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 | d1j18a2 | Bacterial 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 <-- 1.808 --> HitDALI alignment (Z-score: 14.3 Raw score:1623.60) d1m5wa_ 1 --------AELLLGVNIDHiATLRNargtAYPD--PVQAAFIAEQAGADGITVHLREDRR 50 ::::::::::: ::::: :::: ::::::::::::::::::::::::: d1j18a2 1 avngkgmnPDYKAYLMAPL-KKIPE----VTNWetFENDLRWAKQNGFYAITVDFWWGDM 55 d1m5wa_ 51 ------hiTDRDVRILRQTL---DTRMNLEMA---------------------------- 73 :::::::::::: ::::::::: d1j18a2 56 ekngdqqfDFSYAQRFAQSVknaGMKMIPIISthqcggnvgddcnvpipswvwnqksdds 115 d1m5wa_ 74 -------------------------vTEEMLAIAVETK------PHFCCLVPEkrqevtT 102 :::::::::::: ::::::::: : d1j18a2 116 lyfksetgtvnketlnplasdvirkeYGELYTAFAAAMkpykdvIAKIYLSGG------P 169 d1m5wa_ 103 EGGLD------------------------------------------------------- 107 ::::: d1j18a2 170 AGELRypsyttsdgtgypsrgkfqaytefakskfrlwvlnkygslnevnkawgtklisel 229 d1m5wa_ 108 -------------------------------VAGQ-RDKMRDACKRLADA-GIQVSLFID 134 :::: :::::::::::::: ::::::::: d1j18a2 230 ailppsdgeqflmngylsmygkdylewyqgiLENHtKLIGELAHNAFDTTfQVPIGAKIA 289 d1m5wa_ 135 A----------------------DEEQIKAAAEVGApFIEIHTgcyADAKT---DAEQaq 169 : ::::::::::::: :::::: ::::: :::: d1j18a2 290 GvhwqynnptiphgaekpagyndYSHLLDAFKSAKL-DVTFTC-leMTDKGsypEYSM-- 345 d1m5wa_ 170 ELARIAKAATFAASLGLKVNAGHGL------TYHNVKAIAAIPEMHELNIGHaIIGRAVM 223 ::::::::::::::::::::::::: ::::::::::::::::::::: ::::::: d1j18a2 346 PKTLVQNIATLANEKGIVLNGENALsigneeEYKRVAEMAFNYNFAGFTLLR-YQDVMYN 404 d1m5wa_ 224 TglkDAVAEMKRLMlearg 242 : :::::::::: d1j18a2 405 N---SLMGKFKDLL---gv 417 FAST alignment (Normalized score: 8.35 Raw score:2654.00) d1m5wa_ 1 --------AELLLGVNIDHIATLRNAR---------GTAYPDPVQAAFIAEQAGADGITV 43 :::::::: :::: ::::::::::::::::::: d1j18a2 1 AVNGKGMNPDYKAYLM-----------APLKKIPEVTNWE-TFENDLRWAKQNGFYAITV 48 d1m5wa_ 44 HLREDRRHI---------------TDRDVRILRQTLDTRMNLEMAV-------------- 74 :::: ::::::::: :::::::::: d1j18a2 49 DFWW-----GDMEKNGDQQFDFSYAQRFAQSVK-NAGMKMIPII--STHQCGGNVGDDCN 100 d1m5wa_ 75 --------------------------------------TEEMLAIAVETK---------- 86 :::::::::: d1j18a2 101 VPIPSWVWNQKSDDSLYFKSETGTVNKETLNPLASDVIRKEYGELYTA--FAAAMKPYKD 158 d1m5wa_ 87 -PHFCCLVPEKRQEVTTEGGLDVAG----------------------------------- 110 ::::::::: d1j18a2 159 VIAKIYLSGG---------------PAGELRYPSYTTSDGTGYPSRGKFQAYTEFAKSKF 203 d1m5wa_ 111 ---------------------------------------------------------QRD 113 ::: d1j18a2 204 RLWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQFLMNGYLSMYGKDYLEWYQGILEN 263 d1m5wa_ 114 KMRDACKRLAD-----AGIQVSLFIDA-----------------------DEEQIKAAAE 145 ::::::::::: :::::::::: :::::::::: d1j18a2 264 HTKLIGELAHNAFDTTFQVPIGAKIA-GVHWQYNNPTIPHGAEKPAGYNDYSHLLDAFKS 322 d1m5wa_ 146 VGAPFIEIHTGCYADAKTDAEQ----------AQELARIAKAATFAASLGLKVNAGHG-- 193 :: ::::: :::: ::::::::::::::::::::::: d1j18a2 323 AK-LDVTF--TCLE--------MTDKGSYPEYSMPKTLVQNIATLANEKGIVLNG---EN 368 d1m5wa_ 194 ----LTYHNVKAIAAI----PEMHELN--IGHAIIGRAVMTGLKDAVAEMKRLMLEARG- 242 ::::::::::: ::::::: ::::::: ::::::::::: d1j18a2 369 ALSIGNEEEYKRVAE-MAFNYNFAGFTLLRYQDVMY------NNSLMGKFKDL------L 415 d1m5wa_ 243 -- 243 d1j18a2 416 GV 417 TMalign alignment (TM-score: 0.74 Raw score:179.92) d1m5wa_ 1 ------A-E-LLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRR-- 50 : : :::::::::::: ::: :::::::::::::::::::::::::::::: d1j18a2 1 AVNGKGMNPDYKAYLMAPLKKI-PEV--TNWETFENDLRWAKQNGFYAITVDFWWGDMEK 57 d1m5wa_ 51 --------HITDRDVRILRQTLDTRMNLEMAV---------------------------- 74 ::::::::::::::::::::::: d1j18a2 58 NGDQQFDF-SYAQRFAQSVKNAGMKMIPIISTHQCGGNVGDDCNVPIPSWVWNQKSDDSL 116 d1m5wa_ 75 -------------------------T-EEMLAIAV--E-TK--PHFCCLVPEKRQEVTTE 103 : :::::::: : :: :::::::::: :: d1j18a2 117 YFKSETGTVNKETLNPLASDVIRKEYGELYTAFAAAMKPYKDVIAKIYLSGGP-----AG 171 d1m5wa_ 104 GGL--------------------------------------------------------- 106 ::: d1j18a2 172 ELRYPSYTTSDGTGYPSRGKFQAYTEFAKSKFRLWVLNKYGSLNEVNKAWGTKLISELAI 231 d1m5wa_ 107 ----------------------------DVAGQ-RDKMRDACKRLADA-GIQVSLFIDA- 135 ::::: :::::::::::::: :::::::::: d1j18a2 232 LPPSDGEQFLMNGYLSMYGKDYLEWYQGILENHTKLIGELAHNAFDTTFQVPIGAKIAGV 291 d1m5wa_ 136 ---------------------DEEQIKAAAEVGAPFIEIHTGCYADAKTDA---EQAQEL 171 ::::::::::::: ::::::: :: : ::: :::::: d1j18a2 292 HWQYNNPTIPHGAEKPAGYNDYSHLLDAFKSAKL-DVTFTCL-EM-T-DKGSYPEYSMPK 347 d1m5wa_ 172 ARIAKAATFAASLGLKVNAGHGL-T-Y-HNVKAIAAI---PEMHELNIGHAIIGRAVMTG 225 ::::::::::::::::::::::: : : ::::::::: :::::::::: :::::: :: d1j18a2 348 TLVQNIATLANEKGIVLNGENALSIGNEEEYKRVAEMAFNYNFAGFTLLR-YQDVMY-NN 405 d1m5wa_ 226 LKDAVAEMKRLMLEARG 242 :::::::::::: d1j18a2 406 --SLMGKFKDLLGV--- 417 HHsearch alignment (Probability: 0.38 E-value:0.00) d1m5wa_ 27 VQAAFIAEQAGADGITVH 44 :::::::::::::::::: d1j18a2 32 ENDLRWAKQNGFYAITVD 49