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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.289 --> Intermediate <-- 0.951 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1eexa_) through the intermediate protein (d1twda_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1twda_ Copper homeostasis protein CutCCutC-​like (Pfam 03932)TIM beta/​alpha-​barrelα/β
Hit d1eexa_ Diol dehydratase,​ alpha subunitCobalamin (vitamin B12)-​dependent enzymesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.289 --> Intermediate
DALI alignment (Z-score: 8.2 Raw score:868.70) query 1 mietpyylidkakltrnmeriahvreksgAKALLALkcFATWsvFDLMRD-YMDGTTS-- 57 ::::::: :::: :::::: ::::::: d1twda_ 1 -----------------------------ALLEICC--YSME-cALTAQQnGADRVELca 28 query 58 -------SSLF-EVRLGRERFGKETHAYSVA-------------yGDNEIDEVVS-HADK 95 :::: ::::::::::::::::::: :::::::::: :::: d1twda_ 29 apkegglTPSLgVLKSVRQRVTIPVHPIIRPrggdfcysdgefaaILEDVRTVRElGFPG 88 query 96 IIFNS--------ISQLERFADKAAGIARGLR-LNPQrlgEWDVPKV-ERVMD-RINGFM 144 ::::: ::::::::::::::::::: :::: ::::::: ::::: :::::: d1twda_ 89 LVTGVldvdgnvdMPRMEKIMAAAGPLAVTFHrAFDM---CANPLYTlNNLAElGIARVL 145 query 145 IHnncenkdfglfDRMLGEIEErFGALiARVDWVSLGGGIHFtgddypvdaFSARLRAFS 204 :: ::::::::: :::: :::::::::::::: ::::::::: d1twda_ 146 TS-----gqksdaLQGLSKIME-LIAH-RDAPIIMAGAGVRA--------eNLHHFLDAG 190 query 205 drygvqIYLEPGeaSITKsTTLE-VTVLdtlynknlaivdssieahmldlliyretakvl 263 :::::: :::: :::: :::: d1twda_ 191 -----vLEVHSS--AGAW-QASPmRYRN-------------------------------- 210 query 264 pnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGYtmvkknwfngvkmpai 323 ::::: d1twda_ 211 ---------------------------------------YSRYI---------------- 215 query 324 aireldgsvrtvreftyadyeqsls 348 d1twda_ 216 ------vdgaavaemkgiierhqak 234 FAST alignment (Normalized score: 4.77 Raw score:1361.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFA--TWSVFDLMRD-YMDGTTS 57 :::::: :::::::::: ::::::: d1twda_ 1 -----------------------------ALLEIC-----CYSMECALTAQQNGADRVEL 26 query 58 ----------SSLFEVRLGRERFGKETHAYSVAY----------------GDNEIDEVVS 91 ::::::::::::::::::::: :::::::::: d1twda_ 27 CAAPKEGGLTPSLGVLKSVRQRVTIPVHPII---RPRGGDFCYSDGEFAAILEDVRTVRE 83 query 92 -HADKIIFN---------SISQLERFADKAAGIARGLRLNPQRLGEW---------DVPK 132 ::::::: ::::::::::::::::::: :::: d1twda_ 84 LGFPGLVT-GVLDVDGNVDMPRMEKIMAAAGPLAVTF----------HRAFDMCANPLYT 132 query 133 VERVMD-RINGFMIHNNCENKDFG--------LFDRMLGEIEERFGALIARV----DWVS 179 :::::: ::::::: ::::::::::: :::: d1twda_ 133 LNNLAELGIARVLT----------SGQKSDALQGLSKIMELIA---------HRDAPIIM 173 query 180 LGGGIHFTGDD--YPVDAFSARLRAFSDRYGVQ---IYLEPGEASITK----STTLEVTV 230 ::::: :::::::: ::::: :::::::: d1twda_ 174 AGAGV------RAENLHHFLD------------AGVLEVHS-------SAGAWQASPMRY 208 query 231 LDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFA 290 d1twda_ 209 ------------------------------------------------------------ 209 query 291 EELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-- 348 d1twda_ 209 ----------------------------------------------------------RN 210 query 349 ------------------------ 349 d1twda_ 211 YSRYIVDGAAVAEMKGIIERHQAK 234 TMalign alignment (TM-score: 0.42 Raw score:146.57) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSS-- 58 ::::: ::: ::::::::::::::::::: d1twda_ 1 ----------------------------ALLEI-CCY--SMECALTAQQNGADRVELCAA 29 query 59 ------SLF--EVRLGRERFGKETHAYSVA-------------YGDNEIDEVVS-HADKI 96 ::: ::::::::::::::::::: ::::::::::: ::::: d1twda_ 30 PKEGGLTPSLGVLKSVRQRVTIPVHPIIRPRGGDFCYSDGEFAAILEDVRTVRELGFPGL 89 query 97 IFNS------IS--QLERFADKAAGIARGLRLNPQRLGEWD-VPKVERVMD-RINGFMIH 