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 <-- 2.203 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1i4na_) 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 d1i4na_ Indole-​3-​glycerophosphate synthase,​ IPGSRibulose-​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 <-- 2.203 --> Hit
DALI alignment (Z-score: 17.7 Raw score:1607.30) d1tqja_ 1 --------------------------------------KNIVVAPSILS-------ADFS 15 ::::::::::: :::: d1i4na_ 1 rrlweiveakkkdileidgenlivqrrnhrflevlsgkERVKIIAEFKKaspsagdINAD 60 d1tqja_ 16 -RLGEEIKAVDEaGADWIHVDVMDGrfvpNITIGPLIVDAIRPLTKKTLDVHLMIVEpEK 74 ::::::::::: :::::::::::: :::::::::::::::::::::::::::: :: d1i4na_ 61 aSLEDFIRMYDE-LADAISILTEKH----YFKGDPAFVRAARNLTCRPILAKDFYID-TV 114 d1tqja_ 75 YVEDFAKAGADIISVHVEhnASPH--LHRTLCQIRELGKKAGAVLnPSTP-LDFL-EYVL 130 :::::::::::::::::: :::: ::::::::::::::::::: :::: :::: :::: d1i4na_ 115 QVKLASSVGADAILIIAR--ILTAeqIKEIYEAAEELGMDSLVEV-HSREdLEKVfSVIR 171 d1tqja_ 131 pvCDLILIMSVNP---QSFIPEVLPKIRALRQmcderglDPWIEVDGGLK-PNNTWQvLE 186 ::::::::::: :::::::::::::::: ::::::::::: :::::: :: d1i4na_ 172 --PKIIGINTRDLdtfEIKKNVLWELLPLVPD-------DTVVVAESGIKdPRELKD-LR 221 d1tqja_ 187 AGANAIVAGSAVFNAPNYAEAIAGVRNSkr 216 :::::::::::::::::::::::::::: d1i4na_ 222 GKVNAVLVGTSIMKAENPRRFLEEMRAWse 251 FAST alignment (Normalized score: 13.04 Raw score:3036.00) d1tqja_ 1 --------------------------------------KNIVVAPSILSADF-------- 14 ::::::::: d1i4na_ 1 RRLWEIVEAKKKDILEIDGENLIVQRRNHRFLEVLSGKERVKIIAEF-----KKASPSAG 55 d1tqja_ 15 -----SRLGEEIKAVDEAGADWIHVDVMDGRFVPNI----TIGPLIVDAIRPLTKKTLDV 65 :::::::::::: :::::::::: :::::::::::::::::::: d1i4na_ 56 DINADASLEDFIRMYDE-LADAISILTE--------KHYFKGDPAFVRAARNLTCRPILA 106 d1tqja_ 66 HLMIVEPEKYVEDFAKAGADIISVHVEHNASP------HLHRTLCQIRELGKKAGAVLNP 119 ::::: :::::::::::::::::::: ::::::::::::::::::: d1i4na_ 107 KDFYI-DTVQVKLASSVGADAILIIA------RILTAEQIKEIYEAAEELGMDSLVE--- 156 d1tqja_ 120 ST-----PLDFLEYVLP-----VCDLILIMSVNPQSFIPE-------VLPKIRALRQMCD 162 :::: :::::::::: ::::::::::: d1i4na_ 157 --VHSREDLEK------VFSVIRPKIIGINTR--------DLDTFEIKKNVLWELLPL-- 198 d1tqja_ 163 ERG--LDPWIEVDGGL-KPNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSKR--- 216 ::::::::::: :::::::::: ::::::::::::::::::::::::: d1i4na_ 199 ---VPDDTVVVAESGIKDPRELKDLRG-KVNAVLVGTSIMKAENPRRFLEEMR----AWS 250 d1tqja_ 217 - 217 d1i4na_ 251 E 251 TMalign alignment (TM-score: 0.77 Raw score:166.78) d1tqja_ 1 ------------------------------------K--NIVVAPSILS--------ADF 14 : :::::::::: ::: d1i4na_ 1 RRLWEIVEAKKKDILEIDGENLIVQRRNHRFLEVLSGKERVKIIAEFKKASPSAGDINAD 60 d1tqja_ 15 SRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK 74 :::::::::::: :::::::::::: :::::::::::::::::::::::::: :::: d1i4na_ 61 ASLEDFIRMYDE-LADAISILTEKH----YFKGDPAFVRAARNLTCRPILAKDFY-IDTV 114 d1tqja_ 75 YVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPVCD 134 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: d1i4na_ 115 QVKLASSVGADAILIIARILTAEQIKEIYEAAEELGMDSLVEVHSREDLEKVFSVIR-PK 173 d1tqja_ 135 LILIMSVNP--QSFIPEVLPKIRALRQMCDERGLDPWIEVDGGLK-PNNTWQVLEAGANA 191 ::::::::: :::::::::::::: ::: ::: :::::::: :::::: ::::::: d1i4na_ 174 IIGINTRDLDTFEIKKNVLWELLPL--VPD---DTV-VVAESGIKDPRELKD-LRGKVNA 226 d1tqja_ 192 IVAGSAVFNAPNYAEAIAGVRNSK-R 216 :::::::::::::::::::::::: d1i4na_ 227 VLVGTSIMKAENPRRFLEEMRAWSE- 251 HHsearch alignment (Probability: 0.99 E-value:0.00) d1tqja_ 6 APSILSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTL-- 63 ::::::::::::::::::::::::::::::::: :: ::::::::::::::::::: d1i4na_ 51 SPSAGDINADASLEDFIRMYDELADAISILTEK-HY---FKGDPAFVRAARNLTCRPILA 106 d1tqja_ 64 -DVHLMIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPSTP 122 :: :::::: ::::::::::::::::::::::::::::::::::::::::::::::: d1i4na_ 107 KDF---YIDTVQ-VKLASSVGADAILIIARILTAEQIKEIYEAAEELGMDSLVEVHSRED 162 d1tqja_ 123 LDFLEYVLPVCDLILIMSVNPQSFIPEV--LPKIRALRQMCDERGLDPWIEVDGGLKPNN 180 ::::::: ::::::::::::::::: :::::::::: ::::::::::::::::: d1i4na_ 163 LEKVFSV----IRPKIIGINTRDLDTFEIKKNVLWELLPL---VPDDTVVVAESGIKDPR 215 d1tqja_ 181 TWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSK 215 ::::::::::::::::::::::::::::::::::: d1i4na_ 216 ELKDLRGKVNAVLVGTSIMKAENPRRFLEEMRAWS 250