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 <-- 1.163 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1k77a_) 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 d1k77a_ Hypothetical protein YgbM (EC1530)Xylose isomerase-​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 <-- 1.163 --> Hit
DALI alignment (Z-score: 10.4 Raw score:1183.30) d1j93a_ 1 tqpllldavrgkeveRPPVWLM--RQAGRymksyqllcekyplfrdrsenvdLVVEISLQ 58 ::::::: ::::: :::::::: d1k77a_ 1 ---------------MPRFAANlsMMFTE----------------------vPFIERFAA 23 d1j93a_ 59 PWKVfRPDGVILfsDILTplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvp 118 :::: ::::::: :::: d1k77a_ 24 ARKA-GFDAVEF-lFPYN------------------------------------------ 39 d1j93a_ 119 YVGEALTILRKEVNnqAAVLGFVGapftLASYvvEGGSsknftkikrlafaepkvLHALl 178 :::::::::::::: :::::::: :::: :::: :::: d1k77a_ 40 YSTLQIQKQLEQNH--LTLALFNT---aPGDI--NAGE------------wglsaLPGR- 79 d1j93a_ 179 QKFATSMAKYIRYQADSGAQAVQIFDswATEL----sPVDFEEFSLPYLKQIVDSVKLth 234 :::::::::::::::::::::::::: :::: ::::::::::::::::::::: d1k77a_ 80 EHEAHADIDLALEYALALNCEQVHVM--AGVVpagedAERYRAVFIDNIRYAADRFAP-- 135 d1j93a_ 235 PNLPLILYAS----------GSGGLLERLPL----TGVDvVSLD-WTVD-----MADGRR 274 :::::::::: ::::::::::: :::: :::: :::: :::::: d1k77a_ 136 HGKRILVEALspgvkphylfSSQYQALAIVEevarDNVF-IQLDtFHAQkvdgnLTHLIR 194 d1j93a_ 275 RlGPNV-AIQGnVDPG-----VLFGskefitnRINDTVKKAG--KGKHILNLghGIKVG- 325 : :::: :::: :::: :::: :::::::::: :::::::: ::::: d1k77a_ 195 D-YAGKyAHVQ-IAGLpdrhePDDG-----eiNYPWLFRLFDevGYQGWIGC--EYKPRg 245 d1j93a_ 326 ---tPEENFAHFFEIakglry 343 ::::::::::: d1k77a_ 246 lteeGLGWFDAWRGS------ 260 FAST alignment (Normalized score: 4.46 Raw score:1331.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVD---------L 51 :::::: : d1k77a_ 1 ---------------MPRFAA-----------------------------NLSMMFTEVP 16 d1j93a_ 52 VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF 111 :::::::::: :::::: d1k77a_ 17 FIERFAAARK-AGFDAV------------------------------------------- 32 d1j93a_ 112 IPEK--------SVPYVGEALTILRKEVNNQAA-----VLGFVGAPFTLASYVVEGGSSK 158 ::::::::::: :::: d1k77a_ 33 ----EFLFPYNYSTLQIQKQLEQ----------NHLTLALFN------------------ 60 d1j93a_ 159 NFTKIKRLAFAEP----------------KVLHALLQKFATSMAKYIRYQADSGAQAVQI 202 :::::::::::::::::::: :::::::: d1k77a_ 61 -------------TAPGDINAGEWGLSALPGREHEAHADIDLALEYALA---LNCEQVHV 104 d1j93a_ 203 FDSWATELSPVDFEE-----------FSLPYLKQIVDSVKLTH---PNLPLILYASGSGG 248 : :::::::::::::::: ::::::::: d1k77a_ 105 M--------------AGVVPAGEDAERYRAVFIDNIRYAADR-FAPHGKRILVEA----- 144 d1j93a_ 249 ------------LLERLPLTGV---------DVVSLDWT---------VDMADGRRRLGP 278 ::::::: ::::: ::::::::: d1k77a_ 145 LSPGVKPHYLFSSQYQALA---IVEEVARDNVFIQL---DTFHAQKVDGNLTHLIRD--- 195 d1j93a_ 279 N-----VAIQGNVDPGVLFGSKEFITN---------------RINDTVKKAGKG------ 312 :::: :::::::: d1k77a_ 196 -YAGKYAHVQ-----------------IAGLPDRHEPDDGEINYPWLFRL----FDEVGY 233 d1j93a_ 313 KHILNLGHGIKVGTPEEN-----------FAHFFEIAKGLRY-- 343 ::::: ::::::::: d1k77a_ 234 QGWIG-------------CEYKPRGLTEEGLGWFDAWR----GS 260 TMalign alignment (TM-score: 0.55 Raw score:187.48) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::::::::::: ::::: :::: :::: d1k77a_ 1 ---------------MPRFAANLSMM-FTEVP-------------------FIER-FAAA 24 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 :::::::::::::: : :: d1k77a_ 25 RKAGFDAVEFLFPY-N------------------------------------------YS 41 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKI-KRLAFAEPKVLHALLQ 179 :::::::::::: ::::::::: :: :: ::::: : : : ::::: d1k77a_ 42 TLQIQKQLEQNH--LTLALFNTA--PG--DI--NAGEW-G--LS---A------LPGRE- 80 d1j93a_ 180 KFATSMAKYIRYQADSGAQAVQIFDSWATE--LSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 :::::::::::::::::::::::::::::: ::::::::::::::::::::::: :: : d1k77a_ 81 HEAHADIDLALEYALALNCEQVHVMAGVVPAGEDAERYRAVFIDNIRYAADRFAP-HG-K 138 d1j93a_ 238 PLILYASG---------SG-GLLERLPL-T---GVDVVSLDWTV----D-MADGRRRLGP 278 :::::::: :: :::::::: : ::::::::::: : :::::::::: d1k77a_ 139 RILVEALSPGVKPHYLFSSQYQALAIVEEVARDNVFIQLDTFHAQKVDGNLTHLIRDYAG 198 d1j93a_ 279 NVAIQGNVDP-GVLFGSKEFITNRINDTVKKA--GKGKHILNLGHGIKVGTPEENFAHFF 335 :::::::::: ::::: : ::::::::::::: ::::::::: ::::::::::::::: d1k77a_ 199 KYAHVQIAGLPDRHEP-D-DGEINYPWLFRLFDEVGYQGWIGC--EYKPRGLTEEGLGWF 254 d1j93a_ 336 EIAKGLRY 343 :::::: d1k77a_ 255 DAWRGS-- 260 HHsearch alignment (Probability: 0.79 E-value:0.00) d1j93a_ 169 AEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDS-WATELSPVDFEEFSLPYLKQIV 227 :::::::::: ::::::::::::::::::::::: :::::::::::::::::::::: d1k77a_ 75 ALPGREHEAH----ADIDLALEYALALNCEQVHVMAGVVPAGEDAERYRAVFIDNIRYAA 130 d1j93a_ 228 DSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVD 287 ::::::: :::::::::::: :::::::::::::::::::::: ::::::: d1k77a_ 131 DRFAPHG--KRILVEALSPGV---------KPHYLFSSQYQALAIVEEVARD-NVFIQLD 178 d1j93a_ 288 PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 ::::::::::::::::::::::: :::::::::::::::::::::::::::::::: d1k77a_ 179 TFHAQKVDGNLTHLIRDYAGKYA-HVQIAGLPDRHEPDDGEINYPWLFRLFDEVGY 233