146 :::: :: ::::::::::::::::::::: :::: ::::::::: :::::::: d1twda_ 90 VTGVLDVDGNVDMPRMEKIMAAAGPLAVTFHRAFD--MCANPLYTLNNLAELGIARVLTS 147 query 147 -NNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSD 205 ::: : :::::::::: :::: :::::::::::::: :: ::::::::: d1twda_ 148 GQKS-D-----ALQGLSKIME-LIAH-RDAPIIMAGAGVRA----EN---LHHFLDAGV- 191 query 206 RYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPN 265 :::: :: : ::: ::::: :: d1twda_ 192 ----LEVH-SS-A-GAW-QASPM--------------RY--------------------- 208 query 266 EGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTM---------------- 309 :: :::::: d1twda_ 209 ----------RN--------------------------YSRYIVDGAAVAEMKGIIERHQ 232 query 310 --VKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1twda_ 233 AK--------------------------------------- 234 HHsearch alignment (Probability: 0.20 E-value:0.04) query 45 FDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYG-------------DNEIDEVVS 91 :::::::::::::::::::::::::::::::::::::: ::::::::: d1twda_ 24 VELCAAPKEGGLTPSLGVLKSVRQRVTIPVHPIIRPRGGDFCYSDGEFAAILEDVRTVRE 83 query 92 HADKIIF---------NSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRING 142 ::::::: :::::::::::::::::::: ::::::::::::::::::: d1twda_ 84 LGFPGLVTGVLDVDGNVDMPRMEKIMAAAGPLAVTF-----HRAFDMCANPLYTLNNLAE 138 query 143 FMI-HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGI 184 ::: ::::::::::: :::::::::::::::::: ::::::: d1twda_ 139 LGIARVLTSGQKSDA-LQGLSKIMELIAHRDAPI--IMAGAGV 178
Intermediate <-- 0.951 --> Hit
DALI alignment (Z-score: 9.9 Raw score:1232.90) d1twda_ 1 ------------------------------------------------------------ 1 d1eexa_ 1 mrskrfealakrpvnqdgfvkewieegfiamespndpkpsikivngavteldgkpvsdfd 60 d1twda_ 1 ------------------------------------------------------------ 1 d1eexa_ 61 lidhfiaryginlnraeevmamdsvklanmlcdpnvkrseivplttamtpakivevvshm 120 d1twda_ 1 -----------------ALLEICCY--------SMECALTAQQNGADRVELCAApkeggl 35 :::::::: ::::::::::::::::::::: d1eexa_ 121 nvvemmmamqkmrarrtPSQQAHVTnvkdnpvqIAADAAEGAWRGFDEQETTVA----va 176 d1twda_ 36 tpSLGVLKSVRQRVT-----IPVHPIIRprggdfcysdgefaaILEDVRTVRELGFPGLV 90 ::::::::::::: :::::::: ::::::::::::::::: d1eexa_ 177 ryAPFNAIALLVGSQvgrpgVLTQCSLE---------------EATELKLGMLGHTCYAE 221 d1twda_ 91 -TGVL-DVDGN----vDMPRMEKIMAAAG--PLAVTFHRaFDMCA-------------NP 129 :::: ::::: ::::::::::::: :::::::: ::::: :: d1eexa_ 222 tISVYgTEPVFtdgddTPWSKGFLASSYAsrGLKMRFTS-GSGSEvqmgyaegksmlyLE 280 d1twda_ 130 LYTLNNLAELGIARVLTSG--QKSD---alqGLSKIMELIAH--RDAPIIMAGAG----- 177 ::::::::::::::::::: :::: ::::::::::: ::::::::::: d1eexa_ 281 ARCIYITKAAGVQGLQNGSvsCIGVpsavpsGIRAVLAENLIcsSLDLECASSNDqtfth 340 d1twda_ 178 ---vrAENLHHFLDAGVLE-VHSSA--GAWQaspmryrnysryivDGAAvAEMKGIIERH 231 :::::::::::::: ::::: :::: :::: :::::::::: d1eexa_ 341 sdmrrTARLLMQFLPGTDFiSSGYSavPNYD------nmfagsneDAED-FDDYNVIQRD 393 d1twda_ 232 QA---------------------------------------------------------- 233 :: d1eexa_ 394 LKvdgglrpvreedviairnkaaralqavfagmglppitdeeveaatyahgskdmperni 453 d1twda_ 234 ------------------------------------------------------------ 234 d1eexa_ 454 vedikfaqeiinknrnglevvkalaqggftdvaqdmlniqkakltgdylhtsaiivgdgq 513 d1twda_ 234 -------------------------------------k 234 d1eexa_ 514 vlsavndvndyagpatgyrlqgerweeiknipgaldpn 551 FAST alignment (Normalized score: 5.35 Raw score:1921.00) d1twda_ 1 ------------------------------------------------------------ 1 d1eexa_ 1 MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFD 60 d1twda_ 1 ------------------------------------------------------------ 1 d1eexa_ 61 LIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHM 