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 <-- 1.254 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1nofa2) 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 d1nofa2 Glycosyl hydrolase family 5 xylanase,​ catalytic domain(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 <-- 1.254 --> Hit
DALI alignment (Z-score: 13.5 Raw score:1364.50) d1m5wa_ 1 aELLLGVNIDhIATLrnargtayPDPVQ-AAFIAEQ-----AGADGITVHLREDRrhiTD 54 ::::::::: :::: ::::: ::::::: :::::::::::::: :: d1nofa2 1 -IQGFGGMSG-VGWI--------NDLTTeQINTAYGsgvgqIGLSIMRVRIDPDS--sKW 48 d1m5wa_ 55 RDVRILRQTLD---TRMNLEMA-------------------------vTEEMLAIAVET- 85 ::::::::::: :::::::: ::::::::::: d1nofa2 49 NIQLPSARQAVslgAKIMATPWsppaymksnnslinggrllpanysayTSHLLDFSKYMq 108 d1m5wa_ 86 ----KPHFCCLVP--ekrQEVTTEgglDVAGQ-RDKMRDACKRLAdaGIQVSLFID--AD 136 ::::::::: :::::: ::::: :::::::::::: ::::::::: :: d1nofa2 109 tngaPLYAISIQNepdwkPDYESC--eWSGDEfKSYLKSQGSKFG--SLKVIVAESlgFN 164 d1m5wa_ 137 EEQIKAAA-----EVGAPFIEIHTGCYadaktdaeqaqelarIAKAaTFAASLGLKVNAG 191 :::::::: :::::::::::::: :::: ::::::::::::: d1nofa2 165 PALTDPVLkdsdaSKYVSIIGGHLYGT--------------tPKPY-PLAQNAGKQLWMT 209 d1m5wa_ 192 HGLT--------------YHNV-KAIAAIpEMHELNIGHaIIGR---AVMTGLKD-AVAE 232 :::: :::: :::::: ::::::::: :::: :::::::: :::: d1nofa2 210 EHYVdskqsannwtsaieVGTElNASMVS-NYSAYVWWY-IRRSyglLTEDGKVSkRGYV 267 d1m5wa_ 233 MKRLMLEarg 242 ::::::: d1nofa2 268 MSQYARFvrp 277 FAST alignment (Normalized score: 7.72 Raw score:2000.00) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPD----PVQAAFIAEQ------AGADGITVHLREDRR 50 ::::::: ::::: ::::::::: ::::::::::::: d1nofa2 1 -IQGFGGM-SGVGW-----------INDLTTEQINTAY-GSGVGQIGLSIMRVRIDPD-- 44 d1m5wa_ 51 HI--TDRDVRILRQT---LDTRMNLEMAV-----------------------TEEMLAIA 82 ::::::::::: ::::::::: :::::::: d1nofa2 45 --SSKWNIQLPSARQAVSLGAKIMATP--WSPPAYMKSNNSLINGGRLLPANYSAYTSHL 100 d1m5wa_ 83 VE---------TKPHFCCL----VPEKRQEVTTE-----GGLDVAGQRDKMRDACKRLAD 124 :: ::::::: :::: :::::::::::::::::: d1nofa2 101 LDFSKYMQTNGAPLYAIS-IQNEPDWK-------PDYESCEWSGDEFKSYLKSQGSK--- 149 d1m5wa_ 125 -AGIQVS-LFI-DADEEQIKAAAEV------GAPFIEIHTGCYADAKTDAEQAQELARIA 175 :::::: ::: :::::::::::: :::::::::: d1nofa2 150 FGSLKVIVAESLGFNPALTDPVLK-DSDASKYVSIIGGHLY------------------- 189 d1m5wa_ 176 KA------ATFAASLGLKVNAGHGL------------------TYHNVKAIAAIPEMHEL 211 :::::::::::::: :::::::::: :::::: d1nofa2 190 --GTTPKPYPLAQNAGKQLWMT---EHYVDSKQSANNWTSAIEVGTELNASMV-SNYSAY 243 d1m5wa_ 212 NIGHAIIGRAVMTG--------------LKDAVAEMKRLMLEARG--- 242 ::: :::::::::::::: d1nofa2 244 VWW-----------YIRRSYGLLTEDGKVSKRGYVMSQYARF---VRP 277 TMalign alignment (TM-score: 0.54 Raw score:131.26) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPDPVQAAFI---AEQAGADGITVHLR-E-DRR-HITD 54 ::::::::: ::::: ::::::::::::: ::: ::::::::: : ::: ::: d1nofa2 1 --IQGFGGMSG-VGWIN--DLTTEQINTAYGSGVGQIG--LSIMRVRIDPDSSKWN-IQL 52 d1m5wa_ 55 RDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKR------QEVTTEGGLDV 108 ::::::::: ::::: : ::::::: :::: :::::: d1nofa2 53 PSARQAVSL-GAKIM-A-------------------TPWSPPAYMKSNNSLIN-GGRLLP 90 d1m5wa_ 109 AGQRDKMRDACK-RL-ADA---GIQVSLFI-------------D-A--DEEQIKAAAEVG 147 :::::::::::: :: ::: :::::::: : : :::::::::::: d1nofa2 91 ANYSAYTSHLLDFSKYMQTNGAPLYAISIQNEPDWKPDYESCEWSGDEFKSYLKSQGSKF 150 d1m5wa_ 148 AP-FIEIHTGCYADAKTDAEQAQELARIAKAATFA-ASLGLKVNAGHGLTYHNVKAIAAI 205 :: :::::::::: :::::::::::: :::::::::: ::::::::::::: d1nofa2 151 GSLKVIVAESLGF----------NPALTDPVLKDSDASKYVSIIGG-HLYGTTPKPYPLA 199 d1m5wa_ 206 P-E-MHELNIGHAIIG-RAVMTG--LKDAVAEMKRLMLEARG------------------ 242 : : :::::::::::: :::::: :::::::::::::::: d1nofa2 200 QNAGKQLWMTEHYVDSKQSANNWTS-AIEVGTELNASMVSNYSAYVWWYIRRSYGLLTED 258 d1m5wa_ 243 ------------------- 243 d1nofa2 259 GKVSKRGYVMSQYARFVRP 277 HHsearch alignment (Probability: 0.01 E-value:0.22) d1m5wa_ 79 LAIAVETKPHFCCLVPEKRQEVTTE-----GGL----DVAGQRDKMRDACKRLADAGIQV 129 ::::::::::::::::::::::::: ::: ::::::::::::::::::::::: d1nofa2 55 ARQAVSLGAKIMATPWSPPAYMKSNNSLINGGRLLPANYSAYTSHLLDFSKYMQTNGAPL 114 d1m5wa_ 130 ---SLFIDADE------------EQIKAAAEVG--APFIEIHTGCYADAKTDAEQAQELA 172 :::::::: :::::::::: ::::::::::::: :::::::::: d1nofa2 115 YAISIQNEPDWKPDYESCEWSGDEFKSYLKSQGSKFGSLKVIVAESLG--FNPALTDPVL 172 d1m5wa_ 173 RIAKAATFAASLGLKVN--AGHGLTYHNVKAIAAIPEMHELNIGHA 216 :::::::::: ::::: ::::::::::::::::::::::::::: d1nofa2 173 KDSDASKYVS--IIGGHLYGTTPKPYPLAQNAGKQLWMTEHYVDSK 216