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 <-- 1.231 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1geqa_) 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 d1geqa_ Trp synthase alpha-​subunitRibulose-​phoshate 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 <-- 1.231 --> Hit
DALI alignment (Z-score: 10.7 Raw score:1195.20) d1j93a_ 1 tqplLLDAvrgkeverPPVWLMRqagrymksyqllcekyplfrdRSENVDLVVEISLQPW 60 :::: ::::::: :::::::::::::::: d1geqa_ 1 ----MFKD--------GSLIPYL-------------------taGDPDKQSTLNFLLALD 29 d1j93a_ 61 kvFRPDGVILFSDILtplsgmnipfdiikgkgpvifdplrtaadvekvrefipekSVPYV 120 ::::::::::::: ::::: d1geqa_ 30 --EYAGAIELGIPFS-------------------dpiadgktiqeshyralkngfKLREA 68 d1j93a_ 121 GEALTILRKEVNnqAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhallqk 180 :::::::::::: :::::::::: d1geqa_ 69 FWIVKEFRRHSS--TPIVLMTYYN----------------------------------pi 92 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDswatelspvdfeefSLPYLKQIVDSVKLTHpnLPLI 240 :::::::::::::::::::::::: :::::::::::::::: :::: d1geqa_ 93 YRAGVRNFLAEAKASGVDGILVVD-------------lPVFHAKEFTEIAREEG--IKTV 137 d1j93a_ 241 LYASGSGG--LLERLPlTGVD-VVSLDWT--------VDMADGRRRLgpNVAIQGNVDPG 289 :::::::: :::::: :::: ::::::: :::::::::: ::::::::::: d1geqa_ 138 FLAAPNTPdeRLKVID-DMTTgFVYLVSLyeipktayDLLRRAKRIC--RNKVAVGFGVS 194 d1j93a_ 290 vlfgskefITNRINDTVKKAgkgkHILNlghGIKV------------gtpEENFAHFFEI 337 :::::::::::: :::: :::: :::::::::: d1geqa_ 195 --------KREHVVSLLKEG---aNGVV--vGSALvkiigekgreateflKKKVEELLGI 241 d1j93a_ 338 akglry 343 d1geqa_ 242 ------ 242 FAST alignment (Normalized score: 5.56 Raw score:1597.00) d1j93a_ 1 TQPLLLDAVRGKEVER----PPVWLMRQAGRYMKSYQLLCEKYPLFRDR-----SENVDL 51 ::::: :::::: d1geqa_ 1 ----------------MFKDGSLIP------------------------YLTAGDPDKQS 20 d1j93a_ 52 VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF 111 :::::::::: :::::::::: d1geqa_ 21 TLNFLLALDE--YAGAIELGIP-------------------------------------- 40 d1j93a_ 112 IPEKS------------------------VPYVGEALTILRKEVNN-QAAVLGFVGAPFT 146 :::::::::::::: ::::::::: d1geqa_ 41 -----FSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRH---SSTPIVLMTY---- 88 d1j93a_ 147 LASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFAT-------SMAKYIRYQADSGAQA 199 :::::::::::::::: d1geqa_ 89 -------------------------------------YNPIYRAGVRNFLAEAKASGVDG 111 d1j93a_ 200 VQIFDSWATELSPVDFEEF---SLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLT 256 ::: :::::::::::::: :::::: d1geqa_ 112 ILV----------------VDLPVFHAKEFTEIARE--EGIKTV---------------- 137 d1j93a_ 257 GVDVVSLDWTVDMADGRRRLGPN------VAIQGNVDPGVLFGS----KEFITNRINDTV 306 ::::::: ::::::: ::::::: :::::::::::: d1geqa_ 138 ----FLAAPNT-PDERLKV----IDDMTTGFVYLVS--------LYEIPKTAYDLLRRAK 180 d1j93a_ 307 KKAGKG---KHILNLGHGIKVGTPEEN-----FAHFFEIAKGLRY--------------- 343 :: :::: :::::::::: d1geqa_ 181 RI----CRNKVAV--------------GFGVSKREHVVSLLK---EGANGVVVGSALVKI 219 d1j93a_ 344 ---------------------- 344 d1geqa_ 220 IGEKGREATEFLKKKVEELLGI 241 TMalign alignment (TM-score: 0.48 Raw score:164.38) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 : : : :::::::::::: : :::::::::: d1geqa_ 1 -----M-F-----K-DGSLIPYLTAGD----P------------------DKQSTLNFLL 26 d1j93a_ 61 KVFR-PDGVILFSDILT------------PLSGMNIPFDIIKG-KGP---VIFDPLRTAA 103 :::: :::::::::::: :: :: d1geqa_ 27 ALDEYAGAIELGIPFSDPIADGKTIQESH------------YRA-LKNGF---------- 63 d1j93a_ 104 DVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKI 163 ::::::::::::::: :: ::::::::: :: d1geqa_ 64 ------------KLREAFWIVKEFRRH-SS-TPIVLMTYY---NP--------------- 91 d1j93a_ 164 KRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYL 223 ::::::::::::::::::::::::: : ::::: d1geqa_ 92 ----------------IYRAGVRNFLAEAKASGVDGILVVD--L-----------PVFHA 122 d1j93a_ 224 KQIVDSVKLTHPNLPLILYASGSGGLLE-RLPLT--GVD-VVSLDW------TVD--MAD 271 ::::::::::: ::::::: :::::: ::::: ::: :::::: ::: ::: d1geqa_ 123 KEFTEIAREEG--IKTVFLA--APNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRR 178 d1j93a_ 272 GRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI-KVG--T-- 326 ::: :::::::::::: : ::::::::::::: ::::: ::: ::: : d1geqa_ 179 AKR--ICRNKVAVGFGV--S------KREHVVSLLKEGA---NGVVV-GSALVKIIGEKG 224 d1j93a_ 327 -----PE-ENFAHFFEIAKGLRY 343 :: :::::: :: : d1geqa_ 225 REATEFLKKKVEEL-LG--I--- 241 HHsearch alignment (Probability: 0.81 E-value:0.00) d1j93a_ 90 GKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLAS 149 ::::::: ::::::::: ::::::::::::::::: :::::: ::: d1geqa_ 46 ADGKTIQ-----ESHYRALKN---GFKLREAFWIVKEFRRH--SSTPIV--------LMT 87 d1j93a_ 150 YVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATE 209 :: ::::::: :: :::::::::::::::::: d1geqa_ 88 YY------------------NPIYRAG-VR-------NFLAEAKASGVDGILVVD----- 116 d1j93a_ 210 LSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYA--SGSGGLLERLPLTGVDVV------ 261 ::::::::::::: ::: :::::::: :::::::::::::::::: d1geqa_ 117 LPVFHAKEFTEIA--------REE--GIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLY 166 d1j93a_ 262 --SLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLG 319 :::::::::::::::::::::::::: ::::: :::::::: :::::::: d1geqa_ 167 EIPKTAYDLLRRAKRICRNKVAVGFGVS------KREHV----VSLLKEGA-NGVVVGSA 215 d1j93a_ 320 -HGIKVGTPEENFAHFFEIAKGL 341 :::::::::::::::::::::: d1geqa_ 216 LVKIIGEKGREATEFLKKKVEEL 238