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 <-- 1.524 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1s2wa_) 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 d1s2wa_ Phosphoenolpyruvate mutasePhosphoenolpyruvate/​pyruvate domainTIM 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 <-- 1.524 --> Hit
DALI alignment (Z-score: 11.7 Raw score:1254.90) d1j93a_ 1 ---tqPLLLDAVRgkeVERPPVWLMrqagrymksyqllcekyplfrdrsenvdlVVEISL 57 :::::::: ::::::::: :::::: d1s2wa_ 1 kvkktTQLKQMLN---SKDLEFIME---------------------------ahNGLSAR 30 d1j93a_ 58 QPWKVFrPDGVILFSdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksV 117 :::::: :::::::: : d1s2wa_ 31 IVQEAG-FKGIWGSG-------------------------------------lsvsaqlW 52 d1j93a_ 118 PYVGEALTILRKEVNnqAAVLGFVGapftlasyvveggssknftkikrlafaepkvlhal 177 ::::::::::::::: :::::::: d1s2wa_ 53 TQVVEVLEFMSDASD--VPILLDAD----------------------------------t 76 d1j93a_ 178 lqKFATSMAKYIRYQADSGAQAVQIFDSWatELSPvdfeeFSLPYLKQIVDSVKLTH--P 235 ::::::::::::::::::::::::::: :::: ::::::::::::::::: : d1s2wa_ 77 gyGNFNNARRLVRKLEDRGVAGACLEDKLfgRAQP----lADIEEFALKIKACKDSQtdP 132 d1j93a_ 236 NLPLILYASGS-----GGLLER-LPLT---GVDVVSLDWT----vDMADGRRRLGPNVAI 282 ::::::::::: :::::: :::: :::::::::: ::::::::::::::: d1s2wa_ 133 DFCIVARVEAFiagwgLDEALKrAEAYrnaGADAILMHSKkadpsDIEAFMKAWNNQGPV 192 d1j93a_ 283 QGNVDPGVLfgskefitNRINDTVKKAGkgkHILNlgHGIK------------------v 324 ::::::::: ::::::::::: :::: :::: d1s2wa_ 193 VIVPTKYYK--------TPTDHFRDMGV---SMVI--WANHnlrasvsaiqqttkqiydd 239 d1j93a_ 325 gtpeenfahffeiakglry 343 d1s2wa_ 240 qslvnvedkivsvkeifrl 258 FAST alignment (Normalized score: 7.53 Raw score:2241.00) d1j93a_ 1 TQ-----PLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL---V 52 :::::: ::: ::::::: : d1s2wa_ 1 --KVKKTTQLKQM-LNS--KDLEFIM------------------------------EAHN 25 d1j93a_ 53 VEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFI 112 ::::::::: ::::::: d1s2wa_ 26 GLSARIVQE-AGFKGIW------------------------------------------- 41 d1j93a_ 113 PEKS----------VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTK 162 ::::::::::::::: ::::::: d1s2wa_ 42 ----GSGLSVSAQLWTQVVEVLEFMSDAS--DVPILLD---------------------- 73 d1j93a_ 163 IKRLAFAEPKVLHALLQK------FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFE 216 :::::::::::::::::::::::: d1s2wa_ 74 ------------------ADTGYGNFNNARRLVRKLEDRGVAGACLED------------ 103 d1j93a_ 217 EF----------SLPYLKQIVDSVKL--THPNLPLILYASG-----------SGGLLERL 253 :::::::::::::: ::::::::::: :::::::: d1s2wa_ 104 --KLFGRAQPLADIEEFALKIKACKDSQTDPDFCIVARV--EAFIAGWGLDEALKRAEAY 159 d1j93a_ 254 PLTGVDVVSLDWTV--------DMADGRRRLGPNVAIQGNVDPGVLFGSKEFITN--RIN 303 :::::::::: ::::::::::::::: :::::::: ::: d1s2wa_ 160 RNAGADAILM----HSKKADPSDIEAFMKAWNNQGPV-VIVPTKYY---------KTPTD 205 d1j93a_ 304 DTVKKAGKGK---HILNLGHGIKVGTPEENFAHFFEIAKGLRY----------------- 343 :::: :::: d1s2wa_ 206 HFRD------MGVSMVI--------------------------WANHNLRASVSAIQQTT 233 d1j93a_ 344 ------------------------- 344 d1s2wa_ 234 KQIYDDQSLVNVEDKIVSVKEIFRL 258 TMalign alignment (TM-score: 0.47 Raw score:162.87) d1j93a_ 1 -TQ--PLLLDAVRGKE-V-----------------ERPPVWLMRQAGRYMKSYQLLCEKY 39 :: ::::::::::: : ::::::::::::: : : : d1s2wa_ 1 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEA-GFKGIWGSGLSVS-A--Q--L--- 51 d1j93a_ 40 PLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPL 99 : ::::::::::::::::::::::::: :: : d1s2wa_ 52 ------W---TQVVEVLEFMSDASDVPILLDADTG-YG--N------------------- 80 d1j93a_ 100 RTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKN 159 :: : :::::::::::: :: :::::: :: : : d1s2wa_ 81 -------------FN--N--ARRLVRKLEDRG---VA-GACLED--KL--F--------G 107 d1j93a_ 160 FTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSG---AQAVQIFDSWATELSPVDFE 216 : :: :: ::::::::::::::::: :::::::::::::: ::: d1s2wa_ 108 R--AQ------------PL-ADIEEFALKIKACKDSQTDPDFCIVARVEAFIAG---WGL 149 d1j93a_ 217 EFSLPYLKQIVDSVKLTHPNLPLILYASGS--GGLLERLP-LT--GVDVVSLDW--T-VD 268 ::::::::::: :: : :::::::::: :::::::: :: ::::::::: : :: d1s2wa_ 150 DEALKRAEAYR-NA---G--ADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTP 203 d1j93a_ 269 MADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIK-VGTP 327 :::::: :: ::::: :::: : :: :::: d1s2wa_ 204 TDHFRD-MG--VSMVI-WANH-N------------------------------LRASVSA 228 d1j93a_ 328 E--------------------ENFA--------HFFEIAKGLRY 343 : : d1s2wa_ 229 IQQTTKQIYDDQSLVNVEDKI---VSVKEIFRL----------- 258 HHsearch alignment (Probability: 0.72 E-value:0.00) d1j93a_ 183 TSMAKYIRYQADSGAQAVQIFDSWATELS-PVDFEEFSLPYLKQIVDSVKLTHPNLPLIL 241 ::::::::::::::::::::: :::: ::::::: ::::: ::::::: d1s2wa_ 150 DEALKRAEAYRNAGADAILMH----SKKADPSDIEAF--------MKAWN---NQGPVVI 194 d1j93a_ 242 YASG-SGGLLERLPLTGVDVVSLD 264 :::: ::::::::::::::::::: d1s2wa_ 195 VPTKYYKTPTDHFRDMGVSMVIWA 218