HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.905 --> Intermediate <-- 1.293 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1f8fa2) through the intermediate protein (d1vl2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1f8fa2 Benzyl alcohol dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.905 --> Intermediate
DALI alignment (Z-score: 12.5 Raw score:953.20) query 1 dadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 ySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK----DV 157 :::::::::::::: :::::::: :::: :::: :::::: :: d1vl2a1 95 IAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpefLA 149 query 158 YK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaivaag 216 :: :::::::::: :::: d1vl2a1 150 KFkTDLINYAMEK----------GIPI--------------------------------- 166 query 217 ydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1vl2a1 167 -------------------------------------------------- 167 FAST alignment (Normalized score: 7.91 Raw score:1662.00) query 1 DADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 :::::::::::::::::::::: ::: ::::::::: d1vl2a1 1 -----------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVANV 35 query 60 KYSSDHSKGDAAELARRTG-LNFRTVSIEPMFD-AYMA---SLGLTGL-------AEENL 107 :::: ::::::::::::: ::::::::::::: :::: :::: ::::: d1vl2a1 36 -GQKD-DFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRYLLGTAI 90 query 108 QSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG---------AY 151 ::::::::::::::::: :::::::::: :::: :: d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALNPNLKVI 139 query 152 GPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 201 :: :::::::::: d1vl2a1 140 SP-----WKDPEFLAKFKTDLINYAME--------------------------------- 161 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1vl2a1 162 ------------------------------------------------------------ 162 query 262 WREGH----- 266 d1vl2a1 162 -----KGIPI 166 TMalign alignment (TM-score: 0.47 Raw score:124.53) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 YSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D--VY 158 :::::::::::::: :::::::: : :::::::: :: :::::: : :: d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEFLA 149 query 159 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 218 :::::::::::: : : ::: d1vl2a1 150 -KFKTDLINYAME-K------G-IPI---------------------------------- 166 query 219 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vl2a1 167 ------------------------------------------------ 167 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::: ::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK-GFD-VIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 83 TVSIEPMFDAYMASLGLTGLA--------EENLQSRLRGTTLMAISNQEGHIVLAPG--- 131 ::::::::::::::::::::: :::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 132 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRNRAA 173 :::::::::::::::::: ::: :::::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPNLKV-ISPWKDPEFLAKFKTDLINYAMEKGIPI 166
Intermediate <-- 1.293 --> Hit
DALI alignment (Z-score: 6.0 Raw score:520.70) d1vl2a1 1 ----------------------------KEKVVLAYSGGlDTSVILKWLCEKGF-DVIAY 31 ::::::::::: :::::::::::::: ::::: d1f8fa2 1 vpiellgplgcgiqtgagacinalkvtpASSFVTWGAGA-VGLSALLAAKVCGAsIIIAV 59 d1vl2a1 32 VAnvgqkddFVAIKEKALKTGASKVYVEDLrrefvtdyiftallgnamyegryllgtaia 91 :: ::::::::::::::::::::: d1f8fa2 60 DI-------VESRLELAKQLGATHVINSKT------------------------------ 82 d1vl2a1 92 rpliakRQVEIAEKEG---AQYVAHGAtgkgnDQVRFELTYA-alNPNLKVIS------- 140 :::::::::: :::::::: :::::::::: :::::::: d1f8fa2 83 -----qDPVAAIKEITdggVNFALEST-----GSPEILKQGVdalGILGKIAVvgapqlg 132 d1vl2a1 141 ----------------pwKDPEFLA---kFKTDLINYAMEkgipi 166 ::::::: ::::::::::: d1f8fa2 133 ttaqfdvndlllggktilGVVEGSGspkkFIPELVRLYQQ---gk 174 FAST alignment (Normalized score: 5.93 Raw score:1007.00) d1vl2a1 1 ----------------------------KEKVVLAYSGGLDTSVILKWLCEKGF-DVIAY 31 :::::: ::::::::::::::::::: ::::: d1f8fa2 1 VPIELLGPLGCGIQTGAGACINALKVTPASSFVT-WGAGAVGLSALLAAKVCGASIIIAV 59 d1vl2a1 32 VANVGQKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAI 90 : ::::::::::::::::::: d1f8fa2 60 D--------IVESRLELAKQLGATHVINS------------------------------- 80 d1vl2a1 91 ARP---LIAKRQVEIAEKE---GAQYVAHGATG--KGNDQVRFELTYAAL-NPNLKVISP 141 ::::::::: :::::::: ::::::::::: ::::::::: d1f8fa2 81 ---KTQDPVAAIKEI----TDGGVNFALES---TGSPEILKQGVDA----LGILGKIAVV 126 d1vl2a1 142 WKDPEFLAKF------------------------------------KTDLINYAMEKGIP 165 ::::::::: d1f8fa2 127 ----------GAPQLGTTAQFDVNDLLLGGKTILGVVEGSGSPKKFIPELVRLYQ----- 171 d1vl2a1 166 I--- 166 d1f8fa2 172 -QGK 174 TMalign alignment (TM-score: 0.45 Raw score:74.82) d1vl2a1 1 -----------KEKVVLAYSGGL-DTSVILKW-LCEKGFD--VIAYVANVGQKD-DFVAI 44 :: :::::::: :: :: ::::::: ::: : :: d1f8fa2 1 VPIELLGPLGC----------GIQTGAGACINALK---VTPASSFVTWG--AGAV-G-LS 43 d1vl2a1 45 KEKALKTGAS-KVYV-------------------EDLRREF------------------- 65 :::::::::: :::: ::::::: d1f8fa2 44 ALLAAKVCGASIIIAVDIVESRLELAKQLGATHVINSKTQDPVAAIKEITDGGVNFALES 103 d1vl2a1 66 VTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGNDQVRF 125 :: :::::::::::: :::::::::: :::::: d1f8fa2 104 ----------------------TG--SPEILKQGVDAL--GILGKIAVVG---APQLGT- 133 d1vl2a1 126 ELTYAALN--PN---LKVISPWKDPEFLAKFKTDLINYAMEKGI--PI 166 ::: ::: :: ::::::::: :: :: ::::::::: :: :: d1f8fa2 134 TAQ--FDVNDLLLGGKTILGVVEG--SG-SP-KKFIPELVR-LYQQGK 174 HHsearch alignment (Probability: 0.04 E-value:0.12) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKGF-DVIAYVANVGQKDDFVAIKEKALKTGASKVYVED 60 ::::::::::::::: ::::::::: ::::::: :::::::::::::::: :: d1f8fa2 30 SSFVTWGAGAVGLSA-LLAAKVCGASIIIAVDI-------VESRLELAKQLGATHV--IN 79 d1vl2a1 61 LRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGN 120 ::::::::::::::: ::::::::::::::::::::::::::: ::::::::: :: d1f8fa2 80 SKTQDPVAAIKEITD-----GGVNFALESTGSPEILKQGVDALGILG-KIAVVGAPQ-LG 132 d1vl2a1 121 DQVRFELTYAALNPNLKVIS 140 ::::::: :::::::::::: d1f8fa2 133 TTAQFDV-NDLLLGGKTILG 151