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 <-- 0.687 --> Intermediate <-- 2.679 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1vlia2) through the intermediate protein (d1tx2a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tx2a_ Dihydropteroate synthetaseDihydropteroate synthetase-​likeTIM beta/​alpha-​barrelα/β
Hit d1vlia2 Spore coat polysaccharide biosynthesis protein SpsE,​ N-​terminal domainAldolaseTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.687 --> Intermediate
DALI alignment (Z-score: 2.9 Raw score:483.20) query 1 ---------------SLQLRLALN----qidstvgdiagnAEAILRWTRHSAEQGAHLVA 41 ::::::::: :::::::::::::::::::: d1tx2a_ 1 kwdydlrcgeytlnlNEKTLIMGIlnvtpdsfsdggsyneVDAAVRHAKEMRDEGAHIID 60 query 42 fpemALTGypvedlalrSSFVEASRTALRELAARLAeEGFGeLPVLVGYldrsesaqpky 101 :::: ::::::::::::::::::: :::: ::::::: d1tx2a_ 61 ---iGGES-------faKVSVEEEIKRVVPMIQAVS-KEVK-LPISIDT----------- 97 query 102 gqpagaprnaaavlhrGRVALT-FAKHhlpnygvfdefryfvPGDT-mpivrlhgvdiaL 159 :::::: :::: :::: : d1tx2a_ 98 -----ykaevakqaieAGAHIInDIWG--------------aKAEPkiaevaahydvpiI 138 query 160 AICE---------dlwQDGGR----vpaarsagaglllsvnaspyerdkDDTRLELVRKR 206 :::: ::::: ::::::::::: d1tx2a_ 139 LMHNrdnmnyrnlmadMIADLydsikiakdagvrdeniildpgigfaktPEQNLEAMRNL 198 query 207 aQEAG---ctTAYLAmiggqdelvFDGD------------------sivVDRDGevvara 245 :::: ::::: :::: ::::: d1tx2a_ 199 -EQLNvlgypVLLGT-------srKSFIghvldlpveerlegtgatvclGIEKG------ 244 query 246 pqfsegCVVLdldlpaaeaepptgvvddglridrlviseeplpayeaeLAGGyadrldad 305 :::: :::: d1tx2a_ 245 cefvrvHDVK-----------------------------------emsRMAK-------- 261 query 306 eevysalvvglrayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyss 365 d1tx2a_ 262 ------------------------------------------------------------ 262 query 366 dhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqe 425 d1tx2a_ 262 ------------------------------------------------------------ 262 query 426 ghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtppip 485 d1tx2a_ 262 ------------------------------------------------------------ 262 query 486 easitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgt 545 d1tx2a_ 262 ------------------------------------------------------------ 262 query 546 kisakgfgkdrrlpitnrwregh 568 d1tx2a_ 262 ---------------mmdamigk 269 FAST alignment (Normalized score: 1.23 Raw score:478.70) query 1 ----------------SLQLRLALNQIDSTVGD---IAGNAEAILRWTRHSAEQGAHLVA 41 ::::::::::::::::: :::::::::::::::::::::::: d1tx2a_ 1 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIID 60 query 42 FPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGF-------------------- 81 :: d1tx2a_ 61 IG--------------------------------------GESFAKVSVEEEIKRVVPMI 82 query 82 ------GELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVF 135 ::::::: d1tx2a_ 83 QAVSKEVKLPISI----------------------------------------------- 95 query 136 DEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDK 195 d1tx2a_ 96 ------------------------------------------------------------ 96 query 196 DDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVL 255 d1tx2a_ 96 ------------------------------------------------------------ 96 query 256 DLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVG 315 d1tx2a_ 96 ------------------------------------------------------------ 96 query 316 LRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVS----------------- 358 d1tx2a_ 96 -------------------------------------------DTYKAEVAKQAIEAGAH 112 query 359 ----------------------------MPSKYSSDHSKGDAAELARRTGLNFRTVSIEP 390 :::: d1tx2a_ 113 IINDIWGAKAEPKIAEVAAHYDVPIILMHNRD---------------------------- 144 query 391 MFDAYMASLG----LTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY 446 :::::::::::::::::::: d1tx2a_ 