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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.875 --> Intermediate <-- 0.843 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1viza_) through the intermediate protein (d1j93a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1j93a_ Uroporphyrinogen decarboxylase,​ URODUROD/​MetE-​likeTIM beta/​alpha-​barrelα/β
Hit d1viza_ PcrB protein homolog YerEFMN-​linked oxidoreductasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.875 --> Intermediate
DALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 0.843 --> Hit
DALI alignment (Z-score: 8.2 Raw score:956.50) d1j93a_ 1 tqpllLDAVrgkeverPPVWLMRQ-aGRYMksyqllcekyplfrdrsenvdlvveisLQP 59 :::: :::::::: :::: ::: d1viza_ 1 ---slYDVT------eWKHVFKLDpnKDLP-----------------------deqlEIL 28 d1j93a_ 60 WKvFRPDGVILFSdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksVPY 119 :: :::::::::: ::: d1viza_ 29 CE-SGTDAVIIGG-------------------------------------------tEDN 44 d1j93a_ 120 VGEALTILRKEVnnqAAVLGFVGapftlasyvveggssknftkikrlafaepkvlhallq 179 :::::::::::: :::::::: d1viza_ 45 VLRMMSKVRRFL---VPCVLEVS------------------------------------- 64 d1j93a_ 180 kfatsMAKYIryqaDSGAQAVQIF-DSWAtelspvdfeeFSLPYLKQIVDSVK---LTHP 235 ::::: :::::::::: :::: :::::::::::::: :::: d1viza_ 65 -----AIEAI----VPGFDLYFIPsVLNS----------KNADWIVGMHQKAMkeyGELM 105 d1j93a_ 236 ---NLPLILYASG--------------------SGGLLERLPLTGVDVVSLD----WTVD 268 :::::::::: ::::::::::::::::::: :::: d1viza_ 106 smeEIVAEGYCIAnpdckaaalteadadlnmddIVAYARVSELLQLPIFYLEysgvLGDI 165 d1j93a_ 269 --MADGRRRLgPNVAIQGNVDPGvlfgskefITNRINDTVKKAgkgkHILNlghgIKVGT 326 :::::::: :::::::::::: :::::::::::: :::: ::::: d1viza_ 166 eaVKKTKAVL-ETSTLFYGGGIK--------DAETAKQYAEHA----DVIV--vgNAVYE 210 d1j93a_ 327 PEENFAHFFEIAKGlry 343 :::::::::::::: d1viza_ 211 DFDRALKTVAAVKG--e 225 FAST alignment (Normalized score: 4.21 Raw score:1168.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1viza_ 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 d1viza_ 1 ------------------------------------------------------------ 1 d1j93a_ 121 GEALTILRKEVNNQA--------AVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPK 172 ::::::: d1viza_ 1 ---------------SLYDVTEWKHVFKLD------------------------------ 15 d1j93a_ 173 VLHALLQKFATS-----MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF--SLPYLKQ 225 :::::::::::::::::: ::::::: d1viza_ 16 ------------PNKDLPDEQLEILCESGTDAVII----------------GGTEDNVLR 47 d1j93a_ 226 IVDSVKLTHPNLPLILYASGSGGLLERLPL--TGVDVVSLDWTV----------DMADGR 273 ::::::: :::::::::: :::: :::::::: :::::: d1viza_ 48 MMSKVRR--FLVPCVLEVS-AIEA------IVPGFDLYFI----PSVLNSKNADWIVGMH 94 d1j93a_ 274 RRL--------GPNVA--IQGNVDPGVL----------------FGSKEFITNRINDTVK 307 :: ::::: ::::: :::::::::::::::: d1viza_ 95 QK-AMKEYGELMSMEEIVAEGYC-----IANPDCKAAALTEADADLNMDDIVAYARVSEL 148 d1j93a_ 308 KAGKGK---HILNLGHGIK----VGTPEENFAHFFEIAKGLRY----------------- 343 ::::: :::::::::::::: d1viza_ 149 ------LQLPIFYL-----EYSGVLGDIEAVKKTKAV------LETSTLFYGGGIKDAET 191 d1j93a_ 344 ---------------------------------- 344 d1viza_ 192 AKQYAEHADVIVVGNAVYEDFDRALKTVAAVKGE 225 TMalign alignment (TM-score: 0.40 Raw score:137.34) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYM--------------------KSYQLLCEKYP 40 : : :: :::: ::::::::: ::: d1viza_ 1 -S-L-YD-VTEW----KHVFKLDPN-KDLPDEQLEILCESGTDAVIIGG----------- 40 d1j93a_ 41 LFRDRSENVDLVVEISLQPWKVFR---PDGVILFSDILTPLSGMNIPFDIIKGKGPVIFD 97 ::::::::::::: ::::::::: d1viza_ 41 -----------TEDNVLRMMSKVRRFLVPCVLEVSA------------------------ 65 d1j93a_ 98 PLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSS 157 : ::: : ::: :::::::::: :: : d1viza_ 66 ----------------------I-EAI--V-PGF---DLYFIPSVLN--SK--N------ 86 d1j93a_ 158 KNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRY-QA---D--S--G-AQAVQIFDSWAT 208 : ::: ::::: :: : : : :::::::::::: d1viza_ 87 -----------------------A-DWI-VGMHQKAMKEYGELMSMEEIVAEGYCIANPD 121 d1j93a_ 209 ----------ELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS-GSGG--LLERLPL 255 ::: :::: ::::::::::: : : :::::::: :::: ::::::: d1viza_ 122 CKAAALTEADADL--NMDD-IVAYARVSELL-Q--L--PIFYLEYSGVLGDIEAVKKTKA 173 d1j93a_ 256 TG--VDVVSLD-WT--VDMADGRRRLGPNVAIQGNVDP-GVLFGSKEFITNRINDTVKKA 309 :: ::::::: :: :::::::: :: ::::::::: ::: : ::: :::::: d1viza_ 174 VLETSTLFYGGGIKDAETAKQYAE-HA--DVIVVGNAVYEDF------D-RAL-KTVAAV 222 d1j93a_ 310 GKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 :: : d1viza_ 223 KG-------------------------------E 225 HHsearch alignment (Probability: 0.72 E-value:0.00) d1j93a_ 185 MAKYIRYQADSGAQAVQIFDS 205 ::::::::::::::::::::: d1viza_ 21 PDEQLEILCESGTDAVIIGGT 41