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 <-- 1.075 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1a49a2) 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 d1a49a2 Pyruvate kinase,​ N-​terminal domainPhosphoenolpyruvate/​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 <-- 1.075 --> Hit
DALI alignment (Z-score: 10.9 Raw score:1258.10) d1j93a_ 1 ----------------tqpllldavrgkevERPPVWLMrQAGRYmksyqllcekyplfrd 44 :::::::: ::::: d1a49a2 1 iqtqqlhaamadtflehmcrldidsapitaRNTGIICT-IGPAS---------------- 43 d1j93a_ 45 rsenvdlvveisLQPWKVFrPDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaad 104 ::::::: ::::::::: d1a49a2 44 ------rsvetlKEMIKSG-MNVARMNFS------------------------------- 65 d1j93a_ 105 vekvrefipekSVPYVGEALTILRKEVN---------nQAAVLGFVGAPFtlasyvvegg 155 ::::::::::::::::: :::::::::::: d1a49a2 66 ---------hgTHEYHAETIKNVRTATEsfasdpilyrPVAVALDTKGPA---------- 106 d1j93a_ 156 ssknftkikrlafaepkvlhallqkFATSMAKYIRYQADSGAQAVQIFDSwatelspvdf 215 ::::::::::::::::::::::::: d1a49a2 107 -------------------------VSEKDIQDLKFGVEQDVDMVFASFI---------- 131 d1j93a_ 216 eefSLPYLKQIVDSVKLTHPNLPLILYASG--SGGLLERLPLTgVDVVSLDW-------- 265 ::::::::::::::::::::::::::: ::::::::::: :::::::: d1a49a2 132 --rKAADVHEVRKILGEKGKNIKIISKIENheGVRRFDEILEA-SDGIMVARgdlgieip 188 d1j93a_ 266 ----TVDMADGRRRL-GPNVAIQGNVDPgVLFG-----SKEFITNRINDTVKKAgkgkHI 315 ::::::::::: :::::::::::: :::: :::::::::::::::: :: d1a49a2 189 aekvFLAQKMIIGRCnRAGKPVICATQM-LESMikkprPTRAEGSDVANAVLDG---aDC 244 d1j93a_ 316 LN-lghgikVGTPEENFAHFFEIAKGLRY--------- 343 :: :::::::::::::::::::: d1a49a2 245 IMlsgetakGDYPLEAVRMQHLIAREAEAamfhrklfe 282 FAST alignment (Normalized score: 6.53 Raw score:2031.00) d1j93a_ 1 TQPLLLDAVRGKEVE-------------------------------RPPVWLMRQAGRYM 29 :::::: d1a49a2 1 ---------------IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIIC-------- 37 d1j93a_ 30 KSYQLLCEKYPLFRDRSENVDL-------VVEISLQPWKVFRPDGVILFSDILTPLSGMN 82 ::::::::::: :::::::: d1a49a2 38 ----------------------TIGPASRSVETLKEMIKS-GMNVARMN----------- 63 d1j93a_ 83 IPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS-----VPYVGEALTILRKEVNN---- 133 :::::::::::::: d1a49a2 64 ----------------------------------FSHGTHEYHAETIKNVRTA---TESF 86 d1j93a_ 134 --------QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALL----QKF 181 ::::::::: ::: d1a49a2 87 ASDPILYRPVAVALDTK------------------------------------GPAVSEK 110 d1j93a_ 182 ATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF----SLPYLKQIVDSVKLTHPNL 237 :::::::::: :::::::: ::::::::::::::::::: d1a49a2 111 DIQDLKFGVE---QDVDMVFA----------------SFIRKAADVHEVRKILGEKGKNI 151 d1j93a_ 238 PLILYAS---GSGGLLERLPLTGVDVVSLDWTV----------------DMADGRRRLG- 277 :::::: ::::::::::: ::::::: :::::::: d1a49a2 152 KIISKI-ENHEGVRRFDEILE-ASDGIMV----ARGDLGIEIPAEKVFLAQKMIIGR--C 203 d1j93a_ 278 --PNVAIQGN-VDPGVLFGS---------KEFITNRINDTVKKAGKGK---HILNLGHGI 322 ::::: :::::: ::::::::::::: :::: d1a49a2 204 NRAGKPV---ICATQML---ESMIKKPRPTRAEGSDVANAVL------DGADCIM----- 246 d1j93a_ 323 KVGT----------PEENFAHFFEIAKGLRY------------ 343 :::::::::::::: d1a49a2 247 ----LSGETAKGDYPLEAVRMQHLIARE---AEAAMFHRKLFE 282 TMalign alignment (TM-score: 0.41 Raw score:140.77) d1j93a_ 1 --------------------------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQL 34 d1a49a2 1 IQTQQLHAAMADTFLEHMCRLDIDSA---------------------------------- 26 d1j93a_ 35 LCEKYPLFRDRSENVDLVVEISLQPWK--VFRPDGVILFSDILTPLSGMNIPFDIIKGKG 92 :: :::::::::::::: d1a49a2 27 -------------------------PITA--RNTGIICTIGPASR--------------- 44 d1j93a_ 93 PVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVV 152 ::::::::: ::: :::::::::::: d1a49a2 45 -----------------------SVETLKEMI-KSG--------MNVARMNFSHGT---- 68 d1j93a_ 153 EGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQAD-S------GAQAVQIFDS 205 : ::::::::::::::: : :::::::::: d1a49a2 69 -------------------------H-EYHAETIKNVRTATESFASDPILYRPVAVALDT 102 d1j93a_ 206 WATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGG--LLERLP-LT---G-- 257 :: :::::::::::::::::: : :::::::::: :::::: :: : d1a49a2 103 -KG-PAVSEKDIQDLKFGVEQD--V--------DMVFASFIRKAADVHEVRKILGEKGKN 150 d1j93a_ 258 VDVVSLDWT--VD--MADGRRRLGPNVAIQGNVDP--G--VLFGSKEFITNRINDTVKKA 309 ::::::::: :: :::::::: : ::::::: : ::::: ::::::::::::: d1a49a2 151 IKIISKIENHEGVRRFDEILEAS---D-GIMVARGDLGIEIPAEK--VFLAQKMIIGRCN 204 d1j93a_ 310 GKGKHILNLGHGIKV--------GTPEENF-AHFFEIA---------------------- 338 ::::::::: ::::: ::::::: ::::::: d1a49a2 205 RAGKPVICA-TQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRM 263 d1j93a_ 339 -----------KG---LRY 343 :: ::: d1a49a2 264 QHLIAREAEAAMFHRKLFE 282 HHsearch alignment (Probability: 0.53 E-value:0.01) d1j93a_ 197 AQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPL 255 :::::::: :::::::::::::::::::::::::: :::::: :::::::::: d1a49a2 173 SDGIMVAR---GDLGIEIPAEKVFLAQKMIIGRCNRA--GKPVIC----ATQMLESMIK 222