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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1m5wa_ | Pyridoxine 5'-phosphate synthase | Pyridoxine 5'-phosphate synthase | TIM beta/alpha-barrel | α/β |
| Hit | d1jpdx1 | L-Ala-D/L-Glu epimerase | Enolase C-terminal domain-like | TIM beta/alpha-barrel | α/β |
Query <-- 1.875 --> IntermediateDALI 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 <-- 1.964 --> HitDALI alignment (Z-score: 13.0 Raw score:1190.10) d1m5wa_ 1 ---aeLLLGVNIDHIAtlrnargtaypDPVQAAFIAEQAGADGITVHLREDRrhiTDRDV 57 ::::::::::: ::::::::::::::::::::::::: ::::: d1jpdx1 1 tlpetVITAQTVVIGT---------pdQMANSASTLWQAGAKLLKVKLDNHL---ISERM 48 d1m5wa_ 58 RILRQTL-DTRMNLEMAV------TEEMLAIAVETKPHFCCLVPekrqevtteggldvaG 110 ::::::: :::::::::: :::::::::::::::::::: : d1jpdx1 49 VAIRTAVpDATLIVDANEswraegLAARCQLLADLGVAMLEQPL-------------paQ 95 d1m5wa_ 111 QRDKMRDacKRLAdagIQVSLF--IDADEeQIKAAAeVGAPFIEIHTGCyadaktdaeqa 168 ::::::: :::: :::::: ::::: :::::: :::::::::::: d1jpdx1 96 DDAALEN--FIHP---LPICADesCHTRS-NLKALK-GRYEMVNIKLDK----------t 138 d1m5wa_ 169 QELARIAKAATFAASLGLKVNAGHGLT-YHNVKAIAAI-PEMHELNIGHAIIGravmtgl 226 ::::::::::::::::::::::::::: :::::::::: :::::::::::::: d1jpdx1 139 GGLTEALALATEARAQGFSLMLGCMLCtSRAISAALPLvPQVSFADLDGPTWLavdvepa 198 d1m5wa_ 227 kDAVAeMKRLmlearg 242 :::: :::: d1jpdx1 199 lQFTTgELHL------ 208 FAST alignment (Normalized score: 9.08 Raw score:2037.00) d1m5wa_ 1 ---AELLLGVNIDHIATLRNARGTAYP-------DPVQAAFIAEQAGADGITVHLREDRR 50 :::::::: ::::::::::::::::::::::: d1jpdx1 1 TLPETVITAQT----------------VVIGTPDQMANSASTLWQAGAKLLKVKLDN--- 41 d1m5wa_ 51 HI--TDRDVRILRQT-LDTRMNLEMAV------TEEMLAIAVETKPHFCCLVPEKRQEVT 101 ::::::::::: ::::::::::: :::::::::::::::: d1jpdx1 42 --HLISERMVAIRTAVPDATLIVDANESWRAEGLAARCQLLADLGVAML----------- 88 d1m5wa_ 102 TEGGLDV-----AGQRDKMRDACKRLADA---GIQVSL--FIDADEEQIKAAAEVGAPFI 151 ::::::::: :::::: ::: :::::::::: ::::: d1jpdx1 89 -------EQPLPAQDDAALEN--------FIHPLPICADESCH-TRSNLKALKG-RYEMV 131 d1m5wa_ 152 EIHTGCYADAKTDAEQAQ-----ELARIAKAATFAASLGLKVNA-GHGLTYHNVKAIAA- 204 ::: ::::::::::::::::::::: :::::::::::::: d1jpdx1 132 NIK---------------LDKTGGLTEALALATEARAQGFSLMLGCMLCTSRAISAALPL 176 d1m5wa_ 205 IPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG------------------- 242 ::::::::::::: d1jpdx1 177 VPQVSFADLDGPT-------------------------WLAVDVEPALQFTTGELHL 208 TMalign alignment (TM-score: 0.61 Raw score:147.78) d1m5wa_ 1 A-E--LLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITD-RD 56 : : :::::::: : : :::::::::::::::::::::::::: : :: :: d1jpdx1 1 TLPETVITAQTVV--I---G----TPDQMANSASTLWQAGAKLLKVKLDN-H---LISER 47 d1m5wa_ 57 VRILRQTL-DTRMNLEM---AVTEEMLAIAVETK---PHFCCLVPEKRQEVTTEGGLDVA 109 :::::::: :::::::: :::::::::::::: ::::::::: :: d1jpdx1 48 MVAIRTAVPDATLIVDANESWRAEGLAARCQLLADLGVAMLEQPLP----------AQ-- 95 d1m5wa_ 110 GQRDKMRDACKRLADAGIQVSLF-IDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQA 168 :: :::::: : :: :::::: ::::::::::: :::::::::::::: d1jpdx1 96 DD-AALENF-I-HP---LPICADESCHTRSNLKAL-KGRYEMVNIKLDKT---------- 138 d1m5wa_ 169 QELARIAKAATFAASLGLKVNAGHGLTYH-NVKAIAAI-PEMHELNIGHAIIGRA----- 221 ::::::::::::::::::::::::::::: :::::::: :::::::::::: ::: d1jpdx1 139 GGLTEALALATEARAQGFSLMLGCMLCTSRAISAALPLVPQVSFADLDGPT-WLAVDVEP 197 d1m5wa_ 222 --VMTGLKDAVAEMKRLMLEARG 242 :::::::: : d1jpdx1 198 AL-------QFTTGELH--L--- 208 HHsearch alignment (Probability: 0.02 E-value:0.40) d1m5wa_ 122 LADAGIQVSLFIDADEEQIKAAAEV-G-APFIEIHTGCYADAKTDAEQAQELARIAKAAT 179 ::::::::::::::::::::::::: : :::::::::::: :::::::::: d1jpdx1 100 LENFIHPLPICADESCHTRSNLKALKGRYEMVNIKLDKTG----------GLTEALALAT 149 d1m5wa_ 180 FAASLGLKVNAGHGLT 195 :::::::::::::::: d1jpdx1 150 EARAQGFSLMLGCMLC 165