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 <-- 1.679 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1oyba_) 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 d1oyba_ Old yellow enzyme (OYE)FMN-​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 <-- 1.679 --> Hit
DALI alignment (Z-score: 12.5 Raw score:1509.70) d1j93a_ 1 -------------tqplllDAVRgkeverPPVWLMRQagrymksyqllcekyplfrDRSE 47 :::: :::::::: :::: d1oyba_ 1 sfvkdfkpqalgdtnlfkpIKIG-nnellHRAVIPPL-----------------trMRAL 42 d1j93a_ 48 ------NVDLVVEISLQPWKvFRPDGVILFsDILTPLSgmnipFDIIkgkgpvifdplrt 101 :::::::::::::: ::::::::: ::::::: :::: d1oyba_ 43 hpgnipNRDWAVEYYTQRAQ-RPGTMIITE-GAFISPQ---agGYDN------------- 84 d1j93a_ 102 aadvekvrefiPEKSVpyvGEALTILRKE-VNNQAAVLGFVGapftLASYvveGGSS--- 157 ::::: :::::::::: :::::::::::: :::: :::: d1oyba_ 85 -------apgvWSEEQ---MVEWTKIFNAiHEKKSFVWVQLW----VLGW---AAFPdnl 127 d1j93a_ 158 ---knftKIKRL---------------afaepkVLHALLQKFATSMAKYIRYQADSGAQA 199 ::::: ::::::::::::::::::::::::::: d1oyba_ 128 ardglryDSASDnvfmdaeqeakakkannpqhsLTKDEIKQYIKEYVQAAKNSIAAGADG 187 d1j93a_ 200 VQIFDS-----WATEL-------------SPVDFEeFSLPYLKQIVDSVKlthpnLPLIL 241 :::::: ::::: :::::: :::::::::::::: ::::: d1oyba_ 188 VEIHSAngyllNQFLDphsntrtdeyggsIENRAR-FTLEVVDALVEAIG----hEKVGL 242 d1j93a_ 242 YASG------------------SGGLLERLPL-----tGVDVVSLDWT------------ 266 :::: :::::::::: :::::::::: d1oyba_ 243 RLSPygvfnsmsggaetgivaqYAYVAGELEKrakagkRLAFVHLVEPrvtnpfltegeg 302 d1j93a_ 267 ----vDMADGRRRLGpnVAIQGNvDPGVLfgskefITNRINDTVKkagKGKHILNLghGI 322 :::::::::: :::::: ::::: :::::::::: :::::::: :: d1oyba_ 303 eyeggSNDFVYSIWK--GPVIRA-GNFAL------HPEVVREEVK---DKRTLIGY--GR 348 d1j93a_ 323 KVgtpeenFAHFFEI------------------------------akglry 343 :: ::::::: d1oyba_ 349 FFisnpdlVDRLEKGlplnkydrdtfyqmsahgyidyptyeealklgwdkk 399 FAST alignment (Normalized score: 6.39 Raw score:2365.00) d1j93a_ 1 TQPLLLDAVRG------------------------KEVERPPVWLMRQAGRYMKSYQLLC 36 ::::: ::::::: d1oyba_ 1 -----------SFVKDFKPQALGDTNLFKPIKIGNNELLH-RAVIPPL------------ 36 d1j93a_ 37 EKYPLFRDRSE------------NVDLVVEISLQPWKVFRP----DGVILFSDILTPLSG 80 ::::::::::::: ::::: d1oyba_ 37 -----------TRMRALHPGNIPNRDWAVEYYTQRA-----QRPGTMIIT---------- 70 d1j93a_ 81 MNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS-------------------VPYVG 121 ::::: d1oyba_ 71 ------------------------------------EGAFISPQAGGYDNAPGVWSEEQM 94 d1j93a_ 122 EALTILRKEVNN----QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV---- 173 ::::::::: :::::::: d1oyba_ 95 VEWTKIFNA---IHEKKSFVWVQL--------------------------------WVLG 119 d1j93a_ 174 ------------------------------------------LHALLQKFATSMAKYIRY 191 :::::::::::::::::: d1oyba_ 120 WAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKN 179 d1j93a_ 192 QADSGAQAVQIFD---SWATELSPV----------------DFEEFSLPYLKQIVDSVKL 232 ::::::::::::: :::: :::: :::::::::::::: d1oyba_ 180 SIAAGADGVEIHSANGYLLN-----QFLDPHSNTRTDEYGGSIEN-RARFTLEVVDALVE 233 d1j93a_ 233 T-HPNLPLILYASG----------------SGGLLERLPLT----------GVDVVSLDW 265 : ::: :::::: :::::::::: :::::::: d1oyba_ 234 AIGHE-KVGLRL--SPYGVFNSMSGGAETGIVAQYAYVAG-ELEKRAKAGKRLAFVHLV- 288 d1j93a_ 266 TV-------------------DMADGRRRLGPNVAIQGNVD--PGVLFGSKEFITNRIND 304 ::::::::: ::::: ::::: ::::::: d1oyba_ 289 --EPRVTNPFLTEGEGEYEGGSNDFVYSIW--KGPVI----RAGNFAL-----HPEVVRE 335 d1j93a_ 305 TVKKAGKGKHILNLGHGIKVGTPEENFA---------HFFEIAKGLRY------------ 343 ::: ::::::: ::::::: d1oyba_ 336 EVK---DKRTLIG---------------YGRFFISNPDLVDRLE----KGLPLNKYDRDT 373 d1j93a_ 344 -------------------------- 344 d1oyba_ 374 FYQMSAHGYIDYPTYEEALKLGWDKK 399 TMalign alignment (TM-score: 0.58 Raw score:198.68) d1j93a_ 1 ----------------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEK------ 38 :::::::::::::::::::::::: : ::::::: d1oyba_ 1 SFVKDFKPQALGDTNL----FKPIKIGNNELLHRAVIPPLTRMR-A-LHPGNIPNRDWAV 54 d1j93a_ 39 ---------------------YPLFRD-----RSENVDLVVEISLQPWKVFR-P-DGVIL 70 ::::: :::::::::::::::::::: : ::::: d1oyba_ 55 EYYTQRAQRPGTMIITEGAFI-SPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWV 113 d1j93a_ 71 FSDILTPLSGMNIPFDIIKGKG----PVIFDPLRT-----------------AADVEKVR 109 ::::: : ::::::::: ::::::::: :::::: d1oyba_ 114 QLWVL--G-----WAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQ--HSLTKD 164 d1j93a_ 110 -EFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFT-LASYVVEGGSSKNFTKIKRLA 167 ::::::::::::::::::: : :::::::::: ::::::: : ::: :: d1oyba_ 165 EIKQYIKEYVQAAKNSIAAG--A-----DGVEIHSANGYLLNQFLD------P-HSN-TR 209 d1j93a_ 168 ----FAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATE-----LSP-VDFEE 217 ::::::::::::::::::::::: ::::::::::::: ::: ::::: d1oyba_ 210 TDEY----GGSIENRARFTLEVVDALVEAIG--HEKVGLRLSPYGVFNSMSGGAETGIVA 263 d1j93a_ 218 FSLPYLKQIVDSVKLTHPNLPLILYASGSG------------G--LLERLPLTG-VDVVS 262 :::::::::::::::::: ::::::::::: : ::::::::: ::::: d1oyba_ 264 QYAYVAGELEKRAKAGKR-LAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIR 322 d1j93a_ 263 LDWTV-DMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKK-----AGKGKHIL 316 ::::: :::::::::::::::::::::::: : :: :::::::: d1oyba_ 323 AGNFALHPEVVREEVKDKRTLIGYGRFFIS---N--PD-LVDRLEKGLPLNK-------- 368 d1j93a_ 317 NL---GHGIKVG----TPEENFAHF-FEI--------AKGLRY 343 : :::: :::::: :: :: d1oyba_ 369 -YDRD---TFYQMSAHGYIDYP-TYE-EALKLGWDKK------ 399 HHsearch alignment (Probability: 0.85 E-value:0.00) d1j93a_ 176 ALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSL--------------- 220 :::::::::::::::::::::::::::::::::::: :::: d1oyba_ 164 DEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLN-----QFLDPHSNTRTDEYGGSIE 218 d1j93a_ 221 ---PYLKQIVDSVKLTHPNLPLILYAS 244 :::::::::::::::::::::::: d1oyba_ 219 NRARFTLEVVDALVEAIGHEKVGLRLS 245