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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
YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSAL
REVGKLLAFLKLNMPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGK
NKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVP
ASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQK
QFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARD
TVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF

The query sequence (length=465) 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 5m1d:A 469 468 1.0000 0.9915 0.9936 0.0 5m1d:B, 5m1d:C, 5m1e:A, 5m1e:B, 5m1e:C
2 6h6v:F 446 445 0.3075 0.3206 0.3213 4.40e-56 6h6v:A, 6h6v:B, 6h6v:C, 6h6v:D, 6h6v:E, 6h6x:B, 6h6x:A
3 7ae4:A 476 457 0.2903 0.2836 0.2954 2.80e-48 7ae4:B, 7ae4:C, 7ae4:D, 7ae4:E, 7ae4:F
4 7nf4:A 504 467 0.2839 0.2619 0.2827 4.88e-43 8crd:A, 6ev3:A, 6ev4:A, 6ev5:A, 6ev6:A, 6ev7:A, 6ev8:A, 6ev9:A, 6eva:A, 6evb:A, 6evc:A, 6evd:A, 7nf3:A, 7nf4:B, 8oed:A, 8oeh:A, 8oeo:A, 6r2p:A, 6r2r:A, 6r2t:A, 6r2z:A, 6r30:A, 6r32:A, 6r33:A, 6r34:A, 6r3f:A, 6r3g:A, 6r3i:A, 6r3j:A, 6r3l:A, 6r3n:A, 6r3o:A, 6tib:AAA, 6tic:AAA, 6tie:AAA, 6tih:AAA, 6tij:AAA, 6til:AAA, 6tin:AAA, 6tio:AAA, 4za4:A, 4za5:A, 4za7:A, 4za8:A, 4za9:A, 4zaa:A, 4zab:A
5 4zad:A 511 463 0.2710 0.2466 0.2721 4.91e-40 4zad:B
6 6evf:A 503 431 0.2473 0.2286 0.2668 2.15e-38 6eve:A, 6eve:B, 6eve:C, 6eve:D, 6evf:B, 6evf:C, 6evf:D, 4s13:C, 4s13:F, 4zac:A, 4zac:B, 4zac:C, 4zac:D
7 7pda:A 477 432 0.2731 0.2662 0.2940 2.38e-37
8 7p9q:A 454 445 0.2581 0.2643 0.2697 9.60e-36 7p9q:B, 7p9q:C, 7p9q:D, 7p9q:E, 7p9q:F
9 7ney:A 497 470 0.2839 0.2656 0.2809 3.18e-34 7ney:B, 7nf0:A, 7nf0:B, 7nf1:A, 7nf1:B, 7nf2:A, 7nf2:B
10 6da9:A 463 420 0.2452 0.2462 0.2714 3.74e-34
11 5o3m:A 493 426 0.2559 0.2414 0.2793 8.53e-31 5o3m:B, 5o3m:C, 5o3m:D, 5o3m:E, 5o3m:F
12 5o3n:A 488 498 0.2796 0.2664 0.2610 9.84e-31 5o3n:B
13 4ip2:C 502 458 0.2710 0.2510 0.2751 2.15e-29 7abn:D, 7abn:A, 7abn:H, 7abn:M, 7abo:C, 7abo:B, 7abo:D, 7abo:A, 4ip2:A, 4ip2:B
14 4s13:A 472 430 0.2430 0.2394 0.2628 7.56e-28 4s13:G
15 8oz5:A 514 442 0.2387 0.2160 0.2511 6.68e-15 8oz5:B, 8oz5:C, 8oz5:D, 8oz5:E, 8oz5:F, 8p02:A, 8p02:B, 8p02:C, 8p02:D, 8p02:E, 8p02:F, 8pmk:A, 8pmk:B, 8pmk:C, 8pmk:D, 8pmk:E, 8pmk:F
16 8e5i:A 357 125 0.0710 0.0924 0.2640 0.70
17 4hmd:A 528 72 0.0473 0.0417 0.3056 1.2 4mb4:A, 4mb5:A
18 1oac:B 723 26 0.0280 0.0180 0.5000 1.3 1d6u:A, 1d6u:B, 1d6y:A, 1d6y:B, 1d6z:A, 1d6z:B, 1dyu:A, 1dyu:B, 6ezz:A, 6ezz:B, 6grr:A, 6grr:B, 1jrq:A, 1jrq:B, 1lvn:A, 1lvn:B, 1oac:A, 1qaf:A, 1qaf:B, 1qak:A, 1qak:B, 1qal:A, 1qal:B, 1spu:A, 1spu:B, 2w0q:A, 2w0q:B, 2wgq:A, 2wgq:B, 2wo0:A, 2wo0:B, 2wof:A, 2wof:B, 2woh:A, 2woh:B
19 5zk4:D 73 22 0.0280 0.1781 0.5909 2.0
20 2py2:A 127 20 0.0194 0.0709 0.4500 2.5 2py2:B, 2py2:C, 2py2:D, 2py2:E, 2py2:F
21 3zqj:D 921 172 0.0817 0.0413 0.2209 2.6 3zqj:B, 3zqj:E
22 6dgd:A 704 165 0.0882 0.0582 0.2485 3.9 6dgd:B, 4nl4:H
23 6plm:B 752 56 0.0366 0.0226 0.3036 4.8 6k4r:A, 6k4r:B, 7mir:A, 7mis:A, 6oqq:A, 6oqq:C, 6plm:A, 6s5t:A
24 6jk4:A 126 27 0.0194 0.0714 0.3333 5.2
25 7qok:A 1361 75 0.0387 0.0132 0.2400 6.3
26 6a4z:A 127 38 0.0280 0.1024 0.3421 7.4 6a4z:B, 7w5e:A, 7w5e:B, 7w5e:C, 7w5e:D, 7wb2:A, 7wb2:B, 7wb2:C, 7wb2:D
27 6dcr:B 600 63 0.0430 0.0333 0.3175 9.2

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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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