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 <-- 1.309 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1pbga_) 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 d1pbga_ 6-​phospho-​beta-​D-​galactosidase,​ PGAL(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 <-- 1.309 --> Hit
DALI alignment (Z-score: 11.3 Raw score:1307.30) d1tqja_ 1 ------kNIVVAPSIL---------------------------------saDFSRLGEEI 21 ::::::::: ::::::::: d1pbga_ 1 mtktlpkDFIFGGATAayqaegathtdgkgpvawdkylednywytaepasdFYHKYPVDL 60 d1tqja_ 22 KAVDEAGADWIHVDVMDG---------rfvpnitIGPLIVDAIRPlTKKTLDVHLMIV-- 70 :::::::::::::::::: ::::::::::: :::::::::::: d1pbga_ 61 ELAEEYGVNGIRISIAWSrifptgygevnekgveFYHKLFAECHK-RHVEPFVTLHHFdt 119 d1tqja_ 71 ---------------------EPEKYVEDFAkaGADIISVH--VEHN------------- 94 :::::::::: :::::::: :::: d1pbga_ 120 pealhsngdflnreniehfidYAAFCFEEFP--EVNYWTTFneIGPIgdgqylvgkfppg 177 d1tqja_ 95 --------------aSPHLHRTLCQIR--ELGKKAGAVLNPS------------------ 120 :::::::::::: ::::::::::::: d1pbga_ 178 ikydlakvfqshhnmMVSHARAVKLYKdkGYKGEIGVVHALPtkypydpenpadvraael 237 d1tqja_ 121 ----TPLDFLEYVL-------------------------------------PVCDLILIM 139 :::::::::: ::::::::: d1pbga_ 238 ediiHNKFILDATYlghysdktmegvnhilaenggeldlrdedfqaldaakDLNDFLGIN 297 d1tqja_ 140 SV------------------------------npqSFIPEVLPKIRALRQMCDergLDPW 169 :: :::::::::::::::::: :::: d1pbga_ 298 YYmsdwmqafdgeteikyqikgvgrrvapdyvpwiIYPEGLYDQIMRVKNDYP---NYKK 354 d1tqja_ 170 IEV-DGGL-------------------KPNNTWQVLEAG-----ANAIVAG--------- 195 ::: :::: :::::::::::: ::::::: d1pbga_ 355 IYItENGLgykdefvdntvyddgridyVKQHLEVLSDAIadganVKGYFIWslmdvfsws 414 d1tqja_ 196 ------SAVFN----------APNYAEAIAG-vrNSKR 216 ::::: :::::::::: :::: d1pbga_ 415 ngyekrYGLFYvdfdtqerypKKSAHWYKKLaetQVIE 452 FAST alignment (Normalized score: 6.58 Raw score:2057.00) d1tqja_ 1 ------KNIVVAPSILSA-------------------------------------DFSRL 17 :::::::: ::::: d1pbga_ 1 MTKTLPKDFIFGGA----TAAYQAEGATHTDGKGPVAWDKYLEDNYWYTAEPASDFYHKY 56 d1tqja_ 18 GEEIKAVDEAGADWIHVDVMDGRFVPNITI---------------GPLIVDAIRPL---T 59 :::::::::::::::::::: ::::::::::: : d1pbga_ 57 PVDLELAEEYGVNGIRISIA----------WSRIFPTGYGEVNEKGVEFYHKLFAECHKR 106 d1tqja_ 60 KKTLDVHLMIV-----------------------EPEKYVEDFAK--AGADIISVHV--- 91 ::::::: ::::::::::: ::::::: d1pbga_ 107 HVEPFVT----LHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWT---TFN 159 d1tqja_ 92 -----------------------------EHNAS-PHLHRTLCQIRE--LGKKAGAVLNP 119 :::: :::::::::::: ::::::::: d1pbga_ 160 EIGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNM-MVSHARAVKLYKDKGYKGEIGVVH-- 216 d1tqja_ 120 