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 | d1hkva2 | Diaminopimelate decarboxylase LysA | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1bd0a2 | Alanine racemase | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
Query <-- 1.000 --> IntermediateDALI alignment (Z-score: 19.0 Raw score:1797.70) query 1 mietpyyliDKAKLTRNMERIAHVREksgaKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::::::: :::::::::::::::::::::::::::::: d1hkva2 1 ---------DEDDFRSRCRETAAAFG-sgaNVHYAAKAFLCSEVARWISEEGLCLDVCTG 50 query 61 FEVRLGRERFGK--ETHAYSVAYGDNEIDEVV-SHADKIIFNSISQLERFADKA----AG 113 :::::::::::: :::::::::::::::::: ::::::::::::::::::::: :: d1hkva2 51 GELAVALHASFPpeRITLHGNNKSVSELTAAVkAGVGHIVVDSMTEIERLDAIAgeagIV 110 query 114 IARGLRLNPQ----------------RLGEW----DVPKVERVMD-----RINGFMIHNN 148 :::::::::: ::::: :::::::::: :::::::::: d1hkva2 111 QDVLVRLTVGveahthefistahedqKFGLSvasgAAMAAVRRVFatdhlRLVGLHSHIG 170 query 149 CENKDFGLFDRMLGEIEERFGAL--------iaRVDWVSLGGGIH----ftgDDYPVDAF 196 ::::::::::::::::::::::: :::::::::::: :::::::: d1hkva2 171 SQIFDVDGFELAAHRVIGLLRDVvgefgpektaQIATVDLGGGLGisylpsdDPPPIAEL 230 query 197 SARLRAFSDR-------YGVQIYLEPGEASITKSTtlevtvldtlynknlaivdssieah 249 :::::::::: :::::::::::::::::: d1hkva2 231 AAKLGTIVSDestavglPTPKLVVEPGRAIAGPGT------------------------- 265 query 250 mldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytm 309 d1hkva2 266 ------------------------------------------------------------ 266 query 310 vkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1hkva2 266 --------------------------------------- 266 FAST alignment (Normalized score: 10.67 Raw score:3241.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA-----KALLALKCFATWSVFDLMRDYM--D 53 ::::::::::::::: :::::::::::::::::::: : d1hkva2 1 ---------DEDDFRSRCRETAAA------FGSGANVHYAAKAFLCSEVARWISE--EGL 43 query 54 GTTSSSLFEVRLGRERFGK------ETHAYSVAYGDNEIDEVVS-HADKIIFNSISQLER 106 ::::::::::::::: ::::::::::::::::::: ::::::::::::::: d1hkva2 44 CLDVCTGGELAVALH----ASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIER 99 query 107 FADKAA-----GIARGLRLNP-----------------QRLGEWDV----PKVERVMD-- 138 ::::: ::::::::: ::::: :::::::: d1hkva2 100 LDAIA-GEAGIVQDVLVRLT-VGVEAHTHEFISTAHEDQKFGL---SVASGAAMAAVRRV 154 query 139 ------RINGFMIHNNCENKDFGLFDRMLGEIEERFGALIAR----------------VD 176 :::::::::::::::::::::::::::: :: d1hkva2 155 FATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIG--------LLRDVVGEFGPEKTAQIA 206 query 177 WVSLGGGIHFTGDDY------------PVDAFSARLRAFSDRY--------GVQIYLEPG 216 ::::::: ::::::::::::::: ::::::::: d1hkva2 207 TVDLGGG--------LGISYLPSDDPPPIAELAAKLGTIVSD-ESTAVGLPTPKLVVEPG 257 query 217 EASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGK 276 ::::::: d1hkva2 258 RAIAGPG----------------------------------------------------- 264 query 277 SCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVR 336 d1hkva2 265 ------------------------------------------------------------ 265 query 337 EFTYADYEQSLS- 348 d1hkva2 265 ------------T 265 TMalign alignment (TM-score: 0.54 Raw score:186.58) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::::::: ::::::::::::::::::::::::::::::::: d1hkva2 1 ---------DEDDFRSRCRETAAAFG-SGANVHYAAKAFLCSEVARWISEEGLCLDVCTG 50 query 61 FEVRLGRER-FG-KETHAYSVAYGDNEIDEVVSH-ADKIIFNSISQLERFADKAA---G- 113 ::::::::: :: ::::::::::::::::::::: :::::::::::::::::::: : d1hkva2 51 GELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIV 110 