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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
MRYAETGYVLEVDLTKGSIERVATDPRDTELYLGGLGTNAKILWDRVPPEVEPFSPENLLIFAAGLLCGTPATGCNRTIV
STVSPQTKLMAFSMMGGFWAPELKYAGYDKIIFRGKSPELVYLYINNDKVEIRDASHLKGKGAIETAEIIKKELNEPRAQ
VAAIGKAGENRVFYASIEQGRSSASRGGIGAVMGDKGLKAVVVRGTKDLCVAKPEEYIGLCNEVLDYIKHREENPIPDVM
PILAGLGSPQEMKVHDEKWHTENFNWGNARTRRKDFWTDEVSHAWEKTMDKARTRLISCYNCPMKCGATISMEGLPTYMM
KCFTKLTYTMAAYSDLDFGLRIAQKATEYGLDGFSAPQVMAFAFELLEKGILKDSDFPGLPEGNEERFFYLLDKIVNRDG
IGDILANGTYWAAQEIGNGAEDYAHNNIKKHEQLPLKLSMLNPIYYLMYCTGEKINITQIEGQFPQAPYPKLEQREAFVE
DWIQVPDEKFKKIFLEWEPRGEKSMPNFPTVDMCCDIVDWQEMMHYIDDALGQCAGLSSFPLKPPYHIHNYPKFIAAGAG
IEMDTEKLKKAAKRYRTLVRAFNIRRGMRRVDEQPPANHWKNRFPELEKELLDSYYKLKGWNDDGIPTKETLDDLGLGYV
GDEFIKRGILSAG

The query sequence (length=653) 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 4z3w:C 653 653 1.0000 1.0000 1.0000 0.0 4z3w:A, 4z3w:B, 4z3w:D, 4z3x:A, 4z3x:B, 4z3x:C, 4z3x:D, 4z3y:A, 4z3y:B, 4z3y:C, 4z3y:D, 4z3z:A, 4z3z:B, 4z3z:C, 4z3z:D, 4z40:A, 4z40:B, 4z40:C, 4z40:D
2 1aor:A 605 671 0.3247 0.3504 0.3159 2.44e-70 1aor:B
3 8c0z:A 616 668 0.2864 0.3036 0.2799 3.14e-51 8c0z:B
4 1b25:A 611 661 0.2956 0.3159 0.2920 2.12e-50 1b25:B, 1b25:C, 1b25:D, 1b4n:A, 1b4n:B, 1b4n:C, 1b4n:D
5 6x1o:C 624 450 0.2282 0.2388 0.3311 8.80e-44 6x1o:A, 6x6u:A, 6x6u:C
6 6x1o:C 624 51 0.0276 0.0288 0.3529 1.9 6x1o:A, 6x6u:A, 6x6u:C
7 8oz5:A 514 120 0.0459 0.0584 0.2500 1.9 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
8 7wyu:A 993 118 0.0521 0.0342 0.2881 3.6 3a3y:A, 5avq:A, 5avr:A, 5avs:A, 5avt:A, 5avu:A, 5avv:A, 5avw:A, 5avx:A, 5avy:A, 5avz:A, 5aw0:A, 5aw1:A, 5aw2:A, 5aw3:A, 5aw4:A, 5aw5:A, 5aw6:A, 5aw7:A, 5aw8:A, 5aw9:A, 8jfz:C, 8jfz:A, 7wyu:C, 7wyv:A, 7wyv:C, 7wyw:A, 7wyw:C, 7wyx:A, 7wyx:C, 7wyy:A, 7wyy:C, 7wyz:A, 7wyz:C, 7wz0:A, 7wz0:C, 7y45:C, 7y45:A, 7y46:C, 7y46:A, 2zxe:A
9 5y0t:A 414 38 0.0214 0.0338 0.3684 5.0 5y0t:B, 5y0t:C, 5y0t: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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