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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 2.347 --> Intermediate <-- 2.012 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1ujpa_) through the intermediate protein (d1tqja_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tqja_ D-​ribulose-​5-​phosphate 3-​epimeraseRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1ujpa_ Trp synthase alpha-​subunitRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 2.347 --> Intermediate
DALI alignment (Z-score: 13.0 Raw score:1145.60) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF---aTWSVFDLMRD-YMDGTT 56 ::::::::::: :::::::::: :::::: d1tqja_ 1 ---------------------------kNIVVAPSILSAdfsrLGEEIKAVDEaGADWIH 33 query 57 SSS------------LFEVRLGRERFGKETHAYSV--AYGDnEIDEVVS-HADKIIFNS- 100 ::: :::::::::::::::::::: :::: ::::::: ::::::::: d1tqja_ 34 VDVmdgrfvpnitigPLIVDAIRPLTKKTLDVHLMivEPEK-YVEDFAKaGADIISVHVe 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDRINGFMIHN-NCENkdf 154 :::::::::::: ::::::::::: :::::::::::::::::::: :::: d1tqja_ 93 hnaSPHLHRTLCQIRelGKKAGAVLNPS----TPLDFLEYVLPVCDLILIMSvNPQS--- 145 query 155 glFDRMLGEIEeRFGALIA---RVDWVSLGGGIHFtgddypvdaFSARLRAFSdrygvqI 211 ::::::::: ::::::: ::::::::::::: ::::::::: : d1tqja_ 146 -fIPEVLPKIR-ALRQMCDergLDPWIEVDGGLKP--------nNTWQVLEAG-----aN 190 query 212 YLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsy 271 ::::::::::: d1tqja_ 191 AIVAGSAVFNA------------------------------------------------- 201 query 272 micgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgs 331 d1tqja_ 202 ------------------------------------------------------------ 202 query 332 vrtvreftyadyeqsls 348 d1tqja_ 202 --pnyaeaiagvrnskr 216 FAST alignment (Normalized score: 7.32 Raw score:2007.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALK-CFA--TWSVFDLMRD-YMDGT 55 ::::::::: ::: :::::::::: ::::: d1tqja_ 1 ----------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWI 32 query 56 TS------------SSLFEVRLGRERFGKETHAYSVAY----GDNEIDEVVS-HADKIIF 98 :: ::::::::::::::::::::: :::::::::: ::::::: d1tqja_ 33 HVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHL---MIVEPEKYVEDFAKAGADIISV 89 query 99 N--SISQ---LERFADKA---AGIARGLRLNPQRLGE-WDVPKVERVMDRINGFMIHNNC 149 :::: ::::::: ::::::::::: :::::::::::::::::::: d1tqja_ 90 -HVEHNASPHLHRTLCQ-IRELGKKAGAVLNP-----STPLDFLEYVLPVCDLILIMS-- 140 query 150 ENKD------FGLFDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDA---F 196 ::::::::::::::::: ::::::::: : d1tqja_ 141 ----VNPQSFIPEVLPKIRALRQMCDE-----RGLDPWIEVDGGL-----------KPNN 180 query 197 SARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::: ::::::::: d1tqja_ 181 TWQVLE--------AGANAIVAGSAV---------------------------------- 198 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 d1tqja_ 199 ------------------------------------------------------------ 199 query 314 WFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------------------ 348 d1tqja_ 199 -----------------------------------FNAPNYAEAIAGVRNSKR 216 TMalign alignment (TM-score: 0.43 Raw score:149.23) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A--TWSVFDLMRD-YMDGTT 56 :::::::::::: : :::::::::: :::::: d1tqja_ 1 ---------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWIH 33 query 57 S-S-----------SLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIFNS- 100 : : :::::::::::::::::::::: ::: ::::::: ::::::::: d1tqja_ 34 VDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK-YVEDFAKAGADIISVHVE 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNN--CENKD 153 :::::::::::: ::::::::::: :::: ::::::::::::::::: ::: d1tqja_ 93 HNASPHLHRTLCQIRELGKKAGAVLNPS---TPLD-FLEYVLPVCDLILIMSVNPQSF-- 146 query 154 FGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQ 210 : ::::::::::::::: ::::::::::::: ::: :: :: ::: : d1tqja_ 147 ---I-PEVLPKIRALRQMCDERGLDPWIEVDGGLKP----NNT--WQ-VL-EAG-----A 189 query 211 IYLEPGEASITKST-------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYR 257 :::::::::::::: d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 query 258 ETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNG 317 d1tqja_ 217 ------------------------------------------------------------ 217 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1tqja_ 217 ------------------------------- 217 HHsearch alignment (Probability: 0.21 E-value:0.01) query 75 HAYSVAYGDNEIDEVVSHADKIIFN--SISQLERFADKAAG--IARGLRLNPQRLGEWDV 130 ::::::::::::::::::::::::: :::::::::::::: :::::::::: ::: d1tqja_ 68 MIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPL 123 query 131 PKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDW-VSLG 181 ::::::::::::::::::::::::::::::::::::::::::::::: :::: d1tqja_ 124 DFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175
Intermediate <-- 2.012 --> Hit
DALI alignment (Z-score: 17.1 Raw score:1540.70) d1tqja_ 1 -------------KNIVVAPSIL-sADFS-RLGEEIKAVDEaGADWIHVDVMDGR----- 40 :::::::::: :::: ::::::::::: ::::::::::::: d1ujpa_ 1 mttleafakarseGRAALIPYLTagFPSReGFLQAVEEVLP-YADLLEIGLPYSDgpviq 59 d1tqja_ 41 --------fvpnitIGPLIVDAIRPLTKKTLDVHLMIVEP-----eKYVEDFAKAGADII 87 :::::::::::::::::::::::::: :::::::::::::: d1ujpa_ 60 raselalrkgmsvqGALELVREVRALTEKPLFLMTYLNPVlawgpeRFFGLFKQAGATGV 119 d1tqja_ 88 SVHVEHnaSPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVCD-LILIMSVnpqsf 146 :::::: ::::::::::::::::::::::::::::::::::::::: ::::::: d1ujpa_ 120 ILPDLP--PDEDPGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATgFVYAVSV----- 172 d1tqja_ 147 ipEVLPKIRALRQMCderglDPWIEVDGGLKP-NNTWQVLeaGANAIVAGSAVFNA---- 201 ::::::::::::: :::::::::::: ::::::: :::::::::::::: d1ujpa_ 173 --EVKDLVRRIKART-----ALPVAVGFGVSGkATAAQAA--VADGVVVGSALVRAleeg 223 d1tqja_ 202 PNYAEAIAGVRNS-----kr 216 ::::::::::::: d1ujpa_ 224 RSLAPLLQEIRQGlqrlplp 243 FAST alignment (Normalized score: 12.99 Raw score:2976.00) d1tqja_ 1 -------------KNIVVAPSILS-----ADFSRLGEEIKAVDEAGADWIHVDVMDGRFV 42 :::::::: :::::::::::::: ::::::::::::: d1ujpa_ 1 MTTLEAFAKARSEGRAALIPY---LTAGFPSREGFLQAVEEVL-PYADLLEIGLPYS--- 53 d1tqja_ 43 PNITI---------------------GPLIVDAIRPLTKKTLDVHLMI------VEPEKY 75 ::::::::::::::::::::: :::::: d1ujpa_ 54 -----DGPVIQRASELALRKGMSVQGALELVREVRALTEKPLFLMTY-LNPVLAWGPERF 107 d1tqja_ 76 VEDFAKAGADIISVHVEHNASPH-------LHRTLCQIRELGKKAGAVLNPSTPLDFLEY 128 :::::::::::::: :::::::::::::::::::::::::::::: d1ujpa_ 108 FGLFKQAGATGVIL---------PDLPPDEDPGLVRLAQEIGLETVFLLAPTSTDARIAT 158 d1tqja_ 129 VLPV-CDLILIMSVNPQSFI-PEVLPKIRALRQMCDERGLDPWIEVDGGL-KPNNTWQVL 185 :::: ::::::: :::::::::::: :::::::::::: ::::::::: d1ujpa_ 159 VVRHATGFVYAV--------SVEVKDLVRRIKA-----RTALPVAVGFGVSGKATAAQAA 205 d1tqja_ 186 EAGANAIVAGSAVFNA------PNYAEAIAGVRNSKR--------- 216 :::::::::::: ::::::::::: d1ujpa_ 206 --VADGVVVGSALV--RALEEGRSLAPLLQEIR----QGLQRLPLP 243 TMalign alignment (TM-score: 0.72 Raw score:156.60) d1tqja_ 1 -------K-N-----IVVAPSILS-ADF-SRLGEEIKAVDEAGADWIHVDVMDGR-FV-P 43 : : ::::::::: ::: ::::::::::: :::::::::::::: : : d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVL-PYADLLEIGLPYSDG-PVI 58 d1tqja_ 44 NI-T-------IGP-LIVDAIRPL--TK-KTLDVHLMIVEPE---K--YVEDFAKAGADI 86 :: : ::: ::::::::: :: ::::::::::::: : :::::::::::: d1ujpa_ 59 QRASELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATG 118 d1tqja_ 87 ISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVC-DLILIMSVNPQS 145 ::::::: :::: :::::::::::::::::::::::::::::::::: :::::::: d1ujpa_ 119 VILPDLP-PDED-PGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVYAVSV---- 172 d1tqja_ 146 FIPEVLPKIRALRQMCDERGLDPWIEVDGGLKP-NNTWQVLEAGANAIVAGSAVF-NA-- 201 : :::::::::::: : ::::::::::: :::::::: ::::::::::: :: d1ujpa_ 173 --E-VKDLVRRIKART----A-LPVAVGFGVSGKATAAQAAV--ADGVVVGSALVRALEE 222 d1tqja_ 202 -PNYAEAIAGVRNS--KR--- 216 ::::::::::::: :: d1ujpa_ 223 GRSLAPLLQEIRQGLQRLPLP 243 HHsearch alignment (Probability: 0.99 E-value:0.00) d1tqja_ 4 VVAPSILSAD--FSRLGEEIKAVDEAGADWIHVDV--MDGRFVPNIT-----------IG 48 :::::::::: ::::::::::: ::::::::::: :::::::::: :: d1ujpa_ 17 ALIPYLTAGFPSREGFLQAVEEV-LPYADLLEIGLPYSDGPVIQRASELALRKGMSVQGA 75 d1tqja_ 49 PLIVDAIRPLTKKTLDVHLMI--V-----EPEKYVEDFAKAGADIISVH---VEHNASPH 98 :::::::::::::::: ::: : :::::::::::::::::::: :: : d1ujpa_ 76 LELVREVRALTEKPLF--LMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPD-----E 128 d1tqja_ 99 LHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVCD-LILIMSVNPQSFIPEVLPKIRAL 157 :::::::::::::::::::::::::::::::::::: ::::::: ::::::::: d1ujpa_ 129 DPGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVYAVSV-------EVKDLVRRI 181 d1tqja_ 158 RQMCDERGLDPWIEVDGGLK-PNNTWQVLEAGANAIVAGSAVF----NAPNYAEAIAGVR 212 ::: :::::::::::: :::::: :::::::::::::: ::::::::::::: d1ujpa_ 182 KAR-----TALPVAVGFGVSGKATAAQ--AAVADGVVVGSALVRALEEGRSLAPLLQEIR 234 d1tqja_ 213 NSKR 216 :::: d1ujpa_ 235 QGLQ 238