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 <-- 1.914 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1jpma1) 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 d1jpma1 L-​Ala-​D/​L-​Glu epimeraseEnolase C-​terminal domain-​likeTIM 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 <-- 1.914 --> Hit
DALI alignment (Z-score: 13.0 Raw score:1187.70) d1tqja_ 1 --knIVVAPSIlsADFS--RLGEEIKAVDEAGADWIHVDVMDGrfvpnitIGPLIVDAIR 56 ::::::: :::: :::::::::::::::::::::::: :::::::::: d1jpma1 1 yrdtLETDYTV--SVNSpeEMAADAENYLKQGFQTLKIKVGKD----diaTDIARIQEIR 54 d1tqja_ 57 PLT--KKTLDVHL-MIVE---PEKYVEDFA--KAGADIISV-HVEHNaSPHLHRTLCQIr 107 ::: :::::::: :::: ::::::::: ::::::::: ::::: ::::::::::: d1jpma1 55 KRVgsAVKLRLDAnQGWRpkeAVTAIRKMEdaGLGIELVEQpVHKDD-LAGLKKVTDAT- 112 d1tqja_ 108 elGKKAGAVLnpsTPLDFLEYVL--PVCDLILIMSVnpqsfipEVLPKIRALRQMCDErg 165 :::::::: :::::::::: ::::::::::: ::::::::::::::: d1jpma1 113 --DTPIMADE-svFTPRQAFEVLqtRSADLINIKLM-----kaGGISGAEKINAMAEA-- 162 d1tqja_ 166 LDPWIEVDGG----lKPNN-TWQVLEAG-ANAIVAGSAvFNAP-------nyaEAIAgvR 212 :::::::::: :::: :::::::: ::::::::: :::: :::: : d1jpma1 163 CGVECMVGSMietklGITAaAHFAASKRnITRFDFDAP-LMLKtdvfnggitySGST--I 219 d1tqja_ 213 NSKR----------- 216 :::: d1jpma1 220 SMPGkpglgiigaal 234 FAST alignment (Normalized score: 9.34 Raw score:2100.00) d1tqja_ 1 K---NIVVAPSILSA----DFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITI------ 47 ::::::: :::::::::::::::::::::::: d1jpma1 1 -YRDTLETDYT----VSVNSPEEMAADAENYLKQGFQTLKIKV-----------GKDDIA 44 d1tqja_ 48 -GPLIVDAIRPLT--KKTLDVHLMIV-------EPEKYVEDFAK--AGADIISVHVEHNA 95 :::::::::::: :::::::: ::::::::::: :::::: d1jpma1 45 TDIARIQEIRKRVGSAVKLRLDA---NQGWRPKEAVTAIRKMEDAGLGIELV-------- 93 d1tqja_ 96 SPH-------LHRTLCQIR-ELGKKAGAVLNPS----TPLDFLEYVL--PVCDLILIMSV 141 ::::::::: :::::::: :::::::::: :::::::::: d1jpma1 94 ---EQPVHKDDLAGLKKVTDATDTPIMA-----DESVFTPRQAFEVLQTRSADLINIKL- 144 d1tqja_ 142 NPQSFIPE----VLPKIRALRQMCDERGLDPWIEV-DGGLKPNNTWQVLE-----AGANA 191 :::::::::::::: ::::::: :::::::::::::: ::::: d1jpma1 145 --------MKAGGISGAEKINAMAEA--CGVECMVGSMIETKLGITAAAHFAASKRNITR 194 d1tqja_ 192 IVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 ::::::: d1jpma1 195 FDFDAPL------------------MLKTDVFNGGITYSGSTISMPGKPGLGIIGAAL 234 TMalign alignment (TM-score: 0.69 Raw score:150.01) d1tqja_ 1 -K-NIVVAPSILSADFSRLGEEIKAVDEAGADWIHVDVMDG---RFVPNITIGPLIVDAI 55 : :::::::::::::::::::::::::::::::::::::: ::::::::: d1jpma1 1 YRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIA-------TDIARIQEI 53 d1tqja_ 56 RPLT--KKTLDVHLM-IVE---PEKYVEDFAKA-G-ADIISV-HVEHNASPHLHRTLCQI 106 :::: ::::::::: ::: ::::::::::: : :::::: ::::: ::::::::::: d1jpma1 54 RKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDD-LAGLKKVTDAT 112 d1tqja_ 107 RELGKKAGAVLNPST--PLDFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDER 164 : ::::::::::: :::::::::::: :::::: ::::::::::::::::::: d1jpma1 113 D---TPIMADESVFTPRQAFEVLQTRSAD-LINIKL-----MKAGGISGAEKINAMAEAC 163 d1tqja_ 165 GLDPWIEVDGGLKPNNTWQVLEAG-----ANAIVAGSAVFNAP--------NYAEAIAGV 211 ::::::::::::::::::::::: :::::::::::::: ::::: d1jpma1 164 -GVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGIT--YSGST-- 218 d1tqja_ 212 RNSK----R------- 216 :::: : d1jpma1 219 ISMPGKPGLGIIGAAL 234 HHsearch alignment (Probability: 0.88 E-value:0.00) d1tqja_ 1 KNIVVAPSILSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTK 60 :::::::::::::::::::::::::::::::::::::: :::::::::::::::::: d1jpma1 3 DTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGK----DDIATDIARIQEIRKRVG 58 d1tqja_ 61 KTLDVHLMIVEP-----E---KYVEDFAKAGADIISVHVEH-NASPHLHRTLCQIRELGK 111 : ::::::::: : :::::::::::::::: :: :::::: ::::::::: d1jpma1 59 S--AVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELV--EQPVHKDDL-AGLKKVTDA-- 111 d1tqja_ 112 KAGAVLNPST---PLDFLEYVLP--VCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGL 166 ::::::::: :::::::::: :::::: :::::: :::::::::::::::::: d1jpma1 112 -TDTPIMADESVFTPRQAFEVLQTRSADLIN---IKLMKA--GGISGAEKINAMAEACGV 165 d1tqja_ 167 DPWIE--VDGGLKPNNTWQVL 185 ::::: :::::::::::::: d1jpma1 166 ECMVGSMIETKLGITAAAHFA 186