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 <-- 1.875 --> Intermediate <-- 1.594 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1ceoa_) through the intermediate protein (d1m5wa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1m5wa_ Pyridoxine 5'​-​phosphate synthasePyridoxine 5'​-​phosphate synthaseTIM beta/​alpha-​barrelα/β
Hit d1ceoa_ Endoglucanase CelC(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 1.875 --> Intermediate
DALI alignment (Z-score: 11.1 Raw score:1066.10) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCFA------------TWSVFDLM 48 :::::::::::: :::::::: d1m5wa_ 1 ---------------------------aELLLGVNIDHIAtlrnargtaypdPVQAAFIA 33 query 49 RD-YMDGTTSSS--------LFEVRLGRERFGKETHAYSVaYGDNEIDEVVSH-ADKIIF 98 :: ::::::::: :::::::::::::::::::: :::::::::::: :::::: d1m5wa_ 34 EQaGADGITVHLredrrhitDRDVRILRQTLDTRMNLEMA-VTEEMLAIAVETkPHFCCL 92 query 99 N-----------------sISQLERFADKAA--GIARGLRLNPqrlgewDVPKVERVMD- 138 : :::::::::::: :::::::::: :::::::::: d1m5wa_ 93 VpekrqevtteggldvagqRDKMRDACKRLAdaGIQVSLFIDA------DEEQIKAAAEv 146 query 139 RINGFMIHNNceNKDFG--LFDRMLGEIEERFGALIARVDWVSLGGGIHFtgddypvdaF 196 :::::::::: ::::: ::::::::::::::::::::::::::::::: : d1m5wa_ 147 GAPFIEIHTGcyADAKTdaEQAQELARIAKAATFAASLGLKVNAGHGLTY--------hN 198 query 197 SARLRAFSdrygVQIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldlliy 256 :::::::: :::::::::::::::: d1m5wa_ 199 VKAIAAIP----EMHELNIGHAIIGRAV-------------------------------- 222 query 257 retakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfQDAAgytmvkknwfn 316 :::: d1m5wa_ 223 ---------------------------------------------MTGL----------- 226 query 317 gvkmpaiaireldgsvrtvreftyadyeqsls 348 d1m5wa_ 227 ----------------kdavaemkrlmlearg 242 FAST alignment (Normalized score: 6.41 Raw score:1859.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALKCFA--------------TWSVF 45 :::::::::: ::::: d1m5wa_ 1 ----------------------------AELLLGVNIDH--IATLRNARGTAYPDPVQAA 30 query 46 DLMR-DYMDGTTS--------SSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVS-HADK 95 :::: :::::::: ::::::::::::::::::::: :::::::::::: :::: d1m5wa_ 31 FIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEM-AVTEEMLAIAVETKPHF 89 query 96 IIFN------------------SISQLERFADKA---AGIARGLRLNPQRLGEW----DV 130 ::: ::::::::::: :::::::::: :: d1m5wa_ 90 CCL-VPEKRQEVTTEGGLDVAGQRDKMRDACKR-LADAGIQVSLFID-------ADEEQI 140 query 131 PKVERVMD-RINGFMI--HNNCENKDFGLFDRMLGEIEERFGALIARV--DWVSLGGGIH 185 ::::: ::::::: :::::::::::::::::::::::::::: ::::::::: d1m5wa_ 141 KAAAE---VGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAAS--LGLKVNAGHGL- 194 query 186 FTGDDYPVDA---FSARLRAFSDRYGVQ----IYLEPGEASITKSTTLEVTVLDTLYNKN 238 ::::::: ::::::::: d1m5wa_ 195 ----------TYHNVKAIAA--------IPEMHELNIGHAI------------------- 217 query 239 LAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDR 298 d1m5wa_ 218 ------------------------------------------------------------ 