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 <-- 1.387 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d7a3ha_) 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 d7a3ha_ Endoglucanase Cel5a(Trans)glycosidasesTIM 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 <-- 1.387 --> Hit
DALI alignment (Z-score: 12.0 Raw score:1213.00) d1tqja_ 1 ----------------------KNIVVAPSIL--saDFSR-LGEEIKAVDE-AGADWIHV 34 :::::::::: :::: :::::::::: :::::::: d7a3ha_ 1 svveehgqlsisngelvnergeQVQLKGMSSHglqwYGQFvNYESMKWLRDdWGINVFRA 60 d1tqja_ 35 DVMDGrfvPNIT----iGPLIVDAIRPL---TKKTLDVHLMI----------vEPEKYVE 77 ::::: :::: ::::::::::: ::::::::::: ::::::: d7a3ha_ 61 AMYTS---SGGYiddpsVKEKVKEAVEAaidLDIYVIIDWHIlsdndpniykeEAKDFFD 117 d1tqja_ 78 DFAKAG----aDIISVH---------veHNASPHLHRTLCQIRELG--KKAGAVL--NPS 120 :::::: :::::: :::::::::::::::::: ::::::: ::: d7a3ha_ 118 EMSELYgdypnVIYEIAnepngsdvtwgNQIKPYAEEVIPIIRNNDpnNIIIVGTgtWSQ 177 d1tqja_ 121 TPLDFLEYVLPV-CDLILIMSVnpQSFIP-EVLPKIRALRQMCdergldpWIEV-DGGL- 176 :::::::::::: ::::::::: ::::: ::::::::::::: :::: :::: d7a3ha_ 178 DVHHAADNQLADpNVMYAFHFY--AGTHGqNLRDQVDYALDQG------aAIFVsEWGTs 229 d1tqja_ 177 ------------kpNNTWQVLEaGANAIVAGS-------AVFN---------------AP 202 :::::::: ::::::::: :::: :: d7a3ha_ 230 aatgdggvfldeaqVWIDFMDE-RNLSWANWSlthkdesSAALmpganptggwteaelSP 288 d1tqja_ 203 NYAEAIAGVRNskr 216 ::::::::::: d7a3ha_ 289 SGTFVREKIRE--s 300 FAST alignment (Normalized score: 6.40 Raw score:1630.00) d1tqja_ 1 ----------------------KNIVVAPSILSA------DFSR-LGEEIKAVDE-AGAD 30 :::::::: :::: :::::::::: :::: d7a3ha_ 1 SVVEEHGQLSISNGELVNERGEQVQLKGMS----SHGLQWYGQFVNYESMKWLRDDWGIN 56 d1tqja_ 31 WIHVDVMDGRFVPNITI-----------GPLIVDAIRP---LTKKTLDVHLMIV------ 70 ::::::: :::::::::: :::::::::: d7a3ha_ 57 VFRAAMY----------TSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDW---HILSDN 103 d1tqja_ 71 -------EPEKYVEDFAKAGA------DIISVHVEHNASP--------------HLHRTL 103 :::::::::::: :::: :::::: d7a3ha_ 104 DPNIYKEEAKDFFDEMSEL--YGDYPNVIYE---------IANEPNGSDVTWGNQIKPYA 152 d1tqja_ 104 CQIRE------LGKKAGAVLNPSTPLD-----FLEYVLPVC---------DLILIMSVNP 143 ::::: ::::::::: ::::: :::::: d7a3ha_ 153 EEVIPIIRNNDPNNIIIVGT-------GTWSQDVHHA----ADNQLADPNVMYAFH---- 197 d1tqja_ 144 QS--FIPEVLPKIRALRQMCDERGLDPWIEVDGGL--------------KPNNTWQVLEA 187 ::::::::::::::: ::::::::: :::::::::: d7a3ha_ 198 --FYAGTHGQNLRDQVDYA-LDQGAAIFV------SEWGTSAATGDGGVFLDEAQVWID- 247 d1tqja_ 188 GA------NAIVAGSAVFNAPNYAEAI--------------------------------- 208 ::::: d7a3ha_ 248 --FMDERNLSWAN--------------WSLTHKDESSAALMPGANPTGGWTEAELSPSGT 291 d1tqja_ 209 --AGVRNSKR--- 216 :::: d7a3ha_ 292 FVREKI----RES 300 TMalign alignment (TM-score: 0.72 Raw score:155.61) d1tqja_ 1 ----------------------KNIVVAPSILS---ADFSRLGEEIKAVDEA-GADWIHV 34 ::::::::::: :::::::::::::::: ::::::: d7a3ha_ 1 SVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRA 60 d1tqja_ 35 DVMDGRFVPNIT----IGPLIVDAIRPL---TKKTLDVHLMI--------VE--PEKYVE 77 ::::: :::: :::::::::::: ::::::::::: :: :::::: d7a3ha_ 61 AMYTS---SGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFD 117 d1tqja_ 78 DFAKAG----ADIISVH-VE----HN---AS-PHLHRTLCQIRELG--KKAGAVL-NPST 121 :::::: ::::::: :: :: :: :::::::::::::: ::::::: :::: d7a3ha_ 118 EMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQ 177 d1tqja_ 122 P-LDFLEYVLPV-CDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGGL--- 176 : :::::::::: :::::::: :::::::::::::::::::: : ::::::::: d7a3ha_ 178 DVHHAADNQLADPNVMYAFHF----YAGTHGQNLRDQVDYALDQG-A-AIFVSEWGTSAA 231 d1tqja_ 177 -----KPN-NTWQVL-EA--GANAIVA-GS-------AVFN--------APN--Y---AE 206 ::: :::::: :: ::::::: :: :::: ::: : :: d7a3ha_ 232 TGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGT 291 d1tqja_ 207 AIAGVRNSKR 216 ::::::::: d7a3ha_ 292 FVREKIRES- 300 HHsearch alignment (Probability: 0.21 E-value:0.29) d1tqja_ 101 RTLCQIRELGKKAGAVLNPS 120 :::::::::::::::::::: d7a3ha_ 154 EVIPIIRNNDPNNIIIVGTG 173