query 114 IARGLRLNPQ----------------RLGEW---D-VPKVERVMD-R---IN-GFMIHNN 148 :::::::::: ::::: : ::::::::: : :: ::::::: d1hkva2 111 QDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIG 170 query 149 CENKDFGLFDRMLGEIEERFGALI----A--R--VDWVSLGGGIHFT-----GDDYPVDA 195 :::::::::::::::::::::::: : : ::::::::::::: :::::::: d1hkva2 171 SQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAEL 230 query 196 FSARLRAFS--DR----YGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAH 249 ::::::::: :: :::::::::::::::::: d1hkva2 231 AAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGT------------------------- 265 query 250 MLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTM 309 d1hkva2 266 ------------------------------------------------------------ 266 query 310 VKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1hkva2 266 --------------------------------------- 266 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRER 69 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::: d1hkva2 1 DEDDFRSRCRETAAAFG-SGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHA 59 query 70 FGKETHAYS--VAYGDNEIDEVVSHAD-KIIFNSISQLERFADKAAGIA----RGLRLNP 122 ::::::::: :::::::::::::::: ::::::::::::::::::::: ::::::: d1hkva2 60 SFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTV 119 query 123 ----------------QRLGEWDVP--KVERVMDR-------INGFMIHNNCENKDFGLF 157 ::::::::: :::::::: :::::::::::::::::: d1hkva2 120 GVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGF 179 query 158 DRMLGEIEERFGAL--------IARVDWVSLGGGIHFTGDDYP----VDAFSARLRAFSD 205 :::::::::::::: ::::::::::::::::::::: ::::::::::::: d1hkva2 180 ELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVS 239 query 206 RY-------GVQIYLEPGEASITKS 223 :: :::::::::::::::: d1hkva2 240 DESTAVGLPTPKLVVEPGRAIAGPG 264
Intermediate <-- 0.997 --> HitDALI alignment (Z-score: 16.9 Raw score:1614.70) d1hkva2 1 -DEDDFRSRCRETAAAFGSgaNVHYAAKAFL----CSEVARWISEEGL-CLDVCTGGELA 54 :::::::::::::::::: :::::::::: ::::::::::::: ::::::::::: d1bd0a2 1 vDLDAIYDNVENLRRLLPDdtHIMAVVKANAyghgDVQVARTALEAGAsRLAVAFLDEAL 60 d1hkva2 55 VALHASFPPeRITLHGNnKSVSELTAAVKAGVgHIVVDSMTEIERLDAIAGeAGIVQDVL 114 ::::::::: ::::::: :::::::::::::: :::::::::::::::::: :::::::: d1bd0a2 61 ALREKGIEA-PILVLGA-SRPADAALAAQQRI-ALTVFRSDWLEEASALYS-GPFPIHFH 116 d1hkva2 115 VRLTVGVeahthefistahedQKFGLSvASGAAMAAVRRVFATDHLRLVGLHSHIGsQIF 174 ::::::: :::::: :::::::::::::::::::::::::::: ::: d1bd0a2 117 LKMDTGM--------------GRLGVK-DEEETKRIVALIERHPHFVLEGLYTHFAtADE 161 d1hkva2 175 D-VDGFELAAHRVIGLLRDVVgefgpektAQIATVDLGGGLgisylpsddpppiAELAAK 233 : ::::::::::::::::::: :::::::::::: :::::: d1bd0a2 162 VnTDYFSYQYTRFLHMLEWLP--------SRPPLVHCANSA-----------asLRFPDR 202 d1hkva2 234 lgtivsdestavglptpKLVVEPGRAIA---------------GPGT 265 ::::::::::: :::: d1bd0a2 203 ----------------tFNMVRFGIAMYglapspgikpllpypLKEA 233 FAST alignment (Normalized score: 11.57 Raw score:2874.00) d1hkva2 1 D--EDDFRSRCRETAAAFGSGA----NVHYAAKAFL-------CSEVARWISEEG-LCLD 46 ::::::::::::::: ::::::: :::::::::::: :::: d1bd0a2 1 -VDLDAIYDNVENLRRLL----PDDTHIMAVVK---ANAYGHGDVQVARTALEAGASRLA 52 d1hkva2 47 VCTGGELAVALHASFPPE--RITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIA 104 ::::::::::::::: ::::: ::::::::::::::: ::::::::::::::::: d1bd0a2 53 VAFLDEALALREKGI---EAPILVL-GASRPADAALAAQQR-IALTVFRSDWLEEASAL- 106 d1hkva2 105 G-EAGIVQDVLVRLTVGVEAHTHEFISTAHED--QKFGLSVA--SGAAMAAVRRVFATDH 159 :::::::::::::: ::::: :::::::::::::::: d