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 <-- 1.219 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1uoka2) 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 d1uoka2 Oligo-​1,​6,​ glucosidase(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 <-- 1.219 --> Hit
DALI alignment (Z-score: 11.1 Raw score:1427.60) d1j93a_ 1 tqplllDAVRgkeverPPVWLMRQAGRYMkSYQLLCekyplfrdrsenvdlVVEISLQPW 60 :::: ::::::::::::: :::::: ::::::::: d1uoka2 1 ---mekQWWK------ESVVYQIYPRSFM-DSNGDG-------------igDLRGIISKL 37 d1j93a_ 61 KVFR---PDGVILFS---------DILTPLsgmnipfdiikgkgpvifdplrtaadvekv 108 :::: :::::::: :::::: d1uoka2 38 DYLKelgIDVIWLSPvyespnddnGYDISD------------------------------ 67 d1j93a_ 109 refipekSVPY-----vgEALTILRKEVN-NQAAVLGFVGaPFTL--------------- 147 :::: ::::::::::: :::::::::: :::: d1uoka2 68 -------YCKImnefgtmEDWDELLHEMHeRNMKLMMDLV-VNHTsdehnwfiesrkskd 119 d1j93a_ 148 ----------------------------------asyvvEGGSSKnftkikrlafaepkv 173 :::::: d1uoka2 120 nkyrdyyiwrpgkegkepnnwgaafsgsawqydemtdeyYLHLFS---------kkqpdl 170 d1j93a_ 174 LHALlQKFATSMAKYIRYQADSGAQAVQIF-DSWA------------------tELSPvd 214 :::: ::::::::::::::::::::::::: :::: :::: d1uoka2 171 NWDN-EKVRQDVYEMMKFWLEKGIDGFRMDvINFIskeeglptveteeegyvsgHKHF-m 228 d1j93a_ 215 FEEFSLPYLKQIVDSVKLTHpNLPLILYASGSG-GLLERLP---LTGVDVVSLDWTV--- 267 :::::::::::::::::::: :::::::::::: ::::::: ::::::::::::: d1uoka2 229 NGPNIHKYLHEMNEEVLSHY-DIMTVGEMPGVTtEEAKLYTgeeRKELQMVFQFEHMdld 287 d1j93a_ 268 -------------------DMADGRRRLGPNVAIQGNVDP----GVLFG-------SKEF 297 ::::::::::::::::::::: ::::: :::: d1uoka2 288 sgeggkwdvkpcslltlkeNLTKWQKALEHTGWNSLYWNNhdqpRVVSRfgndgmyRIES 347 d1j93a_ 298 ITNRINDTVKKAgkgkHILNLghgikvgtpeeNFAH------------------------ 333 :::::::::::: ::::: :::: d1uoka2 348 AKMLATVLHMMK----GTPYI--------yqgEEIGmtnvrfesideyrdietlnmykek 395 d1j93a_ 334 ------------------------------------------------------------ 334 d1uoka2 396 vmergediekvmqsiyikgrdnartpmqwddqnhagfttgepwitvnpnykeinvkqaiq 455 d1j93a_ 334 ----fFEIAK-GLRY--------- 343 ::::: :::: d1uoka2 456 nkdsiFYYYKkLIELrknneivvy 479 FAST alignment (Normalized score: 5.54 Raw score:2244.00) d1j93a_ 1 TQPLLLDAVRGKEVER-------PPVWLMRQAGRYMKSYQLLCE------KYPLFRDRS- 46 ::::: :::: :::: d1uoka2 1 ----------------MEKQWWKESVVY-QIYP-----------RSFMDSNGDG-----I 27 d1j93a_ 47 ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVE 106 ::::::::::::: :::::::::: d1uoka2 28 GDLRGIISKLDYL-KELGIDVIWL------------------------------------ 50 d1j93a_ 107 KVRE---------------FIPEKS--------VPYVGEALTILRKEVNN-QAAVLGFVG 142 :::: ::::::::::::: ::::::::: d1uoka2 51 ----SPVYESPNDDNGYDISDYC--KIMNEFGTMEDWDELLHEMHE----RNMKLMMDLV 100 d1j93a_ 143 APFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL------------------------- 177 d1uoka2 101 -----------------------------------VNHTSDEHNWFIESRKSKDNKYRDY 125 d1j93a_ 178 ------------------------------------------------LQKFATSMAKYI 189 :::::::::::: d1uoka2 126 YIWRPGKEGKEPNNWGAAFSGSAWQYDEMTDEYYLHLFSKKQPDLNWDNEKVRQDVYEMM 