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 <-- 1.022 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1jpma1) 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 d1jpma1 L-​Ala-​D/​L-​Glu epimeraseEnolase C-​terminal domain-​likeTIM 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 <-- 1.022 --> Hit
DALI alignment (Z-score: 10.4 Raw score:1158.50) d1j93a_ 1 tqpllldavrgkeVERPPVWlMRQAgrymksyqllcekyplfrdrSENVDLVVEISLQPW 60 ::::::: :::: ::::::::::::::: d1jpma1 1 ------------yRDTLETD-YTVS--------------------VNSPEEMAADAENYL 27 d1j93a_ 61 KVFRPdGVILFSdILTPlsgmnipfdiikgkgpvifdplrtaadvekvrefipeksVPYV 120 ::::: :::::: :::: :::: d1jpma1 28 KQGFQ-TLKIKV-GKDD---------------------------------------IATD 46 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGApftlasyvveggssknftkikrlafaepkvlhallqk 180 ::::::::::::::::::::::: d1jpma1 47 IARIQEIRKRVGSAVKLRLDANQ-----------------------------------gw 71 d1j93a_ 181 FATSMAKYIRYQA--DSGAQAVQI-FDSWatelspvdfeefSLPYLKQIVDSVklthpNL 237 ::::::::::::: ::::::::: :::: :::::::::::: :: d1jpma1 72 RPKEAVTAIRKMEdaGLGIELVEQpVHKD------------DLAGLKKVTDAT-----DT 114 d1j93a_ 238 PLILYA-sGSGGLLERLP-LTGVDVVSLDWTV-----DMADGRRRLGP-NVAIQGNVDPG 289 :::::: :::::::::: ::::::::::::: ::::::::::: ::::::::::: d1jpma1 115 PIMADEsvFTPRQAFEVLqTRSADLINIKLMKaggisGAEKINAMAEAcGVECMVGSMIE 174 d1j93a_ 290 VLfgskeFITNRINDTVKKaGKGKHILNLghgIKVGTP-eenfaHFFEiAKGL------- 341 :: :::::::::::: ::::::::: :::::: :::: :::: d1jpma1 175 TK-----LGITAAAHFAAS-KRNITRFDFdapLMLKTDvfnggiTYSGsTISMpgkpglg 228 d1j93a_ 342 ----ry 343 d1jpma1 229 iigaal 234 FAST alignment (Normalized score: 6.85 Raw score:1940.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRD--RSENVDLVVEISLQ 58 ::::::::: :::::::::::::: d1jpma1 1 ------------YRDTLETDY-----------------------TVSVNSPEEMAADAEN 25 d1j93a_ 59 PWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEK--- 115 ::: ::::::::: d1jpma1 26 YLK-QGFQTLKIK--------------------------------------------VGK 40 d1j93a_ 116 -SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVL 174 :::::::::::::::::::::::::: d1jpma1 41 DDIATDIARIQEIRKRVGSAVKLRLDA--------------------------------- 67 d1j93a_ 175 HALLQK----FATSMAKYIRYQAD--SGAQAVQ--IFDSWATELSPVDFEEF-SLPYLKQ 225 :::::::::::::: :::::: :::: ::::::: d1jpma1 68 ------NQGWRPKEAVTAIRKMEDAGLGIELV-EQPVHK-------------DDLAGLKK 107 d1j93a_ 226 IVDSVKLTHPNLPLILYASG-----SGGLLERLPLT-GVDVVSLDWTV------DMADGR 273 :::: ::::::: ::::::::::: :::::::::: :::::: d1jpma1 108 VTDA-----TDTPIMA----DESVFTPRQAFEVLQTRSADLINIKLM-KAGGISGAEKIN 157 d1j93a_ 274 RRLG---PNVAIQGNVDPGVL-----FGSKEFITNRINDTVKKAGKGKHILNLGHGIKVG 325 :: ::::: :::::::::::::::: d1jpma1 158 AM--AEACGVEC---------MVGSMIETKLGITAAAHFAAS------------------ 188 d1j93a_ 326 TPEENFAHFFEIAKGLRY------------------------------------------ 343 d1jpma1 189 ------------------KRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGII 230 d1j93a_ 344 ---- 344 d1jpma1 231 GAAL 234 TMalign alignment (TM-score: 0.44 Raw score:151.40) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :: d1jpma1 1 --------------YR-------------------------------------------- 2 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 ::::::::::: :: : ::: d1jpma1 3 --DTLETDYTVSV--NS-----------------------------------P----EEM 19 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 :::::::::::: :::::::: :: d1jpma1 20 AADAENYLKQGF---QTLKIKVG--KD--------------------------------- 41 d1j93a_ 181 FATSMAKYIRYQADSG---AQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 :::::::::::::::: ::::::::::: ::::::::::::::::::: d1jpma1 42 DIATDIARIQEIRKRVGSAVKLRLDANQGW-----------RPKEAVTAIRKMEDAGLGI 90 d1j93a_ 238 PLILYASGSGGL--LERLPLTG-VDVVSLD--WT-VDMADGRRRLGPNVAIQGNVDPGVL 291 :::::::::::: :::::::: ::::::: :: ::::::::::: :::::::::::: d1jpma1 91 ELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRS--ADLINIKLMKAG 148 d1j93a_ 292 FGSKEFITNRINDTVKKAGK-GKHILNLGHGIKVGTPEENFAHFFEIAKGLRY------- 343 : : :::::::::::: ::::::: :::: : :::::::::::::::: d1jpma1 149 -G----I-SGAEKINAMAEACGVECMVG--SMIE-T-KLGITAAAHFAASKRNITRFDFD 198 d1j93a_ 344 ------------------------------------ 344 d1jpma1 199 APLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAAL 234 HHsearch alignment (Probability: 0.21 E-value:0.05) d1j93a_ 119 YVGEALTILRKEVNNQAAVLGFVGAPFTLASY 150 :::::::::::::::::::::::::::::::: d1jpma1 45 TDIARIQEIRKRVGSAVKLRLDANQGWRPKEA 76