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 <-- 0.959 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1m7xa3) 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 d1m7xa3 1,​4-​alpha-​glucan branching enzyme,​ central domain(Trans)glycosidasesTIM 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 <-- 0.959 --> Hit
DALI alignment (Z-score: 12.8 Raw score:1527.70) d1j93a_ 1 ----TQPL-LLDAvrgkeverPPVWLMRQAGRymkSYQLlCEKYPlfrdrseNVDLVVEI 55 :::: :::: ::::::::::: :::: ::::: :::::::: d1m7xa3 1 vvqtEERKkANQF------daPISIYEVHLGS---WRRH-TDNNF-----wlSYRELADQ 45 d1j93a_ 56 SLQPWKVFRPDGVILFSDILTplsgmnipFDIIkgkgpvifdplrtaadvekvreFIPE- 114 ::::::::::::::::::::: :::: :::: d1m7xa3 46 LVPYAKWMGFTHLELLPINEH--------PFDG--------------swgyqptgLYAPt 83 d1j93a_ 115 ---ksVPYVGEALTILRKEVnnqAAVLGFVGApfTLASyvvEGGS---------sknfTK 162 ::::::::::::::: ::::::::: :::: :::: :: d1m7xa3 84 rrfgtRDDFRYFIDAAHAAG---LNVILDWVP--GHFP---TDDFalaefdgtnlyehST 135 d1j93a_ 163 IKrlafaepkvLHALlQKFATSMAKYIRYQAD-SGAQAVQIFDS-WATELspVDFEeFSL 220 :: :::: :::::::::::::::: ::::::::::: ::::: :::: ::: d1m7xa3 136 LI--------yNYGR-REVSNFLVGNALYWIErFGIDALRVDAVaSMIYRggRENL-EAI 185 d1j93a_ 221 PYLKQIVDSVKLTHPNLPLILYAsgSGGLlERLP------LTGVDVVSLD--WTVD---- 268 ::::::::::::::::::::::: :::: :::: :::::::::: :::: d1m7xa3 186 EFLRNTNRILGEQVSGAVTMAEE--STDF-PGVSrpqdmgGLGFWYKWNLgwMHDTldym 242 d1j93a_ 269 -------------maDGRRRlGPNVAIQGNV--------dpGVLFG-------SKEFITN 300 ::::: :::::::::: ::::: ::::::: d1m7xa3 243 kldpvyrqyhhdkltFGILY-NYTENFVLPLshdevvhgkkSILDRmpgdawqKFANLRA 301 d1j93a_ 301 RINDTVKKAgkgkHILNLghGIKV-----------------------gtPEENFAHFFEI 337 ::::::::: ::::: :::: ::::::::::: d1m7xa3 302 YYGWMWAFP----GKKLL--FMGNefaqgrewnhdasldwhlleggdnwHHGVQRLVRDL 355 d1j93a_ 338 AKGLRY---------- 343 :::::: d1m7xa3 356 NLTYRHhkamheldfd 371 FAST alignment (Normalized score: 6.47 Raw score:2308.00) d1j93a_ 1 TQP-----LLLDAVRGKEVER---PPVWLMRQ---AGRYMKSYQLLCEKYPLFRDRS--- 46 ::::::: ::::: :::: d1m7xa3 1 ---VVQTEERKKANQ------FDAPISIY---EVHLGSW------------------RRH 30 d1j93a_ 47 ------ENVDLVV-EISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPL 99 ::::::: :::::::: :::::::: d1m7xa3 31 TDNNFWLSYRELADQLVPYAKW-MGFTHLEL----------------------------- 60 d1j93a_ 100 RTAADVEKVREFIPEKS----------------------------VPYVGEALTILRKEV 131 ::::::::::::: d1m7xa3 61 -----------------LPINEHPFDGSWGYQPTGLYAPTRRFGTRDDFRYFIDAAHA-- 101 d1j93a_ 132 NN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL------------- 177 :::::::: d1m7xa3 102 --AGLNVILDW------------------------------------VPGHFPTDDFALA 123 d1j93a_ 178 ------------------LQKFATSMAKYIRYQA-DSGAQAVQI-FDSWATELSPVDF-- 215 :::::::::::::::: ::::::::: ::::: d1m7xa3 