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 <-- 1.210 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1jnda1) 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 d1jnda1 Imaginal disc growth factor-​2(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 <-- 1.210 --> Hit
DALI alignment (Z-score: 12.0 Raw score:1396.80) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQAGRymksYQLLcekyplfrdrsenvdlvveisLQPW 60 ::::::::::: :::: :::: d1jnda1 1 ----------------SNLVCYYDSSS---yTREG----------------lgkllNPDL 25 d1j93a_ 61 KVFR--PDGVILFSDILtpLSGMnipfdiikgkgpvifdplrtaadvekvrefipeksVP 118 :::: ::::::::::: :::: :: d1jnda1 26 EIALqfCSHLVYGYAGL--RGEN----------------------------lqaysmnEN 55 d1j93a_ 119 YVG--EALTILRKEVN--NQAAVLGFVGapftlasyvvEGGSSknftkikrlafaepkvL 174 ::: ::::::::::: :::::::::: ::::: : d1jnda1 56 LDIykHQFSEVTSLKRkyPHLKVLLSVG----gdhdidPDHPN----------kyidllE 101 d1j93a_ 175 HALlQKFATSMAKYIRYQADSGAQAVQIFDSWATE--------lSPVDFEEFSLPYLKQI 226 ::: ::::::::::::::::::::::::::::::: :::::::::::::::: d1jnda1 102 GEK-VRQIGFIRSAYELVKTYGFDGLDLAYQFPKNkprkvivdpHAALHKEQFTALVRDV 160 d1j93a_ 227 VDSVKLthPNLPLILYAS--GSGGLlERLPLT--GVDVVSLDWT---------------- 266 :::::: :::::::::: ::::: :::::: :::::::::: d1jnda1 161 KDSLRA--DGFLLSLTVLpnVNSTWyFDIPALngLVDFVNLATFdfltparnpeeadysa 218 d1j93a_ 267 --------------vDMADGRRRL---GPNV-AIQGNVDPgvlfgskeFITNRINDTVKK 308 ::::::::: :::: :::::::: :::::::::::: d1jnda1 219 piyhpdgskdrlahlNADFQVEYWlsqGFPSnKINLGVAT--------DDPDSASNKAAY 270 d1j93a_ 309 AGK-GKHILNLgHGIKVgTPEE----NFAHFFEIAKGLRy 343 ::: ::::::: ::::: :::: ::::::::::::: d1jnda1 271 ARVkNLGGVAL-FDLSYdDFRGqcsgDKYPILRAIKYRL- 308 FAST alignment (Normalized score: 5.68 Raw score:1847.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL--------- 51 ::::: ::::: d1jnda1 1 ----------------SNLVC-YYDSS------------------------SYTREGLGK 19 d1j93a_ 52 -VVEISLQPWKVF-RPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVR 109 ::::::::: :::::::: d1jnda1 20 LLNPDLEIAL---QFCSHLVYG-------------------------------------- 38 d1j93a_ 110 EFIPEKS---------------VPYVG--EALTILRKEV----NNQAAVLGFVGAPFTLA 148 ::::: :::::::: ::::::::: d1jnda1 39 -------YAGLRGENLQAYSMNENLDIYKHQFSEVTS--LKRKYPHLKVLLS-------- 81 d1j93a_ 149 SYVVEGGSSKNFTKIKRLAFAEPKV---------------------LHALLQKFATSMAK 187 :::::::::::::: d1jnda1 82 -------------------------VGGDHDIDPDHPNKYIDLLEGEKVRQIGFIRSAYE 116 d1j93a_ 188 YIRYQADSGAQAVQIFDSWATEL-----------SPVDFEEFSLPYLKQIVDSVKLTH-- 234 ::: ::::::::::: :::::: :::::::::::::::: d1jnda1 117 LVK---TYGFDGLDLAY------QFPKNKPRKVIVDPHAA-LHKEQFTALVRDVKDS-LR 165 d1j93a_ 235 -PNLPLILYASGSGG-----------LLERLPLTGVDVVSLDWT---------------- 266 :::::::: ::::::: ::::::: d1jnda1 166 