120 d1twda_ 1 -----------------ALLEICCY----------SMECALTAQQNGADRVELCAAPKEG 33 :::::: ::::::::::::::::::: d1eexa_ 121 NVVEMMMAMQKMRARRTPSQQAH--VTNVKDNPVQIAADAAEGAWRGFDEQETT------ 172 d1twda_ 34 GLTP------SLGVLKSVRQRV------TIPVHPIIRPRGGDFCYSDGEFAAILE-DVRT 80 ::::::::::: ::::::: :::: d1eexa_ 173 ----VAVARYAPFNAIALLVG-SQVGRPGVLTQCS--------------------LEEAT 207 d1twda_ 81 VREL-----GFPGL-VTGVLDVDGNV------------DMPRMEKIMAAA---GPLAVTF 119 ::: ::::: :::: ::::::::::: ::::::: d1eexa_ 208 ELK-LGMLGHTCYAETISV-------YGTEPVFTDGDDTPWSKGFLASS-YASRGLKMRF 258 d1twda_ 120 HRAFDMCA--------------------NPLYTLNNLAELGIARVLTSGQKSDAL----- 154 :::::::::::::::::: d1eexa_ 259 --------TSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQ---------NGSVS 301 d1twda_ 155 ---------QGLSKIMELIAHRD-----APIIMAGAGV------------RAENLHHFLD 188 ::::::::::: :::::: :::::::::: d1eexa_ 302 CIGVPSAVPSGIRAVLAENL---ICSSLDLECAS----SNDQTFTHSDMRRTARLLMQFL 354 d1twda_ 189 AGVLE--VHSSAGAWQASPMRYRNYSRYIVDGAAVA---------------EMKGIIERH 231 ::::: ::::: ::::::::: d1eexa_ 355 PGTDFISSGYSA------------------------VPNYDNMFAGSNEDAEDFDDYNVI 390 d1twda_ 232 QAK--------------------------------------------------------- 234 :: d1eexa_ 391 QR-DLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMP 449 d1twda_ 235 ------------------------------------------------------------ 235 d1eexa_ 450 ERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIV 509 d1twda_ 235 ------------------------------------------ 235 d1eexa_ 510 GDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPN 551 TMalign alignment (TM-score: 0.55 Raw score:129.69) d1twda_ 1 ------------------------------------------------------------ 1 d1eexa_ 1 MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFD 60 d1twda_ 1 ---------A-------------------------------------------------- 1 : d1eexa_ 61 LIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHM 120 d1twda_ 2 ----LLEICCYSMECALT-AQQNGADR-VELCAAPKEGGLTPSLGVLKSVRQRVTIPVHP 55 :: :::::::: :::::: d1eexa_ 121 NVVE------------MMMAMQKMRARR--------------------------TPSQQA 142 d1twda_ 56 IIRPRGGDFCYSDGEFAAILEDVRTVRELGFPGLVTGVLDVDGNVDMPRMEKIMAAAG-- 113 ::::: ::: ::::::::::::::::::::::::::: :::::::::::::: d1eexa_ 143 HVTNV-----KDN--PVQIAADAAEGAWRGFDEQETTVAVAR--YAPFNAIALLVGSQVG 193 d1twda_ 114 -P-LAVTFHRAFDMCANPLYTLNNLAELGIARVLTSG------QKSDALQGLSKIMELIA 165 : :::::: ::: : :::::::: ::::::::::: ::::: ::::::::::: d1eexa_ 194 RPGVLTQCS-LEE-A-TELKLGML--GHTCYAETISVYGTEPVFTDGD-DTPWSKGFLAS 247 d1twda_ 166 H--RDAPIIMAGAGV-----------------RAENLHHFLDAGVLEVHSSA---G--AW 201 : :::::::::::: :::::::::::::::::::: : :: d1eexa_ 248 SYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPS 307 d1twda_ 202 QASPMRYRNYSRYIV-DGAAVAEMKGIIE------------------------------- 229 :: : :::: ::::::::::::: d1eexa_ 308 AV-------P-SGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDF 359 d1twda_ 230 ------------------------------------------------------------ 230 d1eexa_ 360 ISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARAL 419 d1twda_ 230 ------------------------------------------------------------ 230 d1eexa_ 420 QAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQ 479 d1twda_ 230 ------------------------------------------------------------ 230 d1eexa_ 480 GGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWE 539 d1twda_ 230 ------------RHQAK 234 d1eexa_ 540 EIKNIPGALDPN----- 551 HHsearch alignment (Probability: 0.01 E-value:0.15) d1twda_ 204 SPMRYRNYS-RYIVDGAA---VAEMKGIIER 230 ::::::::: :::::::: :::::::::: d1eexa_ 520 DVNDYAGPATGYRLQGERWEEIKNIPGALDP 550