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 <-- 1.095 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1jz7a5) 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 d1jz7a5 beta-​Galactosidase,​ domain 3(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 <-- 1.095 --> Hit
DALI alignment (Z-score: 10.5 Raw score:1207.20) d1j93a_ 1 tqpllldAVRG-KEVErPPVWLMRQAGrymksYQLLCekyplfrdRSENvDLVVEISLQP 59 :::: :::: :::::::::: ::::: :::: :::::::::: d1jz7a5 1 evriengLLLLnGKPL-LIRGVNRHEH-----HPLHG--------QVMD-EQTMVQDILL 45 d1j93a_ 60 WKVFRPDGVILfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpy 119 ::::::::::: d1jz7a5 46 MKQNNFNAVRC--------------------------------------------shypn 61 d1j93a_ 120 VGEALTILRKEVnnqAAVLGFVGApftlasyvveggsSKNFtkikrlafaepkvLHALLQ 179 :::::::::::: ::::::::: :::: :::::: d1jz7a5 62 HPLWYTLCDRYG---LYVVDEANI----------ethGMVP-------mnrltdDPRWLP 101 d1j93a_ 180 KFATSMAKYIRYQADSG-AQAVQIFDSWAtelspvdfeefSLPYLKQIVDSVKLTHPNLP 238 ::::::::::::::::: ::::::::::: :::::::::::::::::::: d1jz7a5 102 AMSERVTRMVQRDRNHPsVIIWSLGNESG-----------HGANHDALYRWIKSVDPSRP 150 d1j93a_ 239 LILYAsgsggllerLPLTgVDVVSLDWT-------------VDMADGRRRlGPNVAIQG- 284 ::::: :::: ::::::::: ::::::::: :::::::: d1jz7a5 151 VQYEG------ggaDTTA-TDIICPMYArvdedqpfpavpkWSIKKWLSLpGETRPLILc 203 d1j93a_ 285 NVDPgvLFGSkeFITNrINDTVKKA--GKGKHILNLgHGIKV------------------ 324 :::: :::: :::: :::::::: ::::::::: ::::: d1jz7a5 204 EYAH--AMGN--SLGG-FAKYWQAFrqYPRLQGGFV-WDWVDqslikydengnpwsaygg 257 d1j93a_ 325 --------------------gtPEENFAHFFEIAKglry 343 ::::::::::::: d1jz7a5 258 dfgdtpndrqfcmnglvfadrtPHPALTEAKHQQQ---- 292 FAST alignment (Normalized score: 5.00 Raw score:1584.00) d1j93a_ 1 TQPLLLDAVRGKEV------------ERPPVWL---MRQAGRYMKSYQLLCE---KYPLF 42 ::::: :::: ::::: d1jz7a5 1 --------------EVRIENGLLLLNGKPLL--IRGVNRH------------EHHPLHGQ 32 d1j93a_ 43 RDRS-ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRT 101 ::::::::::::::: :::::::: d1jz7a5 33 ----VMDEQTMVQDILLMKQ-NNFNAVRC------------------------------- 56 d1j93a_ 102 AADVEKVREFIPEKSVPY-----VGEALTILRKEVNN-QAAVLGFVGAPFTLASYVVEGG 155 :::::::::: :::::::: d1jz7a5 57 ------------------SHYPNHPLWYTLCDR----YGLYVVDEA-------------- 80 d1j93a_ 156 SSKNFTKI----------KRLAFAE-PKVLHALLQKFATSMAKYIRYQADS-GAQAVQIF 203 :::: ::::::::::::::::: ::::: :::::: d1jz7a5 81 --------NIETHGMVPMNRLT---DDPRWLPAMSERVTRMVQ---RDRNHPSVIIWS-- 124 d1j93a_ 204 DSWA--TELSPVDF-EEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLT---- 256 :::: :::::::::::::: ::::::::: d1jz7a5 125 ----LGNESG----HGANHDALYRWIKSV----DPSRPVQYE--------------GGGA 158 d1j93a_ 257 ---GVDVVSLDW--------------TVDMADGRRRLG----PNVAIQ---GNVDPGVLF 292 :::::::: :::::::: ::::: :::: d1jz7a5 159 DTTATDIICPM-YARVDEDQPFPAVPKWSIKKWL----SLPGETRPL-ILCEYAH----- 207 d1j93a_ 293 GS-----KEFITNRINDTVKKAGKGKHILNLGHGIKVGT--------------------- 326 ::::::::::::: :::::: d1jz7a5 208 --AMGNSLGGFAKYWQAFRQ---YPRLQG----------GFVWDWVDQSLIKYDENGNPW 252 d1j93a_ 327 ------------------------------PEENFAHFFEIAKGLRY- 343 ::::::::: d1jz7a5 253 SAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQQ--------Q 292 TMalign alignment (TM-score: 0.54 Raw score:185.95) d1j93a_ 1 TQPLLL-DAVRG-KEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQ 58 ::::: ::::: ::: ::::::: :::: :: :: : : :::::::::::: d1jz7a5 1 -EVRIENGLLLLNGKP-LLIRGVN-RHEH----HP---LH--G---Q-VMDEQTMVQDIL 44 d1j93a_ 59 PWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVP 118 ::::::::::::: :: : d1jz7a5 45 LMKQNNFNAVRCS-HY-P------------------------------------------ 60 d1j93a_ 119 YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALL 178 ::::::::::::: ::::::::: : : :: ::::: ::: : ::::: d1jz7a5 61 NHPLWYTLCDRYG---LYVVDEANI--E--T------HG--MVPMN-RLT--D--DPRWL 100 d1j93a_ 179 QKFATSMAKYIRYQADSG-AQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 :::::::::::::::::: ::::::::::: : : ::::::::::::::::: d1jz7a5 101 PAMSERVTRMVQRDRNHPSVIIWSLGNESG-------H---G-ANHDALYRWIKSVDPSR 149 d1j93a_ 238 PLILYASGSGGLLERLPLTGVDVVSLDWT------------V-DMADGRRRLGPNVAIQG 284 :::::: : ::: : :: ::::::::: : ::::::::::::::::: d1jz7a5 150 PVQYEG--G--GAD-T-TA-TDIICPMYARVDEDQPFPAVPKWSIKKWLSLPGETRPLIL 202 d1j93a_ 285 -NVDPGV-LFGSKEFITNRINDTVKKAGKGKHILNLGHGI-------------------- 322 :::::: :::: ::::::::::: ::::::::: ::: d1jz7a5 203 CEYAHAMGNSLG--GFAKYWQAFRQ--YPRLQGGFV-WDWVDQSLIKYDENGNPWSAYGG 257 d1j93a_ 323 ------------KVGT------PEENFAHFFEIAKGLRY 343 :::: ::::::::::::: d1jz7a5 258 DFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQQQ---- 292 HHsearch alignment (Probability: 0.14 E-value:0.12) d1j93a_ 60 WKVFRPDGVILFS-----DILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPE 114 ::::::::::::: ::::::::::::::: ::::::::::::: ::::::: d1jz7a5 46 MKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVD---EANIETHGMVPMN----RLTDDPR 98 d1j93a_ 115 KSVPYVGEALTILRKEVNNQAAVLGFV 141 :::::::::::::::::::::::::: d1jz7a5 99 -WLPAMSERVTRMVQRDRNHPSVIIWS 124