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 | d1u3da2 | Cryptochrome | Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase, N-terminal domain | 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 <-- 0.587 --> HitDALI alignment (Z-score: 2.9 Raw score:270.80) d1m5wa_ 1 aelllgvnidhiatlrnargtaypdpvqaafiaeqagadgitvhlredrrhitdrdvril 60 d1u3da2 1 ------------------------------------------------------------ 1 d1m5wa_ 61 rqtldtrmnlemavteemlaiavetkphfcclvpekrqevtteggldvagqrdkmrdack 120 d1u3da2 1 ------------------------------------------------------------ 1 d1m5wa_ 121 rladagiqVSLFI----------------------------------------------- 133 ::::: d1u3da2 1 --------CSIVWfrrdlrvednpalaaavragpvialfvwapeeeghyhpgrvsrwwlk 52 d1m5wa_ 134 ----------------------daDEEQIKAAAE-VGAPFIEIhTGCYadaktdaeQAQE 170 :::::::::: :::::::: :::: :::: d1u3da2 53 nslaqldsslrslgtclitkrstdSVASLLDVVKsTGASQIFF-NHLY--------DPLS 103 d1m5wa_ 171 LARIAKAATFAASLGLKVNAGHGLTYHNVK----------aiaaipemhelnighaiigr 220 :::::::::::::::::::::::::::::: d1u3da2 104 LVRDHRAKDVLTAQGIAVRSFNADLLYEPWevtdelgrpfsmfaafwerclsmpydpesp 163 d1m5wa_ 221 avmtglkdavaemkrlmlearg 242 d1u3da2 164 llppkkiisgdvskcvadplvf 185 FAST alignment (Normalized score: 2.04 Raw score:431.90) d1m5wa_ 1 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRIL 60 d1u3da2 1 ------------------------------------------------------------ 1 d1m5wa_ 61 RQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACK 120 d1u3da2 1 ------------------------------------------------------------ 1 d1m5wa_ 121 RLADAGIQVSLFIDA--------------------------------------------- 135 ::::: d1u3da2 1 --------CSIVW--FRRDLRVEDNPALAAAVRAGPVIALFVWAPEEEGHYHPGRVSRWW 50 d1m5wa_ 136 --------------------------DEEQIKAAAE-VGAPFIEIHTGCYADAKTDAE-- 166 :::::::::: :::::::::: d1u3da2 51 LKNSLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNH-----------LY 99 d1m5wa_ 167 QAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGL 226 :::::::::::::::::::::::: d1u3da2 100 DPLSLVRDHRAKDVLTAQGIAVRS------------------------------------ 123 d1m5wa_ 227 KD---------------------AVAEMKRLMLEARG----------------------- 242 :::::::::: d1u3da2 124 --FNADLLYEPWEVTDELGRPFSMFAAFWERCL----SMPYDPESPLLPPKKIISGDVSK 177 d1m5wa_ 243 -------- 243 d1u3da2 178 CVADPLVF 185 TMalign alignment (TM-score: 0.30 Raw score:71.97) d1m5wa_ 1 ----------AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRR 50 ::::: : ::: d1u3da2 1 CSIVWFRRDL-------RVEDN-------------------------P-ALA-------- 19 d1m5wa_ 51 HITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPE--------------- 95 ::: ::::::::: d1u3da2 20 -----------------AAV----------------RAGPVIALFVWAPEEEGHYHPGRV 46 d1m5wa_ 96 --------KRQEV-TT------EGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQI 140 ::::: :: :::::: ::::::: d1u3da2 47 SRWWLKNSLAQLDSSLRSLGTC--LITKRS-----------------------TDSVASL 81 d1m5wa_ 141 KAAAE-VGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNV 199 ::::: :::::::::: :: ::::::::::::::::::::::::::::::::: d1u3da2 82 LDVVKSTGASQIFFNH--LY-------DPLSLVRDHRAKDVLTAQGIAVRSFNADLLYEP 132 d1m5wa_ 200 KA------------------IAAIPEMHELNIGHAIIGRAVMT--GLKDAVA-------- 231 :: : :: ::::: d1u3da2 133 WEVTDELGRPFSMFAAFWER------------------C--LSMP--YDPESPLLPPKKI 170 d1m5wa_ 232 ---------------EMKRLMLEARG 242 d1u3da2 171 ISGDVSKCVADPLVF----------- 185 HHsearch alignment (Probability: 0.26 E-value:0.05) d1m5wa_ 78 MLAIAVETKPHFCCLVPEKRQEVTTE-GGLDVAGQRDKMRDACKRLADAGIQVSLFI--D 134 :::::::::::::::::::::::::: :::::::::::::::::::::::::::::: : d1u3da2 17 ALAAAVRAGPVIALFVWAPEEEGHYHPGRVSRWWLKNSLAQLDSSLRSLGTCLITKRSTD 76 d1m5wa_ 135 ADEEQIKAAAEVGAPFIEIH--TGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGH 192 :::::::::::::::::::: ::::: :::::::::::::::::::::: d1u3da2 77 SVASLLDVVKSTGASQIFFNHLYDPLS-----------LVRDHRAKDVLTAQGIAVRSFN 125 d1m5wa_ 193 GLTYH 197 ::::: d1u3da2 126 ADLLY 130