S-------------------------TPLDFLE--------------------------- 127 ::::::: d1pbga_ 217 -ALPTKYPYDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELD 275 d1tqja_ 128 ----------YVLPVCDLILIMSVNPQSFIPE---------------------------- 149 :::::::::::: d1pbga_ 276 LRDEDFQALDAAKDLNDFLGIN----------YYMSDWMQAFDGETEIKYQIKGVGRRVA 325 d1tqja_ 150 --------VLPKIRALRQMCDERGLD------PWIEVDGGL------------------- 176 ::::::::::::: :::::: d1pbga_ 326 PDYVPWIIYPEGLYDQIMRVK-----NDYPNYKKIYIT---ENGLGYKDEFVDNTVYDDG 377 d1tqja_ 177 KPNNTWQVLE---------AGANAIVAGSAVFNAP------------------------- 202 :::::::::: ::::::: d1pbga_ 378 RIDYVKQHLEVLSDAIADGANVKGYF---------IWSLMDVFSWSNGYEKRYGLFYVDF 428 d1tqja_ 203 ------------NYAEAIAGVRNSKR----- 216 ::::::: d1pbga_ 429 DTQERYPKKSAHWYKKLAE-------TQVIE 452 TMalign alignment (TM-score: 0.72 Raw score:155.91) d1tqja_ 1 -----K-NIVVAPSIL---S-----------------------------ADF-SRLGEEI 21 : ::::::::: : ::: ::::::: d1pbga_ 1 MTKTLPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWYTAEPASDFYHKYPVDL 60 d1tqja_ 22 KAVDEAGADWIHVDVMDG-------------RFVPNITIGPLIVDAIRPLTK---KTLDV 65 :::::::::::::::::: ::::::::::::: ::::: d1pbga_ 61 ELAEEYGVNGIRISIAWSRIFPTGYGEVNEK--------GVEFYHKLFAECHKRHVEPFV 112 d1tqja_ 66 HL-M--I---------V-----E--PEKYVEDFA-KA-GADIISVH--V----------- 91 :: : : : : ::::::::: :: :::::::: : d1pbga_ 113 TLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPEVNYWTTFNEIGPIGDGQYLVG 172 d1tqja_ 92 ----------------EHNASPHLHRTLCQIR--ELGKKAGAVLNP-------------- 119 :::::::::::::::: :::::::::::: d1pbga_ 173 KFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPTKYPYDPENPADV 232 d1tqja_ 120 ---------STP--LDFLEY----------------------------------VLPVCD 134 ::: :::::: :::::: d1pbga_ 233 RAAELEDIIHNKFILDATYLGHYSDKTMEGVNHILAENGGELDLRDEDFQALDAAKDLND 292 d1tqja_ 135 LILIMSVNPQSFIPE----------------------------------VL-PKIRALRQ 159 :::::: :::: :: :::::::: d1pbga_ 293 FLGINY-----YMSDWMQAFDGETEIKYQIKGVGRRVAPDYVPWIIYPEGLYDQIMRVKN 347 d1tqja_ 160 MCDERGLDPWIEVDGGL---------------KPNNT-WQ--VL-EA----G-ANAIVA- 194 :: :: ::::::::::: ::::: :: :: :: : :::::: d1pbga_ 348 DY-PN-YKKIYITENGLGYKDEFVDNTVYDDGRIDYVKQHLEVLSDAIADGANVKGYFIW 405 d1tqja_ 195 G--------------SAVFN---------APN-YAEAIAGV--RNSKR 216 : ::::: ::: :::::::: :::: d1pbga_ 406 SLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHWYKKLAETQVIE- 452 HHsearch alignment (Probability: 0.01 E-value:0.27) d1tqja_ 9 ILSADFSRLGEEIKAVDEAGADWIHVDVM------DGRFVPN---ITIGPLIVDAIRPL 58 ::::::::::::::::::::::::::::: ::::::: :::::::::::::: d1pbga_ 48 PASDFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECHKR 106