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 <-- 1.245 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1vyra_) 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 d1vyra_ Pentaerythritol tetranirate reductaseFMN-​linked oxidoreductasesTIM 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 <-- 1.245 --> Hit
DALI alignment (Z-score: 11.3 Raw score:1303.10) d1tx2a_ 1 ----kwdyDLRCgeYTLNlnekTLIMGI--lNVTPDSfSDGGsynEVDAAVRHAKEMRde 54 :::: :::: :::::: :::::: :::: ::::::::::::: d1vyra_ 1 aeklftplKVGA--VTAP----NRVFMApltRLRSIE-PGDI---PTPLMGEYYRQRA-- 48 d1tx2a_ 55 GAHIIDIGGEsfakVSVE-----eEIKR--VVPMIQAVSKEVK---LPISIDTY------ 98 :::::::::: :::: :::: ::::::::::::: :::::::: d1vyra_ 49 SAGLIISEAT-qisAQAKgyagapGLHSpeQIAAWKKITAGVHaedGRIAVQLWhtgris 107 d1tx2a_ 99 ------------------------------------------------------KAEVAK 104 :::::: d1vyra_ 108 hssiqpggqapvsasalnantrtslrdengnairvdtttpraleldeipgivndFRQAVA 167 d1tx2a_ 105 QAIEAGAHIINDIW----------------------------gaKAEPKIAEVAAHYD-V 135 :::::::::::::: :::::::::::::: : d1vyra_ 168 NAREAGFDLVELHSahgyllhqflspssnqrtdqyggsvenrarLVLEVVDAVCNEWSaD 227 d1tx2a_ 136 PIILMHNR-----dNMNYRNLMADMIADLYDSIKIakdagvrdENIILDPGIGFakTPEQ 190 :::::::: ::::::::::::::::::::: ::::::::::: :::: d1vyra_ 228 RIGIRVSPigtfqnVDNGPNEEADALYLIEELAKR--------GIAYLHMSETD-lAGGK 278 d1tx2a_ 191 nlEAMR-NLEQLNVL-GYPVLLGTSRksfighvldlpveerlegTGATVCLGI-EKGCEF 247 :::: :::::::: :::::::::: ::::::::: :::::: d1vyra_ 279 --PYSEaFRQKVRERfHGVIIGAGAY------------------TAEKAEDLIgKGLIDA 318 d1tx2a_ 248 VRV-HDVK---eMSRMAKM-------------------mdamigk 269 ::: :::: ::::::: d1vyra_ 319 VAFgRDYIanpdLVARLQKkaelnpqrpesfygggaegytdypsl 363 FAST alignment (Normalized score: 6.59 Raw score:2060.00) d1tx2a_ 1 KWDY------DLRCGEYTLNLNEKT--LIMGILNV--TPDSFSDGGSYNEVDAAVRHAKE 50 ::::::::: :::::::: ::::::::: :::::::::: d1vyra_ 1 ----AEKLFTPLKVGAVTA------PNRVFMAPLTRLRSIEPGDIP----TPLMGEYYRQ 46 d1tx2a_ 51 MRDEGAHIIDIGGESFAKVS-------------------VEEEIKRVVPMIQAVSKEVKL 91 : :::::::: :::::::::::::::: :::: d1vyra_ 47 R--ASAGLIIS---------EATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVH-AEDG 94 d1tx2a_ 92 PISIDTY----------------------------------------------------- 98 ::::: d1vyra_ 95 RIAVQ--LWHTGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALEL 152 d1tx2a_ 99 ---------KAEVAKQAIEAGAHIINDIWGAKAE-------------------------- 123 :::::::::::::::::: d1vyra_ 153 DEIPGIVNDFRQAVANAREAGFDLVEL-------HSAHGYLLHQFLSPSSNQRTDQYGGS 205 d1tx2a_ 124 -----PKIAEVAAHYDV--------PIILMHNRDNMN-----------YRNLMADMIADL 159 ::::::::: :::::: :::::::::::: d1vyra_ 206 