185 d1j93a_ 190 RYQADSGAQAVQIFDSWATELSPVD-------------------------FEEFSLPYLK 224 ::::::::::::: ::::: :::::::::: d1uoka2 186 KFWLEKGIDGFRM--DVINF-----ISKEEGLPTVETEEEGYVSGHKHFMNGPNIHKYLH 238 d1j93a_ 225 QIVDSVKLTHPNLPLILYASG-SGGLLERLPLT-------GVDVVSLDWTV--------- 267 ::::::::: ::::::::::: ::::::: ::::::: d1uoka2 239 EMNEEVLSH-YDIMTVGEMPGVTTEEAKL----YTGEERKELQMVFQ----FEHMDLDSG 289 d1j93a_ 268 -----------------DMADGRRRLG--PNVAIQGNVDPGVLFG--------------- 293 :::::::: ::::::::: d1uoka2 290 EGGKWDVKPCSLLTLKENLTKWQKA--LEHTGWNSLYW-------NNHDQPRVVSRFGND 340 d1j93a_ 294 ---SKEFITNRINDTVKKAGKGK--HILNLGHGIKVGT---------------------- 326 :::::::::::::: :::: d1uoka2 341 GMYRIESAKMLATVLHM------MKGTPY---------IYQGEEIGMTNVRFESIDEYRD 385 d1j93a_ 327 ------------------------------------------------------------ 327 d1uoka2 386 IETLNMYKEKVMERGEDIEKVMQSIYIKGRDNARTPMQWDDQNHAGFTTGEPWITVNPNY 445 d1j93a_ 327 --------------PEENFAHFFEIAKGLRY---- 343 :::::::::::::::: d1uoka2 446 KEINVKQAIQNKDSIFYYYKKLIELRKNNE-IVVY 479 TMalign alignment (TM-score: 0.53 Raw score:183.28) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::::::::::::::::: :: ::::::: :: ::::::::::::: d1uoka2 1 ----------MEKQWWKESVVYQIYPR---SF--MDSNGDG--IG--DLRGIISKLDYLK 41 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIP-----EK 115 :: :::::: :::: : : :::: ::::: : :::::: d1uoka2 42 EL-GIDVIW-LSPV-Y--E-----SPND--DNGYD--I---------SDYCKIMNEFG-- 76 d1j93a_ 116 SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYV--VE--G----------------- 154 ::::::::::::::: :: :::::::: ::::::: :: : d1uoka2 77 TMEDWDELLHEMHER-NM--KLMMDLVV-NHTSDEHNWFIESRKSKDNKYRDYYIWRPGK 132 d1j93a_ 155 ---------GSSK-NFTKI-----KRLAF-------AEPKVLHALLQKFATSMAKYIRYQ 192 :::: ::::: ::::: :::::::::::::::::::: d1uoka2 133 EGKEPNNWGAAFSGSAWQYDEMTDEYYLHLFSKKQP----DLNWDNEKVRQDVYEMMKFW 188 d1j93a_ 193 ADSGAQAVQIFDSWATELSPV-D----------------F--EEFSLPYLKQIVDSVKLT 233 ::::::::::::: ::::::: : : :::::::::::::::: d1uoka2 189 LEKGIDGFRMDVI-NFISKEEGLPTVETEEEGYVSGHKHFMNGPNIHKYLHEMNEEVL-- 245 d1j93a_ 234 HPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGP-NV---AIQGN-VDP 288 :::::::::::::: : : :::::::: :: ::::: ::: d1uoka2 246 SHYDIMTVGEMPGV-------------------T-T-EEAKLYTGEERKELQMVFQFEHM 284 d1j93a_ 289 GVL----------FGSKEFITNRINDTVKKAGKGKHILNLGHGI-KVGTP---------- 327 ::: ::::::::::::::::::::::::::::::: ::::: d1uoka2 285 DLDSGEGGKWDVKPCSLLTLKENLTKWQKALEHTGWNSLYWNNHDQPRVVSRFGNDGMYR 344 d1j93a_ 328 ---EENFAHFFEIA---------------------------------------------- 338 ::::::::::: d1uoka2 345 IESAKMLATVLHMMKGTPYIYQGEEIGMTNVRFESIDEYRDIETLNMYKEKVMERGEDIE 404 d1j93a_ 339 ------------------------------------------------------------ 339 d1uoka2 405 KVMQSIYIKGRDNARTPMQWDDQNHAGFTTGEPWITVNPNYKEINVKQAIQNKDSIFYYY 464 d1j93a_ 339 ------K----GLRY 343 : :::: d1uoka2 465 KKLIELRKNNEIVVY 479 HHsearch alignment (Probability: 0.10 E-value:0.02) d1j93a_ 234 HPNLPLILY 242 ::::::::: d1uoka2 358 MKGTPYIYQ 366