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I-TASSER I-TASSER-MTD C-I-TASSER CR-I-TASSER QUARK C-QUARK LOMETS MUSTER CEthreader SEGMER DeepFold DeepFoldRNA FoldDesign COFACTOR COACH MetaGO TripletGO IonCom FG-MD ModRefiner REMO DEMO DEMO-EM DMFold SPRING COTH Threpp PEPPI BSpred ANGLOR EDock BSP-SLIM SAXSTER FUpred ThreaDom ThreaDomEx EvoDesign BindProf BindProfX SSIPe GPCR-I-TASSER MAGELLAN ResQ STRUM DAMpred

TM-score TM-align US-align MM-align RNA-align NW-align LS-align EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot MR-REX I-TASSER-MR SVMSEQ NeBcon ResPRE TripletRes DeepPotential WDL-RF ATPbind DockRMSD DeepMSA FASPR EM-Refiner GPU-I-TASSER

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14

BioLiP
>protein
QNLKSTDRAVQQMLDKAKREGIQTVWDRYEAMKPQCGFGETGLCCRHCLQGPCRINPFGDEPKVGICGATAEVIVARGLD
RSIAAGAAGHSGHAKHLAHTLKKAVQGKAASYMIKDRTKLHSIAKRLGIPTEGQKDEDIALEVAKAALADFHEKDTPVLW
VTTVLPPSRVKVLSAHGLIPAGIDHEIAEIMHRTSMGCDADAQNLLLGGLRCSLADLAGCYMGTDLADILFGTPAPVVTE
SNLGVLKADAVNVAVHGHNPVLSDIIVSVSKEMENEARAAGATGINVVGICCTGNEVLMRHGIPACTHSVSQEMAMITGA
LDAMILDYQCIQPSVATIAECTGTTVITTMEMSKITGATHVNFAEEAAVENAKQILRLAIDTFKRRKGKPVEIPNIKTKV
VAGFSTEAIINALSKLNANDPLKPLIDNVVNGNIRGVCLFAGCNNVKVPQDQNFTTIARKLLKQNVLVVATGCGAGALMR
HGFMDPANVDELCGDGLKAVLTAIGEANGLGGPLPPVLHMGSCVDNSRAVALVAALANRLGVDLDRLPVVASAAEWMHEK
AVAIGTWAVTIGLPTHIGVLPPITGSLPVTQILTSSVKDITGGYFIVELDPETAADKLLAAINERRAGLGLPW

The query sequence (length=633) is searched through a non-redundant set of database sequences protein_nr.fasta.gz clustered at 90% identity cutoff to identify representative hits. Homologs that belong to the same sequence cluster of the representative hit are listed in the last column of the table.

