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 <-- 0.642 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1ct5a_) 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 d1ct5a_ ​(​Hypothetical​(​ protein ybl036cPLP-​binding barrelTIM 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 <-- 0.642 --> Hit
DALI alignment (Z-score: 7.1 Raw score:842.20) d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 d1ct5a_ 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefIPEKsVPYV 120 :::: :::: d1ct5a_ 1 -------------------------------------------tgitydedRKTQ-LIAQ 16 d1j93a_ 121 GEALTILRKEVN--nQAAVLGFVGApftlasyvveggssknftkikrlafaepkvlhall 178 :::::::::::: :::::::::: d1ct5a_ 17 YESVREVVNAEAknvKILLLVVSKL----------------------------------- 41 d1j93a_ 179 qkfatSMAKYIRYQADSGAQAVQIFDswatelspvdfeefsLPYLKQIVDSVkltHPNLP 238 ::::::::::::::::::::: ::::::::::: ::::: d1ct5a_ 42 -----KPASDIQILYDHGVREFGENY---------------VQELIEKAKLL---PDDIK 78 d1j93a_ 239 LILYASGSGGLLERLPLTG-VDVVSLDWtvdMADGRRRLGP----------NVAIQGNVD 287 ::::::::::::::::::: :::::::: :::::::::: ::::::::: d1ct5a_ 79 WHFIGGLQTNKCKDLAKVPnLYSVETID---SLKKAKKLNEsrakfqpdcnPILCNVQIN 135 d1j93a_ 288 PGV-lfgskefITNRINDTVKKAGK-----gKHILNLgHGIKVGTPEENFAHFFEIAKGL 341 ::: :::::::::::::: :::::: :::::::::::::::::::::: d1ct5a_ 136 TSHedqksglnNEAEIFEVIDFFLSeeckyiKLNGLM-TIGSWNRDFATLVEWKKKIDAK 194 d1j93a_ 342 RY-------------------------------- 343 :: d1ct5a_ 195 FGtslklsmgmsadfreairqgtaevrigtdifg 228 FAST alignment (Normalized score: 4.50 Raw score:1258.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1ct5a_ 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF--------- 111 d1ct5a_ 1 ---------------------------------------------------TGITYDEDR 9 d1j93a_ 112 --IPEKSVPYVGEALTILRKEVNN--QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLA 167 :::::::::::::::::: ::::::: d1ct5a_ 10 KTQLIAQYESVREVVNAEAK----NVKILLLVV--------------------------- 38 d1j93a_ 168 FAEPKVLHALLQKFATS----MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF-SLPY 222 :::::::::::::::::: :::: d1ct5a_ 39 -----------------SKLKPASDIQILYDHGVREFGE----------------NYVQE 65 d1j93a_ 223 LKQIVDSVKLTHPNLPLILYASG---SGGLLERLPLT-GVDVVSLDWTV-------DMAD 271 ::::::: :::::::::: ::::::::::: ::::: :::: d1ct5a_ 66 LIEKAKL---LPDDIKWHFI---GGLQTNKCKDLAKVPNLYSV------ETIDSLKKAKK 113 d1j93a_ 272 GRRRLGP---------NVAIQGNVDPGVLF---------GSKEFITNRINDTVKKAG--- 310 :::: :::::::::: ::::::::::::: d1ct5a_ 114 LNES---RAKFQPDCNPILCNVQINT----SHEDQKSGLNNEAEIFEVIDFF-----LSE 161 d1j93a_ 311 -KGKHI-LNLGHGIKVGT----PEENFAHFFEIAKGLRY--------------------- 343 ::::: ::::::: ::::::::::::: d1ct5a_ 162 ECKYIKLNGLMTIG----SWNRDFATLVEWKKKID----AKFGTSLKLSMGMSADFREAI 213 d1j93a_ 344 --------------- 344 d1ct5a_ 214 RQGTAEVRIGTDIFG 228 TMalign alignment (TM-score: 0.41 Raw score:141.41) d1j93a_ 1 --------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRD-RSENVDL 51 :: ::::: d1ct5a_ 1 TGITYDED------------------------------------------RKT--QLIAQ 16 d1j93a_ 52 VVEISLQPWKVFR-PDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVRE 110 ::::::::::::: :::::::::::::: : d1ct5a_ 17 YESVREVVNAEAKNVKILLLVVSKLKPA-S------------------------------ 45 d1j93a_ 111 FIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAE 170 :::::::::: :::::::::: d1ct5a_ 46 -----DIQILYDHGV------------REFGENYVQE----------------------- 65 d1j93a_ 171 PKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSV 230 :::::::::::: ::::::::: : : ::::::::: : d1ct5a_ 66 ----------LIEKAKLLPDDI-------KWHFIGGLQ---T--N---KCKDLAKVP--N 98 d1j93a_ 231 KLTHPNLPLILYASGSGGLLERLPLTG--------VDVVSLDW----------TV-D--M 269 :::::::::::::::::::: :::::::: :: : : d1ct5a_ 99 -------LYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQINTSHEDQKSGLNNEAEI 151 d1j93a_ 270 ADGRRRLGP---N-VAIQGNVD-PG-VLFGSKEFITNRINDTVKKAGKGKHILNLGHGIK 323 ::::::::: : :::::::: :: ::::: ::::::::::::::: ::::: :::: d1ct5a_ 152 FEVIDFFLSEECKYIKLNGLMTIGSW-NRDFA-TLVEWKKKIDAKFGT--SLKLS-MGMS 206 d1j93a_ 324 VGTPEENFAHFFEIA----------KGLRY 343 ::::: ::: ::: : d1ct5a_ 207 ADFRE-AIR-QGT-AEVRIGTDIFG----- 228 HHsearch alignment (Probability: 0.05 E-value:0.49) d1j93a_ 216 EEFSLPYLKQIVDSVKLTHPNLPLILYASGSG-GLLERLP 254 :::::::::::::::::::::::: ::::::: ::::::: d1ct5a_ 56 REFGENYVQELIEKAKLLPDDIKW-HFIGGLQTNKCKDLA 94