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 <-- 1.190 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1vkfa_) 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 d1vkfa_ Glycerol uptake operon antiterminator-​related protein TM1436GlpP-​likeTIM 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 <-- 1.190 --> Hit
DALI alignment (Z-score: 7.8 Raw score:815.40) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQagrymksyqllcekyplfrdrsenvdlVVEIslqpw 60 :::::::: :::: d1vkfa_ 1 --------------mfKGIIAALW---------------------------DMDS----i 15 d1j93a_ 61 KVFRPDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksVPYV 120 ::::::::::::: :::: d1vkfa_ 16 GEIEPDVVFLLKS------------------------------------------dILNL 33 d1j93a_ 121 GEALTILRKEVnnqAAVLGFVGapftlasyvveggssknftkikrlafaepkvlhallqk 180 ::::::::::: :::::::: d1vkfa_ 34 KFHLKILKDRG---KTVFVDMD------------------------------------fv 54 d1j93a_ 181 fatSMAK-YIRYQADSGAQAVQIFdswatelspvdfeefslpyLKQIVDSVKLTHpnLPL 239 :::: :::::::::::::::: :::::::::::: ::: d1vkfa_ 55 nglGEGEeAILFVKKAGADGIITI-------------------KPKNYVVAKKNG--IPA 93 d1j93a_ 240 ILYASGSG-GLLE---RLPL-TGVDVVSLDWtvdMADGRRRlGPNVAIQGNVDPgvlfgs 294 :::::::: :::: :::: :::::::::: ::::::: :::::::::::: d1vkfa_ 94 VLRFFALDsKAVErgiEQIEtLGVDVVEVLPgavAPKVARK-IPGRTVIAAGLV------ 146 d1j93a_ 295 kefitnRINDTVKKAGKgKHILNLghgikvgtpeenfAHFFEIakglry 343 ::::::::::: :::::: :::::: d1vkfa_ 147 -----eTEEEAREILKH-VSAIST-----------ssRILWKM------ 172 FAST alignment (Normalized score: 5.49 Raw score:1334.00) d1j93a_ 1 TQPLLLDAVRGKEVERP---PVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL---VVE 54 :::: ::: d1vkfa_ 1 -----------------MFKGIIA------------------------------ALWDMD 13 d1j93a_ 55 ISLQPWKVF----RPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVRE 110 : ::::::: d1vkfa_ 14 S--------IGEIEPDVVFL---------------------------------------- 25 d1j93a_ 111 FIPEKS----VPYVGEALTILRKEVNN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKR 165 ::::::::::::: ::::::: d1vkfa_ 26 ------LKSDILNLKFHLKILKD----RGKTVFVD------------------------- 50 d1j93a_ 166 LAFAEPKVLHALLQKFATS---------MAKYIRYQADSGAQAVQIFDSWATELSPVDFE 216 :::::::::::::::::: d1vkfa_ 51 -------------------MDFVNGLGEGEEAILFVKKAGADGIIT-------------- 77 d1j93a_ 217 EF-SLPYLKQIVDSVKLTHPNLPLILYASG---SGGLLERL----PLTGVDVVSLDWTV- 267 :::::::::: ::::::::: :::::::: :::::::::: d1vkfa_ 78 --IKPKNYVVAKK------NGIPAVLRF--FALDSKAVERGIEQIETLGVDVVEV----L 123 d1j93a_ 268 ---DMADGRRRLGPNVAIQGNVDPGVLFGSKEF-------ITNRINDTVKKAGKGKHILN 317 :::::::: :::::: ::::::::::: d1vkfa_ 124 PGAVAPKVARK-IPGRTV---------------IAAGLVETEEEAREILKH--------- 158 d1j93a_ 318 LGHGIKVGTPEEN-------FAHFFEIAKGLRY-- 343 ::::: d1vkfa_ 159 -------------VSAISTSSRILW--------KM 172 TMalign alignment (TM-score: 0.36 Raw score:123.69) d1j93a_ 1 TQPLLLDAVR---------------GKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDR 45 ::: ::::::::::: d1vkfa_ 1 -------MFKGIIAALWDMDSIGEI-----EPDVVFLLKSD------------------- 29 d1j93a_ 46 SENVDLVVEISLQPWKVFR---PDGVILFSD----ILTPLSGMNIPFDIIKGKGPVIFDP 98 : ::::::::::: ::::::::: d1vkfa_ 30 -----I--LNLKFHLKILKDRGKTVFVDMDFVNGL------------------------- 57 d1j93a_ 99 LRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSK 158 : ::::::::::::: :::::::: d1vkfa_ 58 ------------------G-EGEEAILFVKKAG---ADGIITIK---------------- 79 d1j93a_ 159 NFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF 218 : ::::::::::::::::::: : :: : d1vkfa_ 80 --------------------------P-KNYVVAKKNGIPAVLRFFA-L-------DS-K 103 d1j93a_ 219 SLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTG--VDVVSLD-WTV--DMADGR 273 ::::::::::::: :::::::: :: ::::::::: ::::::: ::: :::::: d1vkfa_ 104 AVERGIEQIETLG-----VDVVEVLP-GA-VAPKVARKIPGRTVIAAGLVETEEEAREIL 156 d1j93a_ 274 RRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAH 333 : : :::::::: : ::::: d1vkfa_ 157 K--H--VSAISTSS----------R-ILWKM----------------------------- 172 d1j93a_ 334 FFEIAKGLRY 343 d1vkfa_ 173 ---------- 173 HHsearch alignment (Probability: 0.43 E-value:0.03) d1j93a_ 249 LLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRIN 303 :::::::::::::::::::::::::::::::::::::: :::::::::::: d1vkfa_ 108 GIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGL-----VETEEEAREILK 157