145 ----------NMNYRNLMADMIADLYDSIKIAKD-------------------------- 168 query 447 GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVD 506 d1tx2a_ 169 ------------------------------------------------------------ 169 query 507 RDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWRE 566 d1tx2a_ 169 ------------------------------------------------------------ 169 query 567 GH---------------------------------------------------------- 568 d1tx2a_ 169 --AGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPV 226 query 569 ------------------------------------------- 569 d1tx2a_ 227 EERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 269 TMalign alignment (TM-score: 0.25 Raw score:142.24) query 1 --SLQL------RLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV 52 :::: ::: : :::: :::: ::: d1tx2a_ 1 KWDYDLRCGEYTLNL------------------------N-EKTL--IMGI--LNV---- 27 query 53 EDLALRSSFV--E-ASRTALRELAARLAEEGFGELPVLVGYLDR---SESAQPKYGQPAG 106 :: ::::: : :::::::::::::: ::: :::::::::: :: : : d1tx2a_ 28 --TP-DSFSDGGSYNEVDAAVRHAKEMR-DEG--AHIIDIGGESFAK---VS--V-E--- 72 query 107 APR-NAA-AV--LHRGRV-ALTFAKHHLPNYGVFDEFRYFVPGDTMPIV-RLHGVDIALA 160 ::: ::: :: :::::: ::::::::: :::::::: : ::::: d1tx2a_ 73 EEIKRVVPMIQAVSKEVKLPISIDTYKA-------------EVAKQAIEA-G---AHIIN 115 query 161 ICEDLWQDGGRVPAARSAGAGLLLSVNASP-YERD-K---DD-TRLELVRKRAQE--AGC 212 :::::::::::::::::: : ::::::::: :::: : :: :::::::::::: ::: d1tx2a_ 116 DIWGAKAEPKIAEVAAHY-D-VPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRD 173 query 213 T-TAYLAMIGG-QDELV-FD--GD--SIVVDRDGEVVARAPQFSE-GCVVLDLDLPAAEA 264 : ::::::::: ::: :: :: ::::: :::::::: ::: d1tx2a_ 174 ENIILDPGIGFA--KTPEQNLEAMRNLEQLN--VLGYPVLL-GTSR-------------- 214 query 265 EPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNG 324 :::::::: ::::: d1tx2a_ 215 ----------------------------------------------KSFIGHVL-DLPVE 227 query 325 FR----------------------------------------SVLIGLSGGIDSALVAAI 344 :: d1tx2a_ 228 ERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK------------------ 269 query 345 ACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGL 404 d1tx2a_ 270 ------------------------------------------------------------ 270 query 405 AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSI 464 d1tx2a_ 270 ------------------------------------------------------------ 270 query 465 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 d1tx2a_ 270 ------------------------------------------------------------ 270 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1tx2a_ 270 -------------------------------------------- 270 HHsearch alignment (Probability: 0.05 E-value:0.02) query 494 YPVLDAILELYVDRDTGADAIV---AAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 550 :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1tx2a_ 156 IADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRK 215 query 551 GF 552 :: d1tx2a_ 216 SF 217
Intermediate <-- 2.679 --> Hit
DALI alignment (Z-score: 18.4 Raw score:1875.10) d1tx2a_ 1 kwdYDLRCgeYTLNL--NEKTLIMGIL--NVTPdsfsdggsynEVDAAVRHAKEMRDEGA 56 ::::: ::::: :::::::::: :::: ::::::::::::::::: d1vlia2 1 ---AAFQI--ANKTVgkDAPVFIIAEAgiNHDG----------KLDQAFALIDAAAEAGA 45 d1tx2a_ 57 HIIDIGGESfaKVSV------------EEEIKRvvpMIQAVSKEVK---LPISIDTYKAE 101 ::::::::: :::: :::::: :::::::::: ::::::::::: d1vlia2 46 DAVKFQMFQ--ADRMyqkdpdvsifslVQSMEMpaeWILPLLDYCRekqVIFLSTVCDEG 103 d1tx2a_ 102 VAKQAIEAGAHIINDIWgAKAEPKIAEVAAHYDVPIILMHNRdnmnyrnlmaDMIADLYD 161 ::::::::::::::::: :::::::::::::::::::::::: :::::::: d1vlia2 104 SADLLQSTSPSAFKIASyEINHLPLLKYVARLNRPMIFSTAG----------AEISDVHE 153 d1tx2a_ 162 SIKIAKDAGVRdeNIILDPGIGF-akTPEQNleAMRNLEQLNVLG--YPVLLGTSRKsfi 218 ::::::::::: :::::::::: ::::: :::::::::::: :::::::::: d1vlia2 154 