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 <-- 1.663 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1w3ia_) 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 d1w3ia_ 2-​keto-​3-​deoxy gluconate aldolase EdaAldolaseTIM 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 <-- 1.663 --> Hit
DALI alignment (Z-score: 13.7 Raw score:1349.50) d1tqja_ 1 knIVVAPSIlsADFS---------RLGEEIKAVDEAGADWIHVD-----VMDGrfvpnit 46 ::::::: :::: :::::::::::::::::::: :::: d1w3ia_ 1 --PEIITPI--ITPFtkdnridkeKLKIHAENLIRKGIDKLFVNgttglGPSL----spe 52 d1tqja_ 47 IGPLIVDAIRPLTKkTLDVHLMIVE---PEKYVEDFAKAGADIISVHVEHN--------a 95 :::::::::::::: :::::::::: ::::::::::::::::::::::: d1w3ia_ 53 EKLENLKAVYDVTN-KIIFQVGGLNlddAIRLAKLSKDFDIVGIASYAPYYyprmsekhl 111 d1tqja_ 96 sPHLHRTLCQIrelGKKAGAVLNP----STPL-DFLEYVlPVCDLILIMSvnpqsfipEV 150 :::::::::: :::::::::: :::: :::::: :::::::::: :: d1w3ia_ 112 vKYFKTLCEVS---PHPVYLYNYPtatgKDIDaKVAKEI-GCFTGVKDTI--------EN 159 d1tqja_ 151 LPKIRALRQMCDerglDPWIEVDGGLkpnNTWQVLEAGANAIVAGsAVFNapnYAEAIAG 210 :::::::::::: :::::::::: :::::::::::::::: :::: ::::::: d1w3ia_ 160 IIHTLDYKRLNP----NMLVYSGSDM---LIATVASTGLDGNVAA-GSNY---LPEVTVT 208 d1tqja_ 211 VRNSKR------------------------------------------------------ 216 :::::: d1w3ia_ 209 IKKLAMerkidealklqflhdevieasrifgslssnyvltkyfqgydlgyprppifpldd 268 d1tqja_ 217 ------------------------- 217 d1w3ia_ 269 eeerqlikkvegiraklvelkilke 293 FAST alignment (Normalized score: 9.09 Raw score:2287.00) d1tqja_ 1 KNIVVAPSILSA-----------DFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI-- 47 :::::: ::::::::::::::::::::: d1w3ia_ 1 --PEIITP----IITPFTKDNRIDKEKLKIHAENLIRKGIDKLF--------------VN 40 d1tqja_ 48 -------------GPLIVDAIRPLTKKTLDVHLMIV---EPEKYVEDFAKAGADIISVHV 91 ::::::::::::: ::::::::: :::::::::::::::::::: d1w3ia_ 41 GTTGLGPSLSPEEKLENLKAVYDVTN-KIIFQVGGLNLDDAIRLAKLSKDFDIVGIASY- 98 d1tqja_ 92 EHNAS----------PHLHRTLCQIRE-LGKKAGAVLNP-------STPLDFLEYVLPVC 133 :::::::::::: ::::::::: ::::::::: :::: d1w3ia_ 99 -----APYYYPRMSEKHLVKYFKTLCEVSPHPVYLYN--YPTATGKDIDAKVAKE-IGCF 150 d1tqja_ 134 DLILIMSVNPQSFIPE---VLPKIRALRQMCDERG-LDPWIEVDGGLKPNNTWQVLEAGA 189 ::::: ::::::::::: :::::::: ::::::::::::: d1w3ia_ 151 TGVKD-----------TIENIIHTLDYKRL-----NPNMLVYSG---SDMLIATVASTGL 191 d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 ::::: :::: ::::::::::: d1w3ia_ 192 DGNVA-AGSN--YLPEVTVTIKK----LAMERKIDEALKLQFLHDEVIEASRIFGSLSSN 244 d1tqja_ 217 ------------------------------------------------- 217 d1w3ia_ 245 YVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE 293 TMalign alignment (TM-score: 0.71 Raw score:153.90) d1tqja_ 1 KNIVVAPSILSAD------F-SRLGEEIKAVDEAGADWIHVDVM--DGRFVPNIT---IG 48 ::::::::::: : ::::::::::::::::::::::: ::::: :: d1w3ia_ 1 --PEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTG----LGPSLSPEEK 54 d1tqja_ 49 PLIVDAIRPLTKKTLDVHLMIV-E--PEKYVEDFAKAGADIISVHVE-----H---NASP 97 :::::::::::: ::::::::: : ::::::::::::::::::::: : :::: d1w3ia_ 55 LENLKAVYDVTN-KIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVK 113 d1tqja_ 98 HLHRTLCQIRELGKKAGAVLNP----ST-PLDFLEYVLPVCDLILIMSVNPQSFIPEVLP 152 ::::::::: : ::::::::: :: ::::::::: ::::::::: :: :: d1w3ia_ 114 YFKTLCEVS--P-HPVYLYNYPTATGKDIDAKVAKEIG-CFTGVKDTI-------EN-II 161 d1tqja_ 153 KIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGVR 212 :::::::::: :::::::: :: :::::::::::::::: ::::: : ::::::: d1w3ia_ 162 HTLDYKRLNP----NMLVYSGS-DM--LIATVASTGLDGNVAA-GSNYL--P-EVTVTIK 210 d1tqja_ 213 N-S-------KR------------------------------------------------ 216 : : :: d1w3ia_ 211 KLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEE 270 d1tqja_ 217 ----------------------- 217 d1w3ia_ 271 ERQLIKKVEGIRAKLVELKILKE 293 HHsearch alignment (Probability: 0.47 E-value:0.01) d1tqja_ 11 SADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIV 70 ::::::::::::::::::::::::: ::::::::::::: d1w3ia_ 16 RIDKEKLKIHAENLIRKGIDKLFVN---GTTGLGPSLSPEE------------------- 53 d1tqja_ 71 EPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPLDFL 126 ::::::::::: ::::::::::::::::::::::::::::::::::::: :::::: d1w3ia_ 54 -KLENLKAVYDV-TNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHL 111 d1tqja_ 127 EYV----LPVCDLILIMSVNPQ----SFIPEVLPKIRALRQMCDER----------GLDP 168 ::: ::::::::::::::: :::::::::::::::::::: :::: d1w3ia_ 112 VKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNP 171 d1tqja_ 169 WIEVDGGLKPNNTWQVLEAGANAIVAGSAV 198 ::::::::: :::::::::::::::::::: d1w3ia_ 172 NMLVYSGSD-MLIATVASTGLDGNVAAGSN 200