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 <-- 1.442 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1iowa1) 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 d1iowa1 D-​Ala-​D-​Ala ligase,​ N-​domainPreATP-​grasp domainPreATP-​grasp domainα/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 <-- 1.442 --> Hit
DALI alignment (Z-score: 4.8 Raw score:336.70) d1vl2a1 1 -KEKVVLAYS--------GGLDTSVILKWLCEKGFDVIAYVANVgqkddfvaikekalkt 51 ::::::::: :::::::::::::::::::::::::: d1iowa1 1 mTDKIAVLLGgtsaerevSLNSGAAVLAGLREGGIDAYPVDPKE---------------- 44 d1vl2a1 52 gaskvyvedlrrefvtdyiftallgnamyegryllgtaiarpliakRQVEIaEKEGAQYV 111 ::::: :::::::: d1iowa1 45 ---------------------------------------------vDVTQL-KSMGFQKV 58 d1vl2a1 112 AHGATgkGNDQ--VRFELTYAALNpnLKVISpwkdpeflakfktdlinyamekgipi 166 ::::: :::: ::::::::::: ::::: d1iowa1 59 FIALH--GRGGedGTLQGMLELMG--LPYTG---------------sgvmasalsmd 96 FAST alignment (Normalized score: 5.31 Raw score:670.10) d1vl2a1 1 -KEKVVLAYSG-----------GLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKA 48 ::::::: :::::::::::::::::::::: d1iowa1 1 MTDKIAVL---LGGTSAEREVSLNSGAAVLAGLREGGIDAYPVD---------------- 41 d1vl2a1 49 LKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL----IAKRQVEIAE 104 ::::::: d1iowa1 42 ----------------------------------------------PKEVDVTQLKS--- 52 d1vl2a1 105 KEGAQYVAHGATGKGND--QVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEK 162 :::::::::: :::: :::::::::: ::::: d1iowa1 53 -MGFQKVFIAL--HGRGGEDGTLQGMLEL--MGLPY------------------------ 83 d1vl2a1 163 GIPI------------- 166 d1iowa1 84 ----TGSGVMASALSMD 96 TMalign alignment (TM-score: 0.33 Raw score:53.98) d1vl2a1 1 ---KEKVVLAYSGGLDTSVILKWLCEK-G--------FDVIAYVANVGQKDDFVAIKEKA 48 ::::::::: :::::::::::::: : ::::::: d1iowa1 1 MTDKIAVLLGGT-SAEREVSLNSGAAVLAGLREGGIDAYPVDPK---------------- 43 d1vl2a1 49 LKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGA 108 :: :::: :::::: d1iowa1 44 -------EV----------------------------------------DVTQ-LKSMGF 55 d1vl2a1 109 -QYVA-HGAT--GKGNDQVRFELTYAALNPNLKVIS----PWK-----DPEFLAKFKTDL 155 :::: :::: :::::::::: ::::::::: : d1iowa1 56 QKVFIALHGRGG----EDGTLQGMLE-LMGLPYTGSGVMA--SALSMD------------ 96 d1vl2a1 156 INYAMEKGIPI 166 d1iowa1 97 ----------- 97 HHsearch alignment (Probability: 0.02 E-value:0.14) d1vl2a1 16 VILKWLCEKGFDVIAYVAN 34 ::::::::::::::::::: d1iowa1 25 AVLAGLREGGIDAYPVDPK 43