AWRTIRAEGNN--QIAIMHCVAKypaPPEYS--NLSVIPMLAAAFpeAVIGFSDHSE--- 206 d1tx2a_ 219 ghvldlpveerleGTGATVCLGIEKGCEFVRVHD-------------------VKEMSRM 259 ::::::::::::::::::::: ::::::: d1vlia2 207 -------------HPTEAPCAAVRLGAKLIEKHFtidknlpgadhsfalnpdeLKEMVDG 253 d1tx2a_ 260 AKMMDAMIG-----------------------k 269 ::::::::: d1vlia2 254 IRKTEAELKqgitkpvsekllgssyktttaieg 286 FAST alignment (Normalized score: 12.09 Raw score:3353.00) d1tx2a_ 1 KWDYDLRCGEYTLNLN-EKTLIMGILNVTPDSFSDGGSYN------EVDAAVRHAKEMRD 53 ::::::::: ::: ::::::::: :::::::::::::: d1vlia2 1 ---AAFQIANKT-VGKDAPVFIIAEA--------------GINHDGKLDQAFALIDAAAE 42 d1tx2a_ 54 EGAHIIDIGGESFAK---------------VSVEE-----EIKRVVPMIQAVSKEVKLPI 93 :::::::::: :::: ::::::::::::: :::::: d1vlia2 43 AGADAVKFQM-----FQADRMYQKDPDVSIFSLV-QSMEMPAEWILPLLDYCR-EKQVIF 95 d1tx2a_ 94 SIDTYKAEVAKQAIEAGAHIINDIWGAK-----AEPKIAEVAAHYDVPIILMHNRDNMNY 148 ::::::::::::::::::::::: :::::::::::::::::::: d1vlia2 96 LSTVCDEGSADLLQSTSPSAFKI-----ASYEINHLPLLKYVARLNRPMIFST------- 143 d1tx2a_ 149 RNLMAD---MIADLYDSIKIAKDAGVRDENIILDPGIGF----AKTPEQNLE-AMRNLEQ 200 ::::::::::::::::: :::::::: :::::: ::::::: d1vlia2 144 ------AGAEISDVHEAWRTIRAEGN--NQIAIMHC---VAKYPAPPEY---SNLSVIPM 189 d1tx2a_ 201 LNV--LGYPVLLGTSRKSFIGHVLDLPVEERLE----GTGATVCLGIEKGCEFVRVH--- 251 ::: :::::::: ::::::::::::::::::: d1vlia2 190 LAAAFPEAVIGFS--------------------DHSEHPTEAPCAAVRLGAKLIEK-HFT 228 d1tx2a_ 252 -----------------DVKEMSRMAKMMDAMIGK------------------------- 269 ::::::::::::::: d1vlia2 229 IDKNLPGADHSFALNPDELKEMVDGIRKTEAE---LKQGITKPVSEKLLGSSYKTTTAIE 285 d1tx2a_ 270 - 270 d1vlia2 286 G 286 TMalign alignment (TM-score: 0.71 Raw score:192.11) d1tx2a_ 1 KWDYDLRCGEYTLNL-NEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHII 59 : ::::: ::::: ::::::::::::::: ::::::::::::::::::::: d1vlia2 1 -A-AFQIA--NKTVGKDAPVFIIAEAGINHD--------GKLDQAFALIDAAAEAGADAV 48 d1tx2a_ 60 DIGGESFAKVS----V-------E-EEIKRVVPMIQAVSKEVK---LPISIDTYKAEVAK 104 :::::: ::: : : :::::::::::::::::: :::::::::::::: d1vlia2 49 KFQMFQ--ADRMYQKDPDVSIFSLVQSMEMPAEWILPLLDYCREKQVIFLSTVCDEGSAD 106 d1tx2a_ 105 QAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIK 164 ::::::::::::::::::::::::::::::::::::::: ::::::::::: d1vlia2 107 LLQSTSPSAFKIASYEINHLPLLKYVARLNRPMIFSTAG----------AEISDVHEAWR 156 d1tx2a_ 165 IAKDAGVRDENIILDPGIGFA-KTPEQNLEAMRNLEQLNV-LG-YPVLLGTSRKSFIGHV 221 :::: :::: ::::::::::: :::::: :::::::::: :: :::::::: : d1vlia2 157 TIRA-EGNN-QIAIMHCVAKYP-APPEYS-NLSVIPMLAAAFPEAVIGFSDH-S------ 205 d1tx2a_ 222 LDLPVEERLEGTGATVCLGIEKGCEFVRV-H--------------D----VKEMSRMAKM 262 :: :::::::::::::::::: : : :::::::::: d1vlia2 206 -------EH--PTEAPCAAVRLGAKLIEKHFTIDKNLPGADHSFALNPDELKEMVDGIRK 256 d1tx2a_ 263 MDAMIGK----------------------- 269 ::::::: d1vlia2 257 TEAELKQGITKPVSEKLLGSSYKTTTAIEG 286 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tx2a_ 5 DLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGE 64 :::::::::::::::::::::: :::::::::::::::::::::::::::::: d1vlia2 2 AFQIANKTVGKDAPVFIIAEAG--------INHDGKLDQAFALIDAAAEAGADAVKFQMF 53 d1tx2a_ 65 SFAKV-------S----------VEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAI 107 ::::: : :::::::: :::: ::::::::::::::::::::: d1vlia2 54 QADRMYQKDPDVSIFSLVQSMEMPAEWILPL---LDYC-REKQVIFLSTVCDEGSADLLQ 109 d1tx2a_ 108 EAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAK 167 :::::::::::::::::::::::::::::::::: :: ::: ::::::::::: d1vlia2 110 STSPSAFKIASYEINHLPLLKYVARLNRPMIFST--AG-AEI-------SDVHEAWRTIR 159 d1tx2a_ 168 DAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYP-VLLGTSRKSFIGHVLDLPV 226 :::: ::::::::::::::::::::: :::::::: ::: :::::::: d1vlia2 160 AEGN--NQIAIMHCVAKYPAPPEYSNL-SVIPMLAA-AFPEAVIGFSDH----------- 204 d1tx2a_ 227 EERLEGTGATVCLGIEKGCEFVRVH 251 :::::::::::::::::::::: d1vlia2 205 ---SEHPTEAPCAAVRLGAKLIEKH 226