ADGFLLSLT------VLPNVNSTWYFDIPALNG-LVDFVNL---ATFDFLTPARNPEEAD 215 d1j93a_ 267 -----------------VDMADGRRR-----LGPNVAIQ---GNVDPGVLFGSKEFITNR 301 ::::::::: :::: :::: :::::::::: d1jnda1 216 YSAPIYHPDGSKDRLAHLNADFQVEYWLSQGFPSN----KINLGVA----TDDPDSASNK 267 d1j93a_ 302 INDTVKKAGKGKHILNLGHGI------KVGTP----------EENFAHFFEIAKGLRY-- 343 :::::: :::: :::: ::::::::: d1jnda1 268 AAYARV--KNLG---------GVALFDLSYD-DFRGQCSGDKYPILRAIKY-------RL 308 TMalign alignment (TM-score: 0.56 Raw score:190.71) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::::::::::: ::::::: : ::::::: d1jnda1 1 ----------------SNLVCYYDSSS---YTREGLG-------------K--LLNPDLE 26 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF---IP--EK 115 ::::::::::::::: : : :: : :::: : d1jnda1 27 IALQFCSHLVYGYAG--L----R--------------GE-----N--LQAYSMN-ENL-- 56 d1j93a_ 116 SVP-YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVL 174 ::: ::::::::::: ::: ::::::::: :: :: :::::: ::::::: ::: d1jnda1 57 DIYKHQFSEVTSLKR-KYP-HLKVLLSVG--GD-HD----IDPDHP-NKYIDLL--EGE- 103 d1j93a_ 175 HALLQKFATSMAKYIRYQADSGAQAVQIFDSWATE--------L-SPVDFEEFSLPYLKQ 225 :::::::::::::::::: : :::::::: :::: : ::::::::::::::: d1jnda1 104 KVRQIGFIRSAYELVKTY--G-FDGLDLAY-QFPKNKPRKVIVDPHAALHKEQFTALVRD 159 d1j93a_ 226 IVDSVKLTHPNLPLILYAS--GSGGLLERLPLT--GVDVVSLDW---------------- 265 :::::: ::: :::::::: :::::::::::: ::::::::: d1jnda1 160 VKDSLR-ADG-FLLSLTVLPNVNSTWYFDIPALNGLVDFVNLATFDFLTPARNPEEADYS 217 d1j93a_ 266 ----------------TVD--MADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVK 307 ::: :::::::::::::::::: :::: ::::::::::::: d1jnda1 218 APIYHPDGSKDRLAHLNADFQVEYWLSQGFPSNKINLGV-ATDD---PDSASNKAAYARV 273 d1j93a_ 308 KAGKGKHILNLGHGIKVGT---PEE-NFAHFFEIAKGLRY 343 : : :::::: ::::::: ::: ::::::::::::: d1jnda1 274 K-N--LGGVAL-FDLSYDDFRGQCSGDKYPILRAIKYRL- 308 HHsearch alignment (Probability: 0.23 E-value:0.01) d1j93a_ 119 YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALL 178 :::::::::::::::::::::: :: ::::: :::::::::: :::::::::::: d1jnda1 61 HQFSEVTSLKRKYPHLKVLLSV-GG-DHDID---PDHPNKYIDL----LEGEKVRQIGFI 111 d1j93a_ 179 QKFATSMAKYIRYQADSGAQAVQIFDSWA---------TELSPVDFEEFSLPYLKQIVDS 229 ::::: :: ::::::::::::::: :::::::: ::::::::::::: d1jnda1 112 RSAYE----LV---KTYGFDGLDLAYQFPKNKPRKVIVDPHAALHK-EQFTALVRDVKDS 163 d1j93a_ 230 VKLTHPNLPLILYAS----------GSGGLLERLPLTGVDVVSL-------DW------- 265 ::::::::::::::: ::::::::::::::::::: :: d1jnda1 164 LRADGFLLSLTVLPNVNSTWYFDIPALNGLVDFVNLATFDFLTPARNPEEADYSAPIYHP 223 d1j93a_ 266 --------TVDMADGRRRLGPNVAIQGNVDPG-----VLFGSKEFITNRINDTVKKAGKG 312 ::::::::::: :::::::: ::::::::::::::::::::::: d1jnda1 224 DGSKDRLAHLNADFQVEYW-----LSQGFPSNKINLGVATDDPDSASNKAAYARVKNLGG 278 d1j93a_ 313 KHILNLGHGI 322 :::::::::: d1jnda1 279 VALFDLSYDD 288