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 <-- 0.999 --> Intermediate <-- 0.999 --> Hit

HHsearch
probability
HHsearch
probability

The query (T542_A.pdb A) is transitively linked to the hit (d1vl2a1) through the intermediate protein (d1gpma1) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1gpma1 GMP synthetase,​ central domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 0.999 --> Intermediate
DALI alignment (Z-score: 17.0 Raw score:1263.90) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 rlDADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMP 360 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::: d1gpma1 1 --WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSS-DHSKGDAAELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLM 419 ::::: :::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRlNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaae 477 :::::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 114 EEALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG----- 163 query 478 rgqtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeyk 537 :::::::: d1gpma1 164 ------LPYDMLYR---------------------------------------------- 171 query 538 rrqyppgtkisakgfgkdrrlpitnrwregh 568 d1gpma1 172 ---------------------------hpfp 175 FAST alignment (Normalized score: 8.89 Raw score:2802.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGV 357 ::::::::::::::::: ::::::::::::::::::::::: :::::::: d1gpma1 1 --WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCV 51 query 358 SMPSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGT 416 :::::::::::::::: :::::::::::::::::::::::::: :::::::::::::::: d1gpma1 52 FVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVE 110 query 417 TLMAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIF 465 :::::::: ::::::::::::: :::::::::::::: d1gpma1 111 VFDEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVR 156 query 466 RLAEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 ::::: :::::::: d1gpma1 157 KIGLE------------LGLPYDMLY---------------------------------- 170 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 568 d1gpma1 171 --------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.27 Raw score:151.12) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 : d1gpma1 1 --------------W--------------------------------------------- 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 2 ------------------------------------------------------------ 2 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::: :: :::::::::::::::::::::::: ::::::::: d1gpma1 2 ---TPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLM 419 ::::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRA 474 ::::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 114 EEALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG-- 163 query 475 AAERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVD 532 :::::::: :: d1gpma1 164 ---------LPYDMLYR-HPFP-------------------------------------- 175 query 533 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1gpma1 176 ------------------------------------ 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 306 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 365 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL 60 query 366 DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQE 425 ::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1gpma1 61 NEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGEN-DPEAKRKIIGRVFVEVFDEEALKL 119 query 426 GHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPI 484 ::: :::::::::::::::::::: ::::::::::::::::::: :::::::::::: d1gpma1 120 EDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLEL-GLPYDMLYRHPF 174 query 485 P 485 : d1gpma1 175 P 175
Intermediate <-- 0.999 --> Hit
DALI alignment (Z-score: 11.2 Raw score:838.90) d1gpma1 1 wtpakiiddavarireqvgDDKVILGLSGGVDSSVTAMLLHRAIGkNLTCVFVDNGLLRl 60 :::::::::::::::::::::::::: ::::::::::::: d1vl2a1 1 -------------------KEKVVLAYSGGLDTSVILKWLCEKGF-DVIAYVANVGQKD- 39 d1gpma1 61 nEAEQVLDMFGdHFGL-NIVHVPAEDRFLS-ALAGEN--------dPEAKRKIIGRVFVE 110 :::::::::: :::: ::::::::::::: :::::: :::::::::::::: d1vl2a1 40 -DFVAIKEKAL-KTGAsKVYVEDLRREFVTdYIFTALlgnamyegrYLLGTAIARPLIAK 97 d1gpma1 111 VFDEEALKLEdVKWLAQGTIYPD---------viesaaKMGLVEPLK----ELFK-DEVR 156 :::::::::: :::::::::::: ::::::::: :::: :::: d1vl2a1 98 RQVEIAEKEG-AQYVAHGATGKGndqvrfeltyaalnpNLKVISPWKdpefLAKFkTDLI 156 d1gpma1 157 KIGLELGLPYdmlyrhpfp 175 :::::::::: d1vl2a1 157 NYAMEKGIPI--------- 166 FAST alignment (Normalized score: 10.27 Raw score:1751.00) d1gpma1 1 WTPAKIIDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGK---NLTCVFVDNGL 57 ::::::::::::::::::::::: :::::::::: d1vl2a1 1 -------------------KEKVVLAYSGGLDTSVILKWLCE----KGFDVIAYVANVG- 36 d1gpma1 58 LRLN---EAEQVLDMFGDHFGL-NIVHVPAEDRFLS----ALAGENDP--------EAKR 101 :::::::: :::::: ::::::::::::: ::::: :::: d1vl2a1 37 ----QKDDFVAIKEK-ALKTGASKVYVEDLRREFVTDYIFTALLG---NAMYEGRYLLGT 88 d1gpma1 102 KIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESA------------------AKMGL 143 ::::::::::::::::: :::::::::: ::::: d1vl2a1 89 AIARPLIAKRQVEIAEK-EGAQYVAHGA---------TGKGNDQVRFELTYAALNPNLKV 138 d1gpma1 144 VEPLKELF----------KDEVRKIGLELGLPYDMLYRHPFP-- 175 ::: ::::::::::::: d1vl2a1 139 ISP-----WKDPEFLAKFKTDLINYAMEKGI-----------PI 166 TMalign alignment (TM-score: 0.62 Raw score:108.49) d1gpma1 1 WTPAKIIDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL 60 :::::::::::::::::::::::::: ::::::::::::: d1vl2a1 1 -------------------KEKVVLAYSGGLDTSVILKWLCEKGF-DVIAYVANVGQKD- 39 d1gpma1 61 NEAEQVLDMFGDHFGL-NIVHVPAEDRFLS-ALA-GE--N-D----PEAKRKIIGRVFVE 110 : ::::::::: :::: ::::::::::::: ::: :: : : :::::::::::::: d1vl2a1 40 D-FVAIKEKAL-KTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAK 97 d1gpma1 111 VFDEEALKLEDVKWLAQGTIYPDV----------------IESAAKMGLV-E----PLKE 149 :::::::::: ::::::::: :: ::::: : :::: d1vl2a1 98 RQVEIAEKEG-AQYVAHGAT--GKGNDQVRFELTYAALNP-----NLKVISPWKDPEFLA 149 d1gpma1 150 LFKDEVRKIGLELGLPYDMLYRHPFP 175 ::::::::::::::::: d1vl2a1 150 KFKTDLINYAMEKGIPI--------- 166 HHsearch alignment (Probability: 1.00 E-value:0.00) d1gpma1 20 DDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGL-NI 78 ::::::::::::::::::::::: ::::::::::::::::: ::::::::::::: :: d1vl2a1 1 KEKVVLAYSGGLDTSVILKWLCE-KGFDVIAYVANVGQKDD---FVAIKEKALKTGASKV 56 d1gpma1 79 VHVPAEDRFLSALAGE---------NDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQGT 129 :::::::::::::::: :::::::::::::::::::::::: :::::::::: d1vl2a1 57 YVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEK-EGAQYVAHGA 115 d1gpma1 130 IY--PDVIE-------SAAKMGLVEP-----LKELFKDEVRKIGLELGLP 165 :: ::::: :::::::::: ::::::::::::::::::: d1vl2a1 116 TGKGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIP 165