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 <-- 1.899 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1ub3a_) 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 d1ub3a_ Deoxyribose-​phosphate aldolase DeoCAldolaseTIM 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 <-- 1.899 --> Hit
DALI alignment (Z-score: 15.7 Raw score:1353.90) d1tqja_ 1 -knIVVAPSILS-aDFSRL-GEEIKAVDEAGADWIHVDvmdgrfvpnitigPLIVDAIRP 57 ::::::::: ::::: :::::::::::::::::: ::::::::: d1ub3a_ 1 dlaAHIDHTLLKptATLEEvAKAAEEALEYGFYGLCIP-------------PSYVAWVRA 47 d1tqja_ 58 L---TKKTLDVHLMI-------vEPEKYVEDFAKAGADIISVHVEHN-----aspHLHRT 102 : ::::::::::: :::::::::::::::::::::::: ::::: d1ub3a_ 48 RyphAPFRLVTVVGFplgyqekeVKALEAALACARGADEVDMVLHLGrakagdldYLEAE 107 d1tqja_ 103 LCQIRE--LGKKAGAVLNPST-----PLDFLEYVLP-VCDLILIMsVNPQSFipeVLPKI 154 :::::: ::::::::::::: :::::::::: :::::::: :::::: ::::: d1ub3a_ 108 VRAVREavPQAVLKVILETGYfspeeIARLAEAAIRgGADFLKTStGFGPRG--aSLEDV 165 d1tqja_ 155 RALRQMCDergLDPWIEVDGGLKP-NNTWQVLEAGANAIVAGSAVfnapnyaeAIAGvrn 213 :::::::: ::::::::::::: :::::::::::::::::::: :::: d1ub3a_ 166 ALLVRVAQ---GRAQVKAAGGIRDrETALRMLKAGASRLGTSSGV--------ALVA--- 211 d1tqja_ 214 skr 216 d1ub3a_ 212 --- 212 FAST alignment (Normalized score: 11.34 Raw score:2420.00) d1tqja_ 1 KNI----VVAPSILSADFSR-----LGEEIKAVDE----AGADWIHVDVMDGRFVPNITI 47 :::::: :::::::::: :::::::: d1ub3a_ 1 ---DLAAHIDHTL-------LKPTATLEEVAKAAEEALEYGFYGLCI------------- 37 d1tqja_ 48 GPLIVDAIRPL---TKKTLDVHLMIV-----------EPEKYVEDFAKAGADIISVHVEH 93 ::::::::::: :::::::: :::::::::::::::::::: d1ub3a_ 38 PPSYVAWVRARYPHAPFRLVTV----VGFPLGYQEKEVKALEAALACARGADEVDMV--- 90 d1tqja_ 94 NAS-----------PHLHRTLCQIRE--LGKKAGAVL-NPST----PLDFLEYVLP-VCD 134 :::::::::::: ::::::::: :::: :::::::::: ::: d1ub3a_ 91 ---LHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGGAD 147 d1tqja_ 135 LILIMSVNPQSFIPE----------VLPKIRALRQMCDERGL---DPWIEVDGGL-KPNN 180 ::: ::::::::::: :::::::::: :::: d1ub3a_ 148 FLK------------TSTGFGPRGASLEDVALLVRV------AQGRAQVKAAGGIRDRET 189 d1tqja_ 181 TWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSKR-- 216 ::::::::::::::: ::::: d1ub3a_ 190 ALRMLKAGASRLGTS-----------SGVAL-----VA 211 TMalign alignment (TM-score: 0.71 Raw score:152.65) d1tqja_ 1 -KN-IVVAPSILS--ADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIR 56 : ::::::::: ::::::::::::::::::::::: ::: :::::: d1ub3a_ 1 D-LAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCI------------PPS-YVAWVR 46 d1tqja_ 57 PLT--K-KTLDVHL-M--I-VE---PEKYVEDFAKAGADIISVHVEHNAS------P--H 98 ::: : ::::::: : : :: ::::::::::::::::::::::::: : : d1ub3a_ 47 ARYPHAPFRLVTVVGFPLGYQEKEVKALEAALACARGADEVDMVLHLGRAKAGDLDYLEA 106 d1tqja_ 99 LHRTLCQIRELGKKAGAVLN-PST----PLDFLEYVLP-VCDLILIMSVNPQSFIPEVLP 152 :::::::::: ::::::::: ::: :::::::::: :::::::::::::::: ::: d1ub3a_ 107 EVRAVREAVP-QAVLKVILETGYFSPEEIARLAEAAIRGGADFLKTSTGFGPRGA--SLE 163 d1tqja_ 153 KIRALRQMCDERGLDPWIEVDGGLK-PNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGV 211 :::::::::: :: :::::::::: :::::::::::::::::: :: : :::: d1ub3a_ 164 DVALLVRVAQ--GR-AQVKAAGGIRDRETALRMLKAGASRLGTS-SG-----V--ALVA- 211 d1tqja_ 212 RNSKR 216 d1ub3a_ 212 ----- 212 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tqja_ 75 YVEDFAKAGADIISVHVE-----HNASPHLHRTLCQIRELGKKAGAVLN---PSTPLDFL 126 :::::::::::::::::: :::::::::::::::::::::::::: :::::::: d1ub3a_ 75 EAALACARGADEVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEI 134 d1tqja_ 127 E---YV--LPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGGLK-PNN 180 : :: ::::::::: :::::::::::::::::::::: :::::::::::: ::: d1ub3a_ 135 ARLAEAAIRGGADFLKT--STGFGPRGASLEDVALLVRVAQ---GRAQVKAAGGIRDRET 189 d1tqja_ 181 TWQVLEAGANAIVAGSA 197 ::::::::::::::::: d1ub3a_ 190 ALRMLKAGASRLGTSSG 206