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 <-- 2.423 --> Intermediate <-- 0.974 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1p3da2) through the intermediate protein (d1gpma1) by significant SVM score (>0.4).

  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 d1p3da2 UDP-​N-​acetylmuramate-​alanine ligase MurCMurD-​like peptide ligases,​ peptide-​binding domainMurD-​like peptide ligases,​ peptide-​binding domainα/β

Supporting Alignments

Query <-- 2.423 --> 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 <-- 0.974 --> Hit
DALI alignment (Z-score: 2.8 Raw score:303.80) d1gpma1 1 -------------------------wtpakiidDAVARIREQVGDDKVILGLSGG----- 30 :::::::::::::::::::::: d1p3da2 1 gagrrfdqlgefirpngkvrlvddyghhptevgVTIKAAREGWGDKRIVMIFQPHrysrt 60 d1gpma1 31 ----vdssVTAMLLhraigknLTCVFVDNGL----LRLN-EAEQVLDMFGDHFGLNIVHV 81 :::::: :::::::::: :::: :::::::::::::::::::: d1p3da2 61 rdlfddfvQVLSQV-------DALIMLDVYAageaPIVGaDSKSLCRSIRNLGKVDPILV 113 d1gpma1 82 PaedrflsalagendpeakrkiigrvFVEVFDEEALKLED-vKWLAQgtiypdviesaak 140 : :::::::::::::: ::::: d1p3da2 114 S-------------------------DTSQLGDVLDQIIQdgDLILA------------- 135 d1gpma1 141 mglveplkelfkdevrkiglelglpydmlyrhpfp 175 d1p3da2 136 ------------------qgagsvskisrglaesw 152 FAST alignment (Normalized score: 2.52 Raw score:410.50) d1gpma1 1 WTPAKIIDDAVARIREQVG----------------DDKVILGLSG----GVDSSVTAMLL 40 :::::::: ::::::::::: d1p3da2 1 -------------------GAGRRFDQLGEFIRPNGKVRLVDD--YGHHPTEVGVTIKAA 39 d1gpma1 41 HRAIGK-NLTCVFVDNGLL-------RLNEAEQVLDMFGDHFG-LNIVHVPAEDRFLSAL 91 :::::: ::::::::: ::::::::::: :::::: d1p3da2 40 REGWGDKRIVMIFQPH---RYSRTRDLFDDFVQVLSQ------VDALIML---------- 80 d1gpma1 92 AGENDPEAKRKIIG---------------------------------------------- 105 d1p3da2 81 --------------DVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQI 126 d1gpma1 106 ------------RVFVEVFDEEALKLEDVKWLAQGTIYPDVIESAAKMGLVEPLKELFKD 153 :::::::::::: d1p3da2 127 IQDGDLILAQGAGSVSKISRGLAE------------------------------------ 150 d1gpma1 154 EVRKIGLELGLPYDMLYRHPFP-- 175 d1p3da2 151 ----------------------SW 152 TMalign alignment (TM-score: 0.34 Raw score:59.08) d1gpma1 1 -----WTPAKIIDDAVARI---REQVG-------DDKVILGLSGGVDSSVTAMLLHRAI- 44 : :: ::::::::::::::::::::::::: d1p3da2 1 GAGRR-------------FDQL---GEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWG 44 d1gpma1 45 -GKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLS-------------- 89 :::::::::::::::::::::: ::::::::::::::::: :::: d1p3da2 45 DKRIVMIFQPHRYSRTRDLFDDF-VQVLSQVDALIMLDVYA-AGEAPIVGADSKSLCRSI 102 d1gpma1 90 -----------------------------------ALAGENDPEAKRKIIGRVFVEVFDE 114 :: :::: d1p3da2 103 RNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQG------------------AG-SVSK 143 d1gpma1 115 EALKLEDVKWLAQGTIYPDVIESAAKMGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPF 174 ::::::::: d1p3da2 144 ISRGLAESW--------------------------------------------------- 152 d1gpma1 175 P 175 d1p3da2 153 - 153 HHsearch alignment (Probability: 0.60 E-value:0.00) d1gpma1 5 KIIDDAVARIREQVGDDKVILGLSGGVDSSVTAML 39 ::::::::::::::::::::::::::::::::::: d1p3da2 30 TEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLF 64