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 <-- 2.356 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1m5wa_) 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 d1m5wa_ Pyridoxine 5'​-​phosphate synthasePyridoxine 5'​-​phosphate synthaseTIM 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 <-- 2.356 --> Hit
DALI alignment (Z-score: 18.7 Raw score:1665.40) d1tqja_ 1 KNIVVAPSILSADF---------SRLGEEIKAVDEAGADWIHVDVMDGrfvpNITIGPLI 51 :::::::::::::: ::::::::::::::::::::::::: :::::::: d1m5wa_ 1 AELLLGVNIDHIATlrnargtayPDPVQAAFIAEQAGADGITVHLRED----RRHITDRD 56 d1tqja_ 52 VDAIRPLTKKTLDVHLMivePEKY-VEDFAKAGADIISVH------------VEHNASP- 97 ::::::::::::::::: :::: ::::::::::::::: ::::::: d1m5wa_ 57 VRILRQTLDTRMNLEMA---VTEEmLAIAVETKPHFCCLVpekrqevtteggLDVAGQRd 113 d1tqja_ 98 HLHRTLCQIRELGKKAGAVLNpsTPLDFLEYVLP-VCDLILIMSVNpqSFIP-------E 149 ::::::::::::::::::::: ::::::::::: ::::::::::: :::: : d1m5wa_ 114 KMRDACKRLADAGIQVSLFID--ADEEQIKAAAEvGAPFIEIHTGC--YADAktdaeqaQ 169 d1tqja_ 150 VLPKIRALRQMCDErgLDPWIEVDGGLKPNNTWQVLEA-GANAIVAGSAVFNA---PNYA 205 :::::::::::::: :::::::::::::::::::::: :::::::::::::: :::: d1m5wa_ 170 ELARIAKAATFAAS--LGLKVNAGHGLTYHNVKAIAAIpEMHELNIGHAIIGRavmTGLK 227 d1tqja_ 206 EAIAGVR-NSKR--- 216 ::::::: :::: d1m5wa_ 228 DAVAEMKrLMLEarg 242 FAST alignment (Normalized score: 14.03 Raw score:3208.00) d1tqja_ 1 KNIVVAPSILSADF------------SRLGEEIKAVDEAGADWIHVDVMDGRFVPN---I 45 ::::::::::: ::::::::::::::::::::::: : d1m5wa_ 1 AELLLGVNIDH---IATLRNARGTAYPDPVQAAFIAEQAGADGITVHLR-------EDRR 50 d1tqja_ 46 TIGPLIVDAIRPLTKKTLDVHLMIV----EPEKYVEDFAKAGADIISVHVEHNASP---- 97 :::::::::::::::::::::: :::::::: ::::::::: d1m5wa_ 51 HITDRDVRILRQTLDTRMNLEM---AVTEEMLAIAVE---TKPHFCCLV-------PEKR 97 d1tqja_ 98 ----------------HLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVL-PVCDLILIMS 140 ::::::::::::::::::::: :::::::::: ::::::::: d1m5wa_ 98 QEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFID--ADEEQIKAAAEVGAPFIEIH- 154 d1tqja_ 141 VNPQSF------------IPEVLPKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLE-A 187 :::::::::::::::::: :::::::::::::::::::: : d1m5wa_ 155 ------TGCYADAKTDAEQAQELARIAKAATFAASL--GLKVNAGHGLTYHNVKAIAAIP 206 d1tqja_ 188 GANAIVAGSAVFNA----PNYAEAIAGVRNSKR-------- 216 ::::::::::::: ::::::::::: d1m5wa_ 207 EMHELNIGHAIIG-RAVMTGLKDAVAEMK----RLMLEARG 242 TMalign alignment (TM-score: 0.79 Raw score:169.83) d1tqja_ 1 KNIVVAPSILSAD--F------S-RLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLI 51 ::::::::::::: : : :::::::::::::::::::::::: :::::::: d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLRED----RRHITDRD 56 d1tqja_ 52 VDAIRPLTKKTLDVHLMIVEPEKYVEDFAKAGADIISVH------------VEHNASPH- 98 :::::::::::::::: : :::::::::::::::::::: :::::::: d1m5wa_ 57 VRILRQTLDTRMNLEM-A-VTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDK 114 d1tqja_ 99 LHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLP-VCDLILIMSVNPQSFI-----P-EVL 151 ::::::::::::::::::: : ::::::::::: ::::::::::: :::: : ::: d1m5wa_ 115 MRDACKRLADAGIQVSLFI-D-ADEEQIKAAAEVGAPFIEIHTGC-YADAKTDAEQAQEL 171 d1tqja_ 152 PKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLEA-GANAIVAGSAVF-NA--P---NY 204 ::::::::::::: ::: :::::::::::::::::: :::::::::::: :: : :: d1m5wa_ 172 ARIAKAATFAASL-GLK-VNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDA 229 d1tqja_ 205 AEAIAGVRNSKR- 216 :::::::::::: d1m5wa_ 230 VAEMKRLMLEARG 242 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tqja_ 14 FSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPE 73 ::::::::::::::::::::::::: ::::::::::::::::::::::: :::::: d1m5wa_ 23 YPDPVQAAFIAEQAGADGITVHLRE----DRRHITDRDVRILRQTLDTRMNL--EMAVTE 76 d1tqja_ 74 KYVEDFAKAGADIISVHVEHN-------------ASPHLHRTLCQIRELGKKAGAVLNPS 120 ::::::::::::::::::::: :::::::::::::::::::::::::: d1m5wa_ 77 EMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDAD 136 d1tqja_ 121 TPLDFLEYVLPVCDLILIMSVN-----PQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175 :::::::::: ::::::::::: ::::::::::::::::::::::::: :::::: d1m5wa_ 137 EEQIKAAAEV-GAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLK--VNAGHG 193 d1tqja_ 176 LKPNNTWQVLEA-GANAIVAGSAVFNA---PNYAEAIAGVRNS 214 :::::::::::: :::::::::::::: ::::::::::::: d1m5wa_ 194 LTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRL 236