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 <-- 0.989 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1lwha2) 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 d1lwha2 4-​alpha-​glucanotransferase(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 <-- 0.989 --> Hit
DALI alignment (Z-score: 9.6 Raw score:1211.80) d1j93a_ 1 tqpllldavrgkeverpPVWLMRqagrymksyqlLCEKyplfrDRSEnvDLVVEIsLQPW 60 :::::: :::: :::: :::::: :::: d1lwha2 1 -----------------MIGYQI---yvrsfrdgNLDG-----VGDF--RGLKNA-VSYL 32 d1j93a_ 61 KVFrPDGVIlfsDILTplsgmniPFDIikgkgpvifdplrtaadvekvrEFIP----eks 116 ::: ::::: :::: :::: :::: d1lwha2 33 KEL-GIDFV-wlMPVF------sSISF----------------hgydvvDFYSfkaeygs 68 d1j93a_ 117 VPYVGEALTILRKEVnnqaAVLGFVGapfTLASYV------------------------- 151 ::::::::::::::: ::::::: :::::: d1lwha2 69 EREFKEMIEAFHDSG----IKVVLDL---PIHHTGflhtwfqkalkgdphyrdyyvwank 121 d1j93a_ 152 ----------------------veggSSKN--FTKIkrlafaepkVLHALLQKFATSMAK 187 :::: :::: ::::::::::::::: d1lwha2 122 etdlderrewdgekiwhpledgrfyrGLFGpfSPDL-------nyDNPQVFDEMKRLVLH 174 d1j93a_ 188 YIRYQAdsgaqAVQIFDSwATEL--SPVDFEEFSLPYLkqivDSVKlthpnlPLILYAsG 245 :::::: ::::::: :::: ::::::::::::: :::: :::::: : d1lwha2 175 LLDMGV-----DGFRFDA-AKHMrdTIEQNVRFWKYFL----SDLK------GIFLAE-I 217 d1j93a_ 246 SGG--LLERLPLTgVDVVSLdwTVDM-------------------aDGRRrlGPNVAIQG 284 ::: :::::::: :::::: :::: :::: :::::::: d1lwha2 218 WAEarMVDEHGRI-FGYMLN--FDTShcikeavwkentrvliesieRAVI--AKDYLPVN 272 d1j93a_ 285 NVD----pGVLF----GSKEFITNRINDTVKKAgkgkHILNLgHGIK------------- 323 ::: :::: ::::::::::::::::: ::::: :::: d1lwha2 273 FTSnhdmsRLASfeggFSKEKIKLSISILFTLP----GVPLV-FYGDelgmkgvyqkpnt 327 d1j93a_ 324 ------------------------------vGTPE--------ENFAHFFEIAKGL---- 341 :::: ::::::::::::: d1lwha2 328 evvldpfpwnesmcvegqtfwkwpayngpfsGISVeyqkrdpdSILSHTLGWTRFRkenq 387 d1j93a_ 342 --ry 343 d1lwha2 388 widr 391 FAST alignment (Normalized score: 5.15 Raw score:1888.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSE------------N 48 :::: :::: : d1lwha2 1 -----------------MIGY-QIYV---------------------RSFRDGNLDGVGD 21 d1j93a_ 49 VDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKV 108 ::::::::::: :::::::::: d1lwha2 22 FRGLKNAVSYL-KELGIDFVWL-------------------------------------- 42 d1j93a_ 109 REFIPEKS--------------------------VPYVGEALTILRKEVNN-QAAVLGFV 141 ::::::::::::: :::::::: d1lwha2 43 --------MPVFSSISFHGYDVVDFYSFKAEYGSEREFKEMIEAFHD----SGIKVVLDL 90 d1j93a_ 142 GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL------------------------ 177 : d1lwha2 91 P-----------------------------------IHHTGFLHTWFQKALKGDPHYRDY 115 d1j93a_ 178 ---------------------------------------------LQKFATSMAKYIRYQ 