# Hit Hit
length
Aligned
length
Identity
(normalized by query)
Identity
(normalized by hit)
Identity (normalized
by aligned length)
E-value Homologs
to hit
1 3i39:X 635 633 0.9984 0.9953 0.9984 0.0 3b51:X, 3b52:X, 3b53:X, 7err:A, 5fle:X, 8omx:X, 8omy:X, 8on0:X, 8on1:X, 8on2:X, 8on3:X, 1su6:A, 1su7:A, 1su8:A, 1suf:A, 4udx:X, 4udy:X, 8x9d:A, 8x9e:A, 8x9f:A, 8x9g:A, 8x9h:A, 7xdm:A, 7xdn:A, 7xdp:A, 2yiv:X, 7zx3:X, 7zx5:X, 7zx6:X, 7zxc:X, 7zxj:X, 7zxl:X, 7zxx:X, 7zy1:X
2 1jqk:A 610 610 0.5513 0.5721 0.5721 0.0 1jqk:B, 1jqk:C, 1jqk:D, 1jqk:E, 1jqk:F
3 6elq:X 630 629 0.5403 0.5429 0.5437 0.0 6elq:A, 6elq:B
4 3i01:A 673 632 0.4882 0.4591 0.4889 0.0 3i01:B, 3i01:C, 3i01:D, 3i04:A, 3i04:B, 3i04:C, 3i04:D, 1mjg:A, 1mjg:B, 1mjg:C, 1mjg:D, 1oao:A, 1oao:B, 6x5k:A, 6x5k:B, 6x5k:C, 6x5k:D, 2z8y:A, 2z8y:B, 2z8y:C, 2z8y:D
5 8cja:A 669 630 0.4850 0.4589 0.4873 0.0 8cjb:A, 8cjc:A, 8cmw:A, 7zkj:A, 7zkk:A, 7zkv:A
6 6t7j:B 632 631 0.4771 0.4778 0.4786 0.0 6t7j:A, 6t7j:D
7 6ytt:C 630 640 0.4423 0.4444 0.4375 0.0 6ytt:B, 6yu9:A, 6yu9:B, 6yu9:C, 6yu9:D, 6yua:B, 6yua:C
8 6b6w:B 628 624 0.4566 0.4602 0.4631 9.16e-172 6b6v:A, 6b6v:B, 6b6w:A, 6b6x:A, 6b6x:B, 6b6y:A, 6b6y:B, 6dc2:A, 6dc2:B, 6dc2:C, 6dc2:D, 6onc:A, 6onc:B, 6onc:C, 6onc:D, 6ond:A, 6ond:B, 6ond:C, 6ond:D, 6ons:A, 7tsj:A, 6vwy:A, 6vwy:B, 6vwz:A, 6vwz:B, 6vx0:A, 6vx0:B, 6vx1:A, 6vx1:B
9 7b7q:A 629 639 0.3207 0.3227 0.3177 8.45e-93 7b7q:B, 7b7t:A, 7b7t:B, 7b95:A, 7b95:B, 7b97:A, 7b97:B, 7b9a:A, 7b9a:B, 7b9a:C, 7b9a:D
10 7e0l:A 491 181 0.0806 0.1039 0.2818 5.49e-10 7e0l:B, 7e0l:K, 7e0l:M, 7wsx:A, 7wsx:B
11 3cf4:A 766 354 0.1248 0.1031 0.2232 3.88e-05
12 3cf4:A 766 164 0.0711 0.0587 0.2744 0.001
13 7de4:A 550 333 0.1201 0.1382 0.2282 6.29e-05
14 1e1d:A 553 172 0.0632 0.0723 0.2326 0.31 1e2u:A, 1e9v:A, 1gnt:A, 1oa1:A, 1w9m:A
15 8ioc:R 272 100 0.0395 0.0919 0.2500 0.41
16 4qfl:A 507 90 0.0332 0.0414 0.2333 0.60 4qfl:B, 4qfn:A, 4qfn:B, 4qfo:A, 4qfo:B, 4qfp:A, 4qfp:B
17 7r2v:B 439 134 0.0521 0.0752 0.2463 1.3
18 1oj7:A 390 126 0.0616 0.1000 0.3095 2.2 1oj7:B, 1oj7:C, 1oj7:D, 4qgs:A
19 7yj0:D 622 169 0.0600 0.0611 0.2249 2.8 7yj0:A, 7yj0:B, 7yj0:C
20 1nos:A 323 77 0.0427 0.0836 0.3506 3.1 2nos:A, 2oro:A, 2orp:A, 2orq:A
21 4xww:A 545 52 0.0269 0.0312 0.3269 4.9 4xwt:A, 4xwt:B, 4xww:B
22 5xga:A 118 59 0.0300 0.1610 0.3220 8.2
23 4eei:B 423 38 0.0269 0.0402 0.4474 8.5 4eei:A, 5hw2:A, 5hw2:C
24 7egq:X 524 54 0.0284 0.0344 0.3333 9.9 5c8s:B, 5c8s:D, 5c8t:B, 5c8t:D, 5c8u:B, 5c8u:D, 7diy:B, 7egq:K, 7eiz:K, 9fw2:B, 9fz4:B, 9fzk:B, 7mc5:A, 7mc6:A, 7n0b:B, 7n0c:B, 7n0d:B, 7n0d:D, 7n0d:F, 7n0d:H, 5nfy:A, 5nfy:B, 5nfy:C, 5nfy:D

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Reference:
  • Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang. BioLiP2: an updated structure database for biologically relevent ligand-protein interactions, Nucleic Acids Research, gkad630 (2023).
  • Jianyi Yang, Ambrish Roy, and Yang Zhang. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Research, 41: D1096-D1103 (2013) (download the PDF file).
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