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 | d1v3ha_ | beta-Amylase | (Trans)glycosidases | 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 <-- 1.645 --> HitDALI alignment (Z-score: 13.8 Raw score:1623.80) d1m5wa_ 1 -----AELLLGVNIdHIATlrnargtAYPD-PVQAAFIAEQAGADGITVHLREDR----- 49 ::::::::: :::: :::: :::::::::::::::::::::::: d1v3ha_ 1 snmllNYVPVYVML-PLGVvnvdnvfEDPDgLKEQLLQLRAAGVDGVMVDVWWGIielkg 59 d1m5wa_ 50 -rhitDRDVRILRQTL---DTRMNLEMA-------------------------------- 73 ::::::::::: ::::::::: d1v3ha_ 60 pkqydWRAYRSLLQLVqecGLTLQAIMSfhqcggnvgdivnipipqwvldigesnhdify 119 d1m5wa_ 74 ------------------------------VTEEMLAIAVETK-------PHFCCLVPEk 96 ::::::::::::: ::::::::: d1v3ha_ 120 tnrsgtrnkeyltvgvdnepifhgrtaieiYSDYMKSFRENMSdflesglIIDIEVGLG- 178 d1m5wa_ 97 rqevtTEGGLD------------------------------------------------- 107 :::::: d1v3ha_ 179 -----PAGQLRypsypqsqgwefpgigefqcydkylkadfkaavaraghpewelpddagk 233 d1m5wa_ 108 --------------------------------VAGQ-RDKMRDACKRLADAGIQVSLFID 134 :::: ::::::::::::::::::::::: d1v3ha_ 234 yndvpestgffksngtyvtekgkffltwysnkLLNHgDQILDEANKAFLGCKVKLAIKVS 293 d1m5wa_ 135 A--------------------------DEEQIKAAAEvGAPFIEIHTgcyADAKTDA--e 166 : :::::::::: ::::::::: ::::::: d1v3ha_ 294 GihwwykvenhaaeltagyynlndrdgYRPIARMLSR-HHAILNFTC-leMRDSEQPsda 351 d1m5wa_ 167 qAQELARIAKAATFAASLGLKVNAGHGL------TYHNVKAIAAI----------pEMHE 210 ::::::::::::::::::::::::::: ::::::::::: :::: d1v3ha_ 352 kSGPQELVQQVLSGGWREDIRVAGENALprydatAYNQIILNARPqgvnnngppklSMFG 411 d1m5wa_ 211 LNIGHaIIGRAVMTGlKDAVAEMKRLMLE------------------------------- 239 ::::: ::::::::: ::::::::::::: d1v3ha_ 412 VTYLR-LSDDLLQKSnFNIFKKFVLKMHAdqdycanpqkynhaitplkpsapkipievll 470 d1m5wa_ 240 ------------------arg 242 d1v3ha_ 471 eatkptlpfpwlpetdmkvdg 491 FAST alignment (Normalized score: 7.19 Raw score:2479.00) d1m5wa_ 1 -----AELLLGVNIDHIATLRNARGTAYP----------------DPVQAAFIAEQAGAD 39 :::::::: ::::::::::::::: d1v3ha_ 1 SNMLLNYVPVYVM----------------LPLGVVNVDNVFEDPDGLKEQLLQLRAAGVD 44 d1m5wa_ 40 GITVHLREDRRHIT------------DRDVRILRQT---LDTRMNLEMAV---------- 74 :::::::: :::::::::: ::::::::: d1v3ha_ 45 GVMVDVWW------GIIELKGPKQYDWRAYRSLLQLVQECGLTLQAIM--SFHQCGGNVG 96 d1m5wa_ 75 --------------------------------------------------TEEMLAIAVE 84 :::::::::: d1v3ha_ 97 DIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKS 156 d1m5wa_ 85 TK-------------PHFCCLVPEKRQEVTTEGGLDVAG--------------------- 110 :::::::: d1v3ha_ 157 --FRENMSDFLESGLIIDIEVGL----------------GPAGQLRYPSYPQSQGWEFPG 198 d1m5wa_ 111 ------------------------------------------------------------ 111 d1v3ha_ 199 IGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFF 258 d1m5wa_ 111 -------QRDKMRDACKRLAD----AGIQVSLFIDA------------------------ 135 :::::::::::::: :::::::::: d1v3ha_ 259 LTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVS-GIHWWYKVENHAAELTAGYYNLND 317 d1m5wa_ 136 ---DEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQA-----------QELARIAKAATFA 181 :::::::::::: ::::: ::::: ::::::::::::: d1v3ha_ 318 RDGYRPIARMLSRHH-AILNF--TCLEM--------RDSEQPSDAKSGPQELVQQVLSGG 366 d1m5wa_ 182 ASLGLKVNAGHG------LTYHNVKAIAAIP---------------EMHELNIGHAIIGR 220 ::::::::: ::::::::::: :::::: d1v3ha_ 367 WREDIRVAG---ENALPRYDATAYNQIIL--NARPQGVNNNGPPKLSMFGVT-------- 413 d1m5wa_ 221 AVMT-----------GLKDAVAEMKRLMLEARG--------------------------- 242 ::::::::::::: d1v3ha_ 414 ----YLRLSDDLLQKSNFNIFKKFVLKM-----HADQDYCANPQKYNHAITPLKPSAPKI 464 d1m5wa_ 243 --------------------------- 243 d1v3ha_ 465 PIEVLLEATKPTLPFPWLPETDMKVDG 491 TMalign alignment (TM-score: 0.75 Raw score:181.63) d1m5wa_ 1 -----AELLLGVNIDHIATLRN-ARGTAYPDPVQAAFIAEQAGADGITVHLREDRR---- 50 ::::::::::::::::: :::::::::::::::::::::::::::::::: d1v3ha_ 1 SNMLLNYVPVYVMLPLGVVNVDN-VFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKG 59 d1m5wa_ 51 ------HITDRDVRILRQTLDTRMNLEMAV------------------------------ 74 ::::::::::::::::::::::: d1v3ha_ 60 PKQYDW-RAYRSLLQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIF 118 d1m5wa_ 75 -------------------------------T-EEMLAIAVET---K----PHFCCLVPE 95 : :::::::::: : ::::::::: d1v3ha_ 119 YTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLG 178 d1m5wa_ 96 KRQEVTTEGGL------------------------------------------------- 106 : ::::: d1v3ha_ 179 P-----AGQLRYPSYPQSQGWEFPGIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGK 233 d1m5wa_ 107 -------------------------------DVAGQ-RDKMRDACKRLADAGIQVSLFID 134 ::::: ::::::::::::::::::::::: d1v3ha_ 234 YNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVS 293 d1m5wa_ 135 A--------------------------DEEQIKAAAEVGAPFIEIHTGCYAD-AKTD-AE 166 : :::::::::: :::::::::::::: :::: :: d1v3ha_ 294 GIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSR-HHAILNFTCLEMRDSEQPSDAK 352 d1m5wa_ 167 QAQELARIAKAATFAASLGLKVNAGHGL-TYH--NVKAIAAI-P------------EMHE 210 : :::::::::::::::::::::::::: ::: :::::::: : :::: d1v3ha_ 353 S-GPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNARPQGVNNNGPPKLSMFG 411 d1m5wa_ 211 LNIGHAIIGRAVMTGLKDAVAEMKRLM-LE------------------------------ 239 ::::: ::::::::::::::::::::: :: d1v3ha_ 412 VTYLR-LSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLL 470 d1m5wa_ 240 --------------ARG---- 242 ::: d1v3ha_ 471 EATKPTLPFPWLPETDMKVDG 491 HHsearch alignment (Probability: 0.46 E-value:0.00) d1m5wa_ 212 NIGHAIIGRAVMTGLKDAVAEMKR 235 :::::::::::::::::::::::: d1v3ha_ 416 RLSDDLLQKSNFNIFKKFVLKMHA 439