192 ::::::::::::::: d1lwha2 116 YVWANKETDLDERREWDGEKIWHPLEDGRFYRGLFGPFSPDLNYDNPQVFDEMKRLVLHL 175 d1j93a_ 193 ADSGAQAVQIFDSWATELSPVDF-----EEFSLPYLKQIVDSVKLTHPNLPLILYASGSG 247 :::::::::: :::: :::::::::::::: ::::::::: d1lwha2 176 LDMGVDGFRF--DAAK-------HMRDTIEQNVRFWKYFLSD-----LKGIFLAEI---- 217 d1j93a_ 248 G--LLERLPLT---GVDVVSLDWTV-----------------DMADGRRRLG--PNVAIQ 283 ::::::: ::::::: :::::::::: ::::: d1lwha2 218 -WAEARMVDE-HGRIFGYMLN----FDTSHCIKEAVWKENTRVLIESIERAVIAKDYLP- 270 d1j93a_ 284 GNVDPGVL-----------------FGSKEFITNRINDTVKKAGKGK--HILNLGHGIKV 324 :::::::::::::::: :::: d1lwha2 271 --------VNFTSNHDMSRLASFEGGFSKEKIKLSISILFT------LPGVPL------- 309 d1j93a_ 325 GT---------------------------------------------------------- 326 d1lwha2 310 --VFYGDELGMKGVYQKPNTEVVLDPFPWNESMCVEGQTFWKWPAYNGPFSGISVEYQKR 367 d1j93a_ 327 ----PEENFAHFFEIAKGLRY------- 343 ::::::::::::: d1lwha2 368 DPDSILSHTLGWTRFRK----ENQWIDR 391 TMalign alignment (TM-score: 0.51 Raw score:173.39) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLC-EKYPLFRDRSENVDLVVEISLQP 59 :::: ::::: :: :: :::: :: :::::::: :::: d1lwha2 1 -----------------MIGY-QIYVR---SF--RDG-NLDG--VG-DFRGLKNA-VSYL 32 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIP---EKS 116 ::: :::::: ::::: : :::: :::: :: :::::: :: d1lwha2 33 KEL-GIDFVW-LMPVF--S------SISF---HGYD--VV--------DFYSFKAEY-GS 68 d1j93a_ 117 VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 :::::::::::::: : ::::::::::: :::::: ::::::::::::::: d1lwha2 69 EREFKEMIEAFHDS-G---IKVVLDLPIHH-TGFLHT--------WFQKALKGDPHYRDY 115 d1j93a_ 177 L--------------------------------LQKFATSMAKYIRYQADSGAQAVQIFD 204 : d1lwha2 116 YVWANKETDLDERREWDGEKIWHPLEDGRFYRG--------------------------- 148 d1j93a_ 205 SWA--TELSPVDFEE-FSLPYLKQIVDSVKLTHPNLPLILYASGSG----G--LLERLPL 255 ::: :::: :::: :::::::::::::: :: :::::::::::: : ::::::: d1lwha2 149 LFGPFSPDL--NYDNPQVFDEMKRLVLHLL-DM-GVDGFRFDAAKHMRDTIEQNVRFWKY 204 d1j93a_ 256 TG--VD-VVSLDWTVDMADGRRRLGPNVAIQGNVD--PGVLFGSK----E-FITNRINDT 305 :: :: ::::::::::::::: ::: :::::::: :::::::: : ::::::::: d1lwha2 205 FLSDLKGIFLAEIWAEARMVDE-HGR-IFGYMLNFDTSHCIKEAVWKENTRVLIESIERA 262 d1j93a_ 306 VKKAGKGKHILNLGHGI-KVGTP----------EE-NFAHFFEIA--------------- 338 ::::: :::::::::: ::::: :: ::::::::: d1lwha2 263 VIAKD--YLPVNFTSNHDMSRLASFEGGFSKEKIKLSISILFTLPGVPLVFYGDELGMKG 320 d1j93a_ 339 ------------------------------------------------------------ 339 d1lwha2 321 VYQKPNTEVVLDPFPWNESMCVEGQTFWKWPAYNGPFSGISVEYQKRDPDSILSHTLGWT 380 d1j93a_ 339 --K--G--LRY 343 : : ::: d1lwha2 381 RFRKENQWIDR 391 HHsearch alignment (Probability: 0.17 E-value:0.01) d1j93a_ 31 SYQLLCEKYPLFRDR 45 ::::::::::::::: d1lwha2 58 DFYSFKAEYGSEREF 72