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 <-- 1.425 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1gvfa_) 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 d1gvfa_ Tagatose-​1,​6-​bisphosphate aldolaseAldolaseTIM 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 <-- 1.425 --> Hit
DALI alignment (Z-score: 13.5 Raw score:1398.20) d1tx2a_ 1 kwdydlrcgeyTLNLNE----KTLIMGILNvtpdsfsdggsynevdaAVRHAKEMRDEG- 55 :::::: ::::::::: :::::::::::: d1gvfa_ 1 -----siistkYLLQDAqangYAVPAFNIH-----------------NAETIQAILEVCs 38 d1tx2a_ 56 ----AHIIDIGGESfakvsveeeikRVVPMIQAVSKEV-----KLPISID-TYKAEVAKQ 105 :::::::::: ::::::::::::: ::::::: ::::::::: d1gvfa_ 39 emrsPVILAGTPGT-------fkhiALEEIYALCSAYSttynmPLALHLDhHESLDDIRR 91 d1tx2a_ 106 AIEAGAHIINDIW------gAKAE-PKIAEVAAHYDVPIILMHNRdnmnYRNLmadMIAD 158 ::::::::::::: :::: :::::::::::::::::::: :::: :::: d1gvfa_ 92 KVHAGVRSAMIDGshfpfaeNVKLvKSVVDFCHSQDCSVEAELGR--lgSAFL--tDPQE 147 d1tx2a_ 159 LYDSIKIAKdagvrdeNIILDPGIG--faktpeqNLEAMRNLEQLNV-LGYPVLLGTSRk 215 ::::::::: ::::::::: ::::::::::::: ::::::::::: d1gvfa_ 148 AKRFVELTG-------VDSLAVAIGtahglysktPKIDFQRLAEIREvVDVPLVLHGAS- 199 d1tx2a_ 216 sfighvldlpveerlEGTGATVCLGIEKGCEFVRVH------------------------ 251 ::::::::::::::::::::: d1gvfa_ 200 ---------------DVPDEFVRRTIELGVTKVNVAtelkiafagavkawfaenpqgndp 244 d1tx2a_ 252 -------------DVKEMSRMAKmmdamigk 269 :::::::::: d1gvfa_ 245 ryymrvgmdamkeVVRNKINVCG--sanris 273 FAST alignment (Normalized score: 8.20 Raw score:2222.00) d1tx2a_ 1 KWDYDLRCGEYTLNLN---------------EKTLIMGILNVTPDSFSDGGSYNEVDA-A 44 ::::::::: : d1gvfa_ 1 ----------------SIISTKYLLQDAQANGYAVPAFNI------------------HN 26 d1tx2a_ 45 VRHAKEMRDEGA--------HIIDIGGESFAKVSVEE-------EIKRVVPMIQAVSKEV 89 ::::::::: :::::: :::::::::::::::: d1gvfa_ 27 AETIQAILE---VCSEMRSPVILAGT-----------PGTFKHIALEEIYALCSAYSTTY 72 d1tx2a_ 90 --KLPISI-DTYKAEVAKQAIEAGAHIINDIWGAKA------------EPKIAEVAAHYD 134 :::::: :::::::::::::::::::::: :::::::::::: d1gvfa_ 73 NMPLALHLDHHESLDDIRRKVHAGVRSAMID-----GSHFPFAENVKLVKSVVDFCHSQD 127 d1tx2a_ 135 VPIILMHNRDNMNYRN----------LMADMIADLYDSIKIAKDAGVRDEN---IILDPG 181 :::::: ::::::::::: :::::: d1gvfa_ 128 CSVEAE----------LGRLGSAFLTDPQEAKRFVEL--------------TGVDSLAVA 163 d1tx2a_ 182 IGFAKTPEQNLE--------------AMRNLEQLN-VLGYPVLLGTSRKSFIGHVLDLPV 226 ::::::::: :::::::::: d1gvfa_ 164 ------------IGTAHGLYSKTPKIDFQRLAEIREVVDVPLVLHG-------------- 197 d1tx2a_ 227 EERLEG----TGATVCLGIEKGCEFVRVH------------------------------- 251 :::::::::::::::::: d1gvfa_ 198 ------ASDVPDEFVRRTIELGVTKVNV-ATELKIAFAGAVKAWFAENPQGNDPRYYMRV 250 d1tx2a_ 252 -------DVKEMSRMAKMMDAMIGK-------- 269 :::::::: d1gvfa_ 251 GMDAMKEVVRNKINV----------CGSANRIS 273 TMalign alignment (TM-score: 0.61 Raw score:165.18) d1tx2a_ 1 --KWDYDLRCGEYTL--NL-NEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRD-E 54 :::::: :: :::::::::::: ::::::::::::: : d1gvfa_ 1 SI-------ISTKYLLQDAQANGYAVPAFNIH-------------NAETIQAILEVCSEM 40 d1tx2a_ 55 -GAHIIDIGGESFAKVSVEEEIKRVVPMIQAVSKEV-----KLPISID-TYKAEVAKQAI 107 ::::::::::: ::::::::::::::::: ::::::: ::::::::::: d1gvfa_ 41 RSPVILAGTPGT-------FKHIALEEIYALCSAYSTTYNMPLALHLDHHESLDDIRRKV 93 d1tx2a_ 108 EAGAHIINDIWG-----AK-AEP-KIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLY 160 :::::::::::: :: ::: :::::::::::::::::::::::: :: :::::: d1gvfa_ 94 HAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQDCSVEAELGRLGSAF--LT--DPQEAK 149 d1tx2a_ 161 DSIKIAKDAGVRDENIILDPG--IGF--AKTPE-QNLEAMRNLEQLN-VLGYPVLLGTSR 214 ::::::: ::::::: ::: ::: :::::::::::: :::::::::::: d1gvfa_ 150 RFVELTG-------VDSLAVAIGTAHGL--YSKT-PKIDFQRLAEIREVVDVPLVLHGAS 199 d1tx2a_ 215 KSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVH----------------------- 251 : :::::::::::::::::::: d1gvfa_ 200 --------------D--VPDEFVRRTIELGVTKVNVATELKIAFAGAVKAWFAENPQGND 243 d1tx2a_ 252 --------------DVKEMSRMAKMMD---AMIGK 269 ::::::::::::: d1gvfa_ 244 PRYYMRVGMDAMKEVVRNKINVCGSANRIS----- 273 HHsearch alignment (Probability: 0.85 E-value:0.00) d1tx2a_ 40 EVDAAVRHAKEMRDEGAH-IIDIGGESFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDT- 97 :::::::::::::::::: ::::: ::::::::::: :::::::::::::::::::: d1gvfa_ 26 NAETIQAILEVCSEMRSPVILAGT-PGTFKHIALEE---IYALCSAYSTTYNMPLALHLD 81 d1tx2a_ 98 --YKAEVAKQAIEAGAH-IINDIWGAKAEPK------IAEVAAHYDVPIILM-HNRDNMN 147 ::::::::::::::: ::::::::::::: ::::::::::::::: ::::::: d1gvfa_ 82 HHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQDCSVEAELGRLGSAF 141 d1tx2a_ 148 YRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIG-----FAKTPEQNLEAMRNLEQLN 202 :::: ::::::::::::: ::::::: ::::::::::::::::::: d1gvfa_ 142 LTDP--------QEAKRFVELTGVD----SLAVAIGTAHGLYSKTPKIDFQRLAEIREVV 189 d1tx2a_ 203 VLGYPVL-LGTS 213 ::::: :::: d1gvfa_ 190 --DVPLVLHGAS 199