VENRARLVLEVVDA---VCNEWSADRIGIRV------SPIGTFQNVDNGPNEEADALYLI 256 d1tx2a_ 160 YDSIKIAKDAGVRDEN---IILDPGIGFAKTPEQNLE---------AMRNLEQLN-VLGY 206 ::::: ::::::: ::::::::: :::: d1vyra_ 257 EELAK-----------RGIAYLHMSE-----------TDLAGGKPYSEAFRQKVRERFHG 294 d1tx2a_ 207 PVLLGTSRKSFIGHVLDLPVEERLEG---TGATVCLGIEK-GCEFVRVHDV------KEM 256 ::::: ::::::::::: :::::::: ::: d1vyra_ 295 VIIGA---------------------GAYTAEKAEDLIGKGLIDAVAFG--RDYIANPDL 331 d1tx2a_ 257 SRMAKMMDAMIGK--------------------------- 269 ::::: d1vyra_ 332 VARLQ--------KKAELNPQRPESFYGGGAEGYTDYPSL 363 TMalign alignment (TM-score: 0.55 Raw score:148.29) d1tx2a_ 1 --------KWDYDLRCGEYTLNLNEKTLIMGILNVT-PDSFS--DGGSYNEVDAAVRHAK 49 :::: :::: : ::::::::: ::::: :::: ::::::::::: d1vyra_ 1 AEKLFTPL----KVGA--VTAP---N-RVFMAPLTRLRSIEPGDIPTP-LMGEYYRQRAS 49 d1tx2a_ 50 EMRDEGAHIIDIG-GE-------SFAKVS-VE-EEIKRVVPMIQAVSKEVKLPISIDTY- 98 : :::::: :: :::::: :: :::::::::::::::::: ::::::: d1vyra_ 50 --A----GLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDG-RIAVQLWH 102 d1tx2a_ 99 -----------------------------------------------------------K 99 : d1vyra_ 103 TGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDF 162 d1tx2a_ 100 AEVAKQAIEAGAHIINDIWG----AKAEPKIAEVAAHYDVPIILMHNRD---NMN----- 147 :::::::::::::::::::: ::::: ::: d1vyra_ 163 RQAVANAREAGFDLVELHSAHGYL--------------------LHQFLSPSSNQRTDQY 202 d1tx2a_ 148 YRNLMADMIADLYDSIKIAKDAGVRDENIILDPGI--GFAKTPEQNLEAMRNLEQLNVL- 204 :::: ::::::::::::::: :::::::::::::: :::::::: ::::::::::::: d1vyra_ 203 GGSV-ENRARLVLEVVDAVC-NEWSADRIGIRVSPIGTFQNVDNG-PNEEADALYLIEEL 259 d1tx2a_ 205 -G-YP-VLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIE-KG--C--EFVRVHDVKEM 256 : :: :::::::: : :: :: :::::::: :: : ::::::: :: d1vyra_ 260 AKRGIAYLHMSETD----------L-AG--GK-PYSEAFRQKVRERFHGVIIGAGA-YT- 303 d1tx2a_ 257 SRMAKMMDAMIGK----------------------------------------------- 269 ::::::::::::: d1vyra_ 304 AEKAEDLIGKGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL 363 HHsearch alignment (Probability: 0.94 E-value:0.00) d1tx2a_ 40 EVDAAVRHAKEMRDEGAHIIDIGGESFAK----------VSVEEEIKRVVPMIQAVSKEV 89 :::::::::::: ::::::::::::::: :::::::::::::::::::: d1vyra_ 36 PTPLMGEYYRQR--ASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAE- 92 d1tx2a_ 90 KLPISIDTYKAEVAKQA-IEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNY 148 ::::::::::::::::: ::::::::::::::::: :::::::::::::::::::::::: d1vyra_ 93 DGRIAVQLWHTGRISHSSIQPGGQAPVSASALNAN-TRTSLRDENGNAIRVDTTTPRALE 151 d1tx2a_ 149 RNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGF 184 ::::::::::::::::::::::::: ::::::::: d1vyra_ 152 LDEIPGIVNDFRQAVANAREAGFDL--VELHSAHGY 185