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 <-- 2.233 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1r85a_) 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 d1r85a_ Xylanase(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 <-- 2.233 --> Hit
DALI alignment (Z-score: 11.9 Raw score:1311.40) d1m5wa_ 1 -----------------AELLLGVNIDhiatlrnargtaypDPVQ--aaFIAEQAGADGI 41 :::::::::: :::: ::::::::::: d1r85a_ 1 kphisalnapqldqrykNEFTIGAAVE-------------pYQLQnekdVQMLKRHFNSI 47 d1m5wa_ 42 TVH--LREDR-----rhiTDRDVRILRQTL---DTRMNLEMAV----------------- 74 ::: ::::: :::::::::::: :::::::::: d1r85a_ 48 VAEnvMKPISiqpeegkfNFEQADRIVKFAkanGMDIRFHTLVwhsqvpqwffldkegkp 107 d1m5wa_ 75 ---------------------TEEMLAIAVETK--PHFCCLVPekrqevtteggLDVA-- 109 :::::::::::: :::::::: :::: d1r85a_ 108 mvnetdpvkreqnkqlllkrlETHIKTIVERYKddIKYWDVVN-----------EVVGdd 156 d1m5wa_ 110 -----------gqRDKMRDACKRLADAG---IQVSLFIDA------DEEQIKAAAEV--- 146 ::::::::::::::: ::::::::: ::::::::::: d1r85a_ 157 gklrnspwyqiagIDYIKVAFQAARKYGgdnIKLYMNDYNtevepkRTALYNLVKQLkee 216 d1m5wa_ 147 --GAPFIEIHTGcyADAKtdaeqAQELARIAKAATFAASLGLKVNA-GHGL--------- 194 :::::::::: :::: ::::::::::::::::::::::: :::: d1r85a_ 217 gvPIDGIGHQSH--IQIG-----WPSEAEIEKTINMFAALGLDNQItELDVsmygwppra 269 d1m5wa_ 195 -----------------tYHNVK-AIAAI-PEMHELNIGHaIIGR--------------- 220 ::::: ::::: :::::::::: :::: d1r85a_ 270 yptydaipkqkfldqaarYDRLFkLYEKLsDKISNVTFWG-IADNhtwldsradvyydan 328 d1m5wa_ 221 -------------------------AVMTGlkdavaemkRLMLEarg 242 ::::: ::::: d1r85a_ 329 gnvvvdpnapyakvekgkgkdapfvFGPDY---kvkpayWAIID-hk 371 FAST alignment (Normalized score: 6.73 Raw score:2018.00) d1m5wa_ 1 -----------------AELLLGVNIDHIATLRNARGTAYPDP-------VQAAFIAEQA 36 :::::::: :::::::::: d1r85a_ 1 KPHISALNAPQLDQRYKNEFTIGAA------------------VEPYQLQNEKDVQMLKR 42 d1m5wa_ 37 GADGITVHLREDRRHI----------------TDRDVRILRQT---LDTRMNLEMAV--- 74 ::::::: ::::::::::: ::::::::: d1r85a_ 43 HFNSIVA---------ENVMKPISIQPEEGKFNFEQADRIVKFAKANGMDIRFHT--LVW 91 d1m5wa_ 75 ---------------------------------TEEMLAIAVET-------KPHFCCLVP 94 :::::::::: :::::: d1r85a_ 92 HSQVPQWFFLDKEGKPMVNETDPVKREQNKQLLLKRLETHIKT-IVERYKDDIKYWD--- 147 d1m5wa_ 95 EKRQEVTTEGGLDVAG---------------------QRDKMRDACKRLAD---AGIQVS 130 :::::::::::::: :::::: d1r85a_ 148 ----------------VVNEVVGDDGKLRNSPWYQIAGIDYIKVAFQAARKYGGDNIKLY 191 d1m5wa_ 131 LFIDA--------DEEQIKAAAE-----VGAPFIEIHTGCYADAKTDAEQAQ-------E 170 ::: :::::::::: :::::::::: : d1r85a_ 192 MND--YNTEVEPKRTALYNLVKQLKEEGVPIDGIGHQS--------------HIQIGWPS 235 d1m5wa_ 171 LARIAKAATFAASLGLKVNAGHGL---------------------------TYHNVKAIA 203 ::::::::::::::::::::: ::::::::: d1r85a_ 236 EAEIEKTINMFAALGLDNQIT---ELDVSMYGWPPRAYPTYDAIPKQKFLDQAARYDRLF 292 d1m5wa_ 204 A-----IPEMHELNIGHAIIGRAVMTGLKDAV---------------------------- 230 : :::::::: d1r85a_ 293 KLYEKLSDKISNVT------------------FWGIADNHTWLDSRADVYYDANGNVVVD 334 d1m5wa_ 231 --------------------------AEMKRLMLEARG--- 242 :::::::: d1r85a_ 335 PNAPYAKVEKGKGKDAPFVFGPDYKVKPAYWAII----DHK 371 TMalign alignment (TM-score: 0.67 Raw score:161.94) d1m5wa_ 1 -----------------AELLLGVNIDHIATLRNARGTAYPDPVQ-AAFIAEQAGADGIT 42 :::::::::: : ::::: :::::::::::::: d1r85a_ 1 KPHISALNAPQLDQRYKNEFTIGAAVE--P----------YQLQNEKDVQMLKRHFNSIV 48 d1m5wa_ 43 V-H-LREDRR-------HITDRDVRILRQTL--D-TRMNLEMAV---------------- 74 : : :::::: :::::::::::: : ::::::::: d1r85a_ 49 AENVMKPISIQPEEGKF--NFEQADRIVKFAKANGMDIRFHTLVWHSQVPQWFFLDKEGK 106 d1m5wa_ 75 ---------------------T-EEMLAIAVETK--PHFCCLVPEKRQEVTTEGGLDV-- 108 : ::::::::::: :::::::: :::: d1r85a_ 107 PMVNETDPVKREQNKQLLLKRLETHIKTIVERYKDDIKYWDVVN----------EVVGDD 156 d1m5wa_ 109 --A----------GQ-RDKMRDACKRLADAGIQVSLFI--DA----D---EEQIKAAAE- 145 : :: :::::::::::::::::::::: :: : ::::::::: d1r85a_ 157 GKLRNSPWYQIAGIDYIKVAFQAARKYGGDNIKLYMNDYNTEVEPKRTALYNLVKQLKEE 216 d1m5wa_ 146 -VGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLT--------- 195 ::::::::::: ::: : ::: ::::::::::::::::::::::::: d1r85a_ 217 GVPIDGIGHQSH--IQI--G-WPS--EAEIEKTINMFAALGLDNQITELDVSMYGWPPRA 269 d1m5wa_ 196 -----------Y--H--NVKAIA-AI--P--EMHELNIGHAI--IG-------------- 219 : : :::::: :: : ::::::::::: :: d1r85a_ 270 YPTYDAIPKQKFLDQAARYDRLFKLYEKLSDKISNVTFWGIADNHTWLDSRADVYYDANG 329 d1m5wa_ 220 ----------------------R-AVMTGLKDAVAEMKRLMLEARG 242 : ::::: :: ::::::::: :: d1r85a_ 330 NVVVDPNAPYAKVEKGKGKDAPFVFGPDY--KV-KPAYWAIID-HK 371 HHsearch alignment (Probability: 0.10 E-value:0.02) d1m5wa_ 140 IKAAAEVGAPFIEIHTGCYADA 161 :::::::::::::::::::::: d1r85a_ 177 FQAARKYGGDNIKLYMNDYNTE 198