124 EFDGTNLYEHSTLIYNYGRREVSNFLVGNALYWIERFGIDALRVDAVASM--------IY 175 d1j93a_ 216 -----EEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGL--LERLP-------LTGVDVV 261 ::::::::::::::::::::::::::::: :::: ::::::: d1m7xa3 176 RGGRENLEAIEFLRNTNRILGEQVSGAVTMAEES-----TDFPGV-SRPQDMGGLGFWYK 229 d1j93a_ 262 SLDWTV-----------------------DMADGRRRLG-PNVAIQGNVDPGVLFG---- 293 :: :::::::: ::::: d1m7xa3 230 WN----LGWMHDTLDYMKLDPVYRQYHHDKLTFGILY--NYTENF-----------VLPL 272 d1j93a_ 294 ----------------------SKEFITNRINDTVKKAGKGK--HILNLGHGIKVGT--- 326 :::::::::::::: :::: d1m7xa3 273 SHDEVVHGKKSILDRMPGDAWQKFANLRAYYGWMWA------FPGKKL---------LFM 317 d1j93a_ 327 ------------------------------PEENFAHFFEIAKGLRY-------- 343 :::::::::::::::: d1m7xa3 318 GNEFAQGREWNHDASLDWHLLEGGDNWHHGVQRLVRDLNLTYRHHK-AMHELDFD 371 TMalign alignment (TM-score: 0.61 Raw score:208.25) d1j93a_ 1 ---TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISL 57 ::: :::::::: : :::::::::::: :::::::: :: :::::::::: d1m7xa3 1 VVQTEE-RKKANQFD-A--PISIYEVHLGSW--RRHTDNNF-----WL--SYRELADQLV 47 d1j93a_ 58 QPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPE-KS 116 ::::::::::::::::: : ::: ::::::::: : :::: : d1m7xa3 48 PYAKWMGFTHLELLPIN-E--------HPF-DGSWGYQPT-----------G-LYAPT-R 84 d1j93a_ 117 V-PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGG----------SSKNFTKIKR 165 : :::::::::::::::::::::::::: : :: :::::: d1m7xa3 85 RFGTRDDFRYFIDAAHAAGLNVILDWVP-G-HF-PTDDFALAEFDGTNLY---------- 131 d1j93a_ 166 LAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPV-DFEEFSLPYLK 224 :: :::::::::::::::::::::::::::::::::::::::::::: ::::::::::: d1m7xa3 132 EH--STLIYNYGRREVSNFLVGNALYWIERFGIDALRVDAVASMIYRGGRENLEAIEFLR 189 d1j93a_ 225 QIVDSVKLTHPNLPLILYASGSGGLLERLP-----LTGVDVVSLD--WTV---------- 267 ::::::::::::::::: : :::::::::: :::::::::: ::: d1m7xa3 190 NTNRILGEQVSGAVTMA-E-ESTDFPGVSRPQDMGGLGFWYKWNLGWMHDTLDYMKLDPV 247 d1j93a_ 268 ----------DMADGRRRLGPNVAIQGNVD--P------GVLF-G------SKEFITNRI 302 ::::::::: ::::::: : :::: : ::::::::: d1m7xa3 248 YRQYHHDKLTFGILYNYTE----NFVLPLSHDEVVHGKKSILDRMPGDAWQKFANLRAYY 303 d1j93a_ 303 NDTVKKAGKGKHILNLGHGI------KV-----GT--P-------EE-NFAHFFEIAKGL 341 ::::::: ::::::::: :: :: : :: :::::::::::: d1m7xa3 304 GWMWAFP----GKKLLFMGNEFAQGREWNHDASLDWHLLEGGDNWHHGVQRLVRDLNLTY 359 d1j93a_ 342 --R-Y------- 343 : : d1m7xa3 360 RHHKAMHELDFD 371 HHsearch alignment (Probability: 0.14 E-value:0.01) d1j93a_ 166 LAFAEPKVLHALLQKFATSMAKYIRYQAD-SGAQAVQIFDSWATELSPVDFEEF--SLPY 222 :::::::::::::: ::::::: :::::: ::::::: ::::::::: :::: d1m7xa3 138 YNYGRREVSNFLVG--------NALYWIERFGIDAL-RVDAVAS-MIYRGGRENLEAIEF 187 d1j93a_ 223 LKQIVDSVKLTHPNLPLI 240 :::::::::::::::::: d1m7xa3 188 LRNTNRILGEQVSGAVTM 205