218 query 299 ISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS---------- 348 d1m5wa_ 218 --------------------------------------------------IGRAVMTGLK 227 query 349 --------------- 349 d1m5wa_ 228 DAVAEMKRLMLEARG 242 TMalign alignment (TM-score: 0.43 Raw score:150.40) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFA------------TWSVFDLM 48 ::::::::::::: :::::::: d1m5wa_ 1 ---------------------------AELLLGVNIDHIATLRNARGTAYPDPVQAAFIA 33 query 49 RD-YMDGTTSSS-------LF-EVRLGRERFGKETHAYSVAYGDNEIDEVV-SHADKIIF 98 :: ::::::::: :: :::::::::::::::::::: :::::::: :::::::: d1m5wa_ 34 EQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVT-EEMLAIAVETKPHFCCL 92 query 99 -------------NSI--S--QLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDR 139 ::: : :::::::::: :::::::::: :::::::::::: d1m5wa_ 93 VPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDA-----DEEQIKAAAEVG 147 query 140 INGFMIHNNCENKD--FG-LFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAF 196 :::::::::::::: : ::::::::::::::::::::::::::::::: ::: : d1m5wa_ 148 APFIEIHTGCYADAKT-DAEQAQELARIAKAATFAASLGLKVNAGHGLTY----HNV--K 200 query 197 SARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIY 256 : ::: :: : ::::::::::::::: d1m5wa_ 201 A-IAA-IP--E--MHELNIGHAIIGRAV-------------------------------- 222 query 257 RETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAG---------- 306 :::: d1m5wa_ 223 ----------------------------------------------MTGLKDAVAEMKRL 236 query 307 ------YTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1m5wa_ 237 MLEARG------------------------------------------ 242 HHsearch alignment (Probability: 0.05 E-value:0.11) query 110 KAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLF-----DRMLGEI 164 :::::::::::::: ::::::::::::::::::::::::::::: ::::::: d1m5wa_ 123 ADAGIQVSLFIDAD-----EEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKA 177 query 165 EERFGALIARVDWVSLGGGI 184 ::::::::::: :::::: d1m5wa_ 178 ATFAASLGLKV---NAGHGL 194
Intermediate <-- 1.594 --> Hit
DALI alignment (Z-score: 13.5 Raw score:1419.90) d1m5wa_ 1 -aelLLGVNIDHIA-TLRNARGT--AYPDPVQAAFIAEQAGADGITVHLREDR------- 49 :::::::::: :::::::: :::::::::::::::::::::::::::: d1ceoa_ 1 mvsfKAGINLGGWIsQYQVFSKEhfDTFITEKDIETIAEAGFDHVRLPFDYPIiesddnv 60 d1m5wa_ 50 ---rhiTDRDVRILRQTL---DTRMNLEMA---------------vTEEMLAIAVETK-- 86 :::::::::::: ::::::::: :::::::::::: d1ceoa_ 61 geykedGLSYIDRCLEWCkkyNLGLVLDMHhapgstlfedpnqqkrFVDIWRFLAKRYin 120 d1m5wa_ 87 ---pHFCCLVPEkrqevtteggldVAGQRDKMRDACKRLA--DAGIQVSLF----IDADe 137 :::::::: :::::::::::::::: ::::::::: :::: d1ceoa_ 121 erehIAFELLNQ-------vvepdSTRWNKLMLECIKAIReiDSTMWLYIGgnnyNSPD- 172 d1m5wa_ 138 eQIKAaAEVG---aPFIEIHTGcYADAK-------------------------------- 162 :::: :::: :::::::: ::::: d1ceoa_ 173 -ELKN-LADIdddyIVYNFHFY-NPFFFthqkahwsesamaynrtvkypgqyegieefvk 229 d1m5wa_ 163 -------------tDAEQAQELARIaKAATFAAS-LGLKVNAGHGLT---------YHNV 199 ::::::::::: :::::::: :::::::::::: :::: d1ceoa_ 230 nnpkysfmmelnnlKLNKELLRKDL-KPAIEFREkKKCKLYCGEFGViaiadlesrIKWH 288 d1m5wa_ 200 KAIAAI--PEMHELNIgHAII----GRAVmTGLKDAvAEMKRLMLEarg 242 :::::: :::::::: :::: :::: :::::: ::::::::: d1ceoa_ 289 EDYISLleEYDIGGAV-WNYKkmdfEIYN-EDRKPVsQELVNILAR--- 332 FAST alignment (Normalized score: 7.26 Raw score:2059.00) d1m5wa_ 1 AEL----LLGVNIDHIATLR-NARGTAYPD--------PVQAAFIAEQAGADGITVHLRE 47 ::::::::::: ::::: :::::::::::::::::::::: d1ceoa_ 1 ---MVSFKAGINLGGWIS--QYQVFS----KEHFDTFITEKDIETIAEAGFDHVRLPFDY 51 d1m5wa_ 48 DRRHI---------------TDRDVRILRQT---LDTRMNLEMAV--------------- 74 ::::::::::: ::::::: d1ceoa_ 52 -----PIIESDDNVGEYKEDGLSYIDRCLEWCKKYNLGLVL----DMHHAPGSTLFEDPN 102 d1m5wa_ 75 --------TEEMLAIAVETKP---HFCCLVPEKRQEVTTEGGL--------DVAGQRDKM 115 ::::::::::: :::: ::::::::: d1ceoa_ 103 QQKRFVDIWRFLAKRYINE--REHIAFE---------------LLNQVVEPDSTRWNKLM 145 d1m5wa_ 116 RDACKRLAD--AGIQVSLFIDADE-------EQIKAAA--EVGA--PFIEIHTGCYADA- 161 ::::::::: :::::::: ::::: :::: ::::::: d1ceoa_ 146 LECIKAIREIDSTMWLYIG-----GNNYNSPDELKN--LADIDDDYIVYNFHF------Y 192 d1m5wa_ 162 ----------------------------------------------------KTDAEQAQ 169 :::::::: d1ceoa_ 193 NPFFFTHQKAHWSESAMAYNRTVKYPGQYEGIEEFVKNNPKYSFMMELNNLKLNKELLRK 252 d1m5wa_ 170 ELARIAKAATFAASLGLKVNAGHGL----------------TYHNVKAIAAIPEMHELNI 213 ::::::::::: :::::::: :::::::::::: ::::: d1ceoa_ 253 DLKPAIEFREK---KKCKLYCG---EFGVIAIADLESRIKWHEDYISLLEEYD--IGGAV 304 d1m5wa_ 214 GHAIIGRAVMTG------------------LKDAVAEMKRLMLEARG- 242 ::::::::: d1ceoa_ 305 ------------WNYKKMDFEIYNEDRKPVSQELVNILA--------R 332 TMalign alignment (TM-score: 0.73 Raw score:177.47) d1m5wa_ 1 --AELLLGVNIDHIA-TLRNARGT--AYPDPVQAAFIAEQAGADGITVHLREDRR----- 50 :::::::::::: :::::::: ::::::::::::::::::::::::::::: d1ceoa_ 1 MV-SFKAGINLGGWISQYQVFSKEHFDTFITEKDIETIAEAGFDHVRLPFDYPIIESDDN 59 d1m5wa_ 51 ------HITDRDVRILRQTLD---TRMNLEM--A-----------V--TEEMLAIAV-ET 85 :::::::::::::: ::::::: : : ::::::::: :: d1ceoa_ 60 VGEYKE-DGLSYIDRCLEWCKKYNLGLVLDMHHAPGSTLFEDPNQQKRFVDIWRFLAKRY 118 d1m5wa_ 86 K----PHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLA-DA-GIQVSLF----IDA 135 : ::::::::: ::::::::::::::::::::: :: ::::::: ::: d1ceoa_ 119 INEREHIAFELLNQ-------VVEPDSTRWNKLMLECIKAIREIDSTMWLYIGGNNYNSP 171 d1m5wa_ 136 DEEQIKAAAEV-G-APFIEIHTGCYADAK-----------------------T------- 163 : :::::::: : ::::::::: ::::: : d1ceoa_ 172 D--ELKNLADIDDDYIVYNFHFY-NPFFFTHQKAHWSESAMAYNRTVKYPGQYEGIEEFV 228 d1m5wa_ 164 -------------DAEQA-QELARIAKAATFAAS-LGLKVNAGHGLT--------YH-NV 199 ::::: ::::::::::::::: :::::::::::: :: :: d1ceoa_ 229 KNNPKYSFMMELNNLKLNKELLRKDLKPAIEFREKKKCKLYCGEFGVIAIADLESRIKWH 288 d1m5wa_ 200 KAIAAI--PEMHELNIGHAII----GRAVMTGLKDAVAEMKRLMLEARG 242 :::::: :::::::::: :: ::::: ::::::::::::::: d1ceoa_ 289 EDYISLLEEYDIGGAVWN-YKKMDFEIYNE-DRKPVSQELVNILAR--- 332 HHsearch alignment (Probability: 0.46 E-value:0.00) d1m5wa_ 113 DKMRDACKRLADAGIQV 129 ::::::::::::::::: d1ceoa_ 69 SYIDRCLEWCKKYNLGL 85