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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.669 --> Intermediate <-- 1.215 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1h2ba2) 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 d1h2ba2 Alcohol dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.669 --> Intermediate
DALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
Intermediate <-- 1.215 --> Hit
DALI alignment (Z-score: 6.0 Raw score:513.60) d1vl2a1 1 --------------------------------KEKVVLAYSGGlDTSVILKWLCE-KGFD 27 ::::::::::: ::::::::::: :::: d1h2ba2 1 isreklvemapladagitayravkkaartlypGAYVAIVGVGG-LGHIAVQLLKVmTPAT 59 d1vl2a1 28 VIAYVAnvgqkddFVAIKEKALKTGASKVYVEDLrrefvtdyiftallgnamyegryllg 87 :::::: ::::::::::::::::::::: d1h2ba2 60 VIALDV-------KEEKLKLAERLGADHVVDARR-------------------------- 86 d1vl2a1 88 taiarpliakRQVEIAEKEG----AQYVAHGAtgkgnDQVRFELTY-aalnPNLKVISP- 141 :::::::::: :::::::: ::::::::: :::::::: d1h2ba2 87 ----------DPVKQVMELTrgrgVNVAMDFV-----GSQATVDYTpyllgRMGRLIIVg 131 d1vl2a1 142 -------------------wKDPEflakFKTDLINYAMEkgipi 166 :::: ::::::::::: d1h2ba2 132 yggelrfptirvissevsfeGSLVgnyvELHELVTLALQ---gk 172 FAST alignment (Normalized score: 6.18 Raw score:1044.00) d1vl2a1 1 --------------------------------KEKVVLAYSGGLDTSVILKWLCE-KGFD 27 :::::: :::::::::::::::: :::: d1h2ba2 1 ISREKLVEMAPLADAGITAYRAVKKAARTLYPGAYVAI-VGVGGLGHIAVQLLKVMTPAT 59 d1vl2a1 28 VIAYVANVGQKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLL 86 ::::: ::::::::::::::::::: d1h2ba2 60 VIALD--------VKEEKLKLAERLGADHVVDA--------------------------- 84 d1vl2a1 87 GTAIARP--LIAKRQVEIAEKE----GAQYVAHGATGKGND--QVRFELTYAAL---NPN 135 ::::::::: :::::::: ::::::::: ::: d1h2ba2 85 -------RRDPVKQVMEL----TRGRGVNVAMDF-------VGSQATVDYTP--YLLGRM 124 d1vl2a1 136 LKVISPWKDPEFLAK-------------------------FKTDLINYAMEKGIPI---- 166 :::::: ::::::::::: d1h2ba2 125 GRLIIV---------GYGGELRFPTIRVISSEVSFEGSLVGNYVELHELVT-----LALQ 170 d1vl2a1 167 -- 167 d1h2ba2 171 GK 172 TMalign alignment (TM-score: 0.46 Raw score:75.79) d1vl2a1 1 --------------KEKVVLAYSGGLDTSVILKWLCEKGFD----VIAYVANVGQKDDFV 42 ::::::::::::: ::: ::::::: ::::: d1h2ba2 1 ISREKLVEMAPLAD---------AGITAYRAVKKAA--RTLYPGAYVAIVGV--GGLGH- 46 d1vl2a1 43 AIKEKALKTGASKVYVEDLR-----------------REF-------------------- 65 :::::::::::::::::::: ::: d1h2ba2 47 IAVQLLKVMTPATVIALDVKEEKLKLAERLGADHVVDARRDPVKQVMELTRGRGVNVAMD 106 d1vl2a1 66 -VTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGNDQVR 124 :::::::::::::: :::::::::: : :: d1h2ba2 107 F------------------------VGSQATVDYTPYLL--GRMGRLIIVG-----Y-GG 134 d1vl2a1 125 FELTYAALNPN----LKVISPWKDPEFLAKFKTDLINYAMEKGI--PI 166 : :: :::::: ::::::: : :: ::::::::: :: :: d1h2ba2 135 E-LR-FPTIRVISSEVSFEGSL-----V-GN-YVELHELVT-LALQGK 172 HHsearch alignment (Probability: 0.07 E-value:0.17) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKG-FDVIAYVANVGQKDDFVAIKEKALKTGAS 54 ::::::::::::::: :::::::: ::::::::: ::::::::::::: d1h2ba2 34 AYVAIVGVGGLGHIA-VQLLKVMTPATVIALDVK-------EEKLKLAERLGAD 79