_:d1vk3a3
d1vk3a3d1w2ia_:d1w2ia_
KASRPGQVIVIFGGATGRDGAGGVLSATSELVAKGNLGAIVHLDRVPLRLFGDVVAEVIEEPVYRVMYR
AIVRAHLKIYGRVQGVGFRWSMQREARKLGVNGWVRNLPDGSVEAVLEGDEERVEALIGWAHQGPPLARVTRVEVKWEQPKGEKGFRIVG
[ [ 4, 2 ], [ 5, 3 ], [ 6, 4 ], [ 7, 5 ], [ 8, 6 ], [ 9, 7 ], [ 10, 8 ], [ 11, 9 ], [ 12, 10 ], [ 13, 11 ], [ 14, 12 ], [ 15, 13 ], [ 16, 14 ], [ 22, 16 ], [ 23, 17 ], [ 24, 18 ], [ 25, 19 ], [ 26, 20 ], [ 27, 21 ], [ 28, 22 ], [ 29, 23 ], [ 30, 24 ], [ 31, 25 ], [ 32, 26 ], [ 33, 27 ], [ 34, 28 ], [ 35, 29 ], [ 36, 30 ], [ 37, 31 ], [ 38, 32 ], [ 39, 33 ], [ 40, 34 ], [ 41, 35 ], [ 42, 36 ], [ 43, 37 ], [ 49, 39 ], [ 50, 40 ], [ 51, 41 ], [ 52, 42 ], [ 53, 43 ], [ 55, 44 ], [ 56, 45 ], [ 57, 46 ], [ 58, 47 ], [ 59, 48 ], [ 61, 83 ], [ 62, 84 ], [ 63, 85 ], [ 64, 86 ], [ 65, 87 ], [ 66, 88 ], [ 67, 89 ] ]
15.384615
[]
{"notes": "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.\nThe motif in 1w2i: the last strand does not belong to the ferredoxin core.\nThese two motifs are analogs. In the superposition, the first ferredoxin strand in 1vk3 will be aligned to the first ferredoxin strand in\n1w2i. But that is OK, since they are aligned back-to-back, i.e. the helix-packing face in one strand is aligned to the\nnon-helix-packing face in the other strand.\n", "source_file": "d1vk3a3d1w2ia_.manual.ali"}
d2csta_d1j4wa1:d2csta_-d1j4wa1
d2csta_d1j4wa1
malisam
d2csta_d1j4wa1:d2csta_
d2csta_d1j4wa1:d1j4wa1
LGLPEFRANASRIALGDDSPAIAQKRVGSVQGLGGTGALRIGAEFLRRWYNGFELFCAQSFSKNFGLYNERVGNLSVVGKDEDNVQRVLSQMEKIVRTTWSNP
GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQ
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11.47541
[]
{"notes": "The motif in 2cst: Although each family in the PLP-dependent transferases superfamily has this motif, this is a hybrid, because PLP-dependent\ntransferases superfamily is homologous to some flavodoxin proteins. So this motif is a hybrid between the Rossmann-like core and the insertions, and\nis therefore analogous to ancient folds like KH.\n", "source_file": "d2csta_d1j4wa1.manual.ali"}
d2gaw.1d1nppa1:d2gaw.1-d1nppa1
d2gaw.1d1nppa1
malisam
d2gaw.1d1nppa1:d2gaw.1
d2gaw.1d1nppa1:d1nppa1
NKPIVLSTWNTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETP
EEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLD
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7.692308
[]
{"notes": "The motif in 2gaw: one strand is insertion, compared to d1pmab_ (d2gaw.1 is circularly permuted). This motif can be analog to motifs in\nSCOP all beta class, like NusG.\n", "source_file": "d2gaw.1d1nppa1.manual.ali"}
d2onea1d1hz6b_:d2onea1-d1hz6b_
d2onea1d1hz6b_
malisam
d2onea1d1hz6b_:d2onea1
d2onea1d1hz6b_:d1hz6b_
SPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQ
EEVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEWTVDVADKGYTLNIKFAG
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16.666667
[]
{"notes": "The ubiquitin motif in 2one is a hybrid consisting of the first TIM strand, an inserted antiparallel strand, and a reversed helix.\nIt is analogous to real ubiquibin-like core motifs like the one in 1hz6.\n", "source_file": "d2onea1d1hz6b_.manual.ali"}
d3pmga1d1e8ca1:d3pmga1-d1e8ca1
d3pmga1d1e8ca1
malisam
d3pmga1d1e8ca1:d3pmga1
d3pmga1d1e8ca1:d1e8ca1
ATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQGVLGKQQFDLENKFKPFTVEIVDS
RNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREMHGVPVIYLSQLNERLSALAGRFYHE
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11.627907
[]
{"notes": "The motif in 3pmg: comparing the three duplicates, the C-terminal beta hairpin in the first duplicate is an addition. Hybrid motif. These\nthree duplicates apparently have a mini-Rossmann core.\nThe 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\nconnecting the two parallel strands. Anyway, this can be regarded as a core motif.\n", "source_file": "d3pmga1d1e8ca1.manual.ali"}
d6mhta_d1vm0b_:d6mhta_-d1vm0b_
d6mhta_d1vm0b_
malisam
d6mhta_d1vm0b_:d6mhta_
d6mhta_d1vm0b_:d1vm0b_
DHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLN
KNRIQVSNTKKPLFFYVNLAKRYMQQYNDVELSALGMAIATVVTVTEILKNNGFAVEKKIMTSIVDIKDDARGRPVQKAKIEITLVKSEKFDELMAAANEEKE
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7.142857
[]
{"notes": "The motif in 6mht: methyltransferase is homologous to Rossmann-like proteins, so the anti-parallel strand is an insertion. So the motif is\nanalogous to IF3-like.\n", "source_file": "d6mhta_d1vm0b_.manual.ali"}