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 <-- 2.119 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1aw1a_) 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 d1aw1a_ Triosephosphate isomeraseTriosephosphate isomerase (TIM)TIM 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 <-- 2.119 --> Hit
DALI alignment (Z-score: 15.2 Raw score:1408.60) d1tqja_ 1 KNIVVAPSILSADFSR-LGEEIKAVDEAG------aDWIHVdvmdgrfvpnitigPLIVD 53 :::::::::::::::: :::::::::::: ::::: ::::: d1aw1a_ 1 RHPVVMGNWKLNGSKEmVVDLLNGLNAELegvtgvdVAVAP-------------pALFVD 47 d1tqja_ 54 AIRPLT-----KKTLDVHLmivePEKY---------VEDFAKAGADIISVH-----veHN 94 :::::: :::::::: :::: ::::::::::::::: :: d1aw1a_ 48 LAERTLteagsAIILGAQN---tDLNNsgaftgdmsPAMLKEFGATHIIIGhserreyHA 104 d1tqja_ 95 AS-PHLHRTLCQIRELGKKAGAVLNPS-----------TPLDFLEYV-----LPVC--DL 135 :: :::::::::::::::::::::::: ::::::::: :::: :: d1aw1a_ 105 ESdEFVAKKFAFLKENGLTPVLCIGESdaqneagetmaVCARQLDAVintqgVEALegAI 164 d1tqja_ 136 ILIMS--VNPQ-SFIP--EVLPKIRALRQMCD--ERGL--DPWIEVDGGLKPNNTWQVLE 186 ::::: :::: :::: :::::::::::::: :::: :::::::::::::::::::: d1aw1a_ 165 IAYEPiwAIGTgKAATaeDAQRIHAQIRAHIAekSEAVakNVVIQYGGSVKPENAAAYFA 224 d1tqja_ 187 A-GANAIVAGSAVFnapnYAEAIAGVRNS----kr 216 : :::::::::::: ::::::::::: d1aw1a_ 225 QpDIDGALVGGAAL----DAKSFAAIAKAaaeaka 255 FAST alignment (Normalized score: 10.45 Raw score:2452.00) d1tqja_ 1 KNIVVAPS-ILSADFSRLGEEIKAVDEAGA---------DWIHVDVMDGRFVPNITIGPL 50 :::::::: :::::::::::::::::: ::::: ::: d1aw1a_ 1 RHPVVMGNWKLNGSKEMVVDLLNGLNA---ELEGVTGVDVAVAP-------------PAL 44 d1tqja_ 51 IVDAIRP-----LTKKTLDVHLMIVEPEK---------------YVEDFAKAGADIISVH 90 ::::::: :::::::: :::::::::::::: d1aw1a_ 45 FVDLAERTLTEAGSAIILGA---------QNTDLNNSGAFTGDMSPAMLKEFGATHII-- 93 d1tqja_ 91 VEHNA-------------SPHLHRTLCQIRELGKKAGAVLNPST---------------P 122 :::::::::::::::::::::: : d1aw1a_ 94 -----IGHSERREYHAESDEFVAKKFAFLKENGLTPVLCI----GESDAQNEAGETMAVC 144 d1tqja_ 123 LDFLEY-----VLPVC---DLILIMSVN------PQSF--IPEVLPKIRALRQMCDERG- 165 :::::: :::: :::::: :::: ::::::::::::::::: d1aw1a_ 145 ARQLDAVINTQGVEA-LEGAIIAYE---PIWAIGTGKAATAEDAQRIHAQIRAHIAE--K 198 d1tqja_ 166 -----LDPWIEVDGGLKPNNTWQVLE-AGANAIVAGSAVFNAP---NYAEAIAGVRNSKR 216 ::::::::::::::::::::: ::::::::::::: :::::::::: d1aw1a_ 199 SEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAAL---DAKSFAAIAKAAA---- 251 d1tqja_ 217 ---- 217 d1aw1a_ 252 EAKA 255 TMalign alignment (TM-score: 0.72 Raw score:155.73) d1tqja_ 1 KNIVVAPSILSADF-SRLGEEIKAVDEAG-----ADWIHVDVMDGRFVPNITIGPLIVDA 54 :::::::::::::: :::::::::::::: ::::::: : :::::: d1aw1a_ 1 RHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAP-----------P-ALFVDL 48 d1tqja_ 55 IRPLT-----KKTLDVHLMIVEPE--------KYVE-DFAKAGADIISVHV---EH--NA 95 ::::: :::::::: ::: :::: :::::::::::::: :: :: d1aw1a_ 49 AERTLTEAGSAIILGAQN---TDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAE 105 d1tqja_ 96 S-PHLHRTLCQIRELGKKAGAVLNPS-----------TPLDFLE--Y--V-LPVC--DLI 136 : :::::::::::::::::::::::: ::::::: : : :::: ::: d1aw1a_ 106 SDEFVAKKFAFLKENGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAII 165 d1tqja_ 137 LIMS--VNPQS-FIP--EVLPKIRALRQMCDE-R-GL--DPWIEVDGGLKPNNT-WQVLE 186 :::: ::::: ::: ::::::::::::::: : :: ::::::::::::::: ::::: d1aw1a_ 166 AYEPIWAIGTGKAATAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQ 225 d1tqja_ 187 AGANAIVAGSAVFNAPNYAEAIAGVRNSK-R 216 ::::::::::::::::::::::::::::: d1aw1a_ 226 PDIDGALVGGAALDAKSFAAIAKAAAEAKA- 255 HHsearch alignment (Probability: 0.95 E-value:0.00) d1tqja_ 10 LSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMI 69 ::::::::::::::::::::::::::: ::::::::::::::::::: : ::::::: d1aw1a_ 11 LNGSKEMVVDLLNGLNAELEGVTGVDV---AVAPPALFVDLAERTLTEA-G--SAIILGA 64 d1tqja_ 70 VEPEK----------YVEDFAKAGADIISV-HVEH-----NASPHLHRTLCQIRELGKKA 113 ::::: ::::::::::::::: :::: :::::::::::::::::::: d1aw1a_ 65 QNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKENGLTP 124 d1tqja_ 114 GAVLNPSTP-------LD----FLEYVLPVCDL----ILIMSVNPQS-----------FI 147 ::::::::: :: ::::::::::: :::::::::: :: d1aw1a_ 125 VLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAATAEDA 184 d1tqja_ 148 PEVLPKIRAL-RQMCDERGLDPWIEVDGGLKPNNTWQVLEA-GANAIVAGSAVFNAPNYA 205 :::::::::: :::::::::::::::::::::::::::::: :::::::::::::::::: d1aw1a_ 185 QRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALDAKSFA 244 d1tqja_ 206 EAIAGVRNSK 215 :::::::::: d1aw1a_ 245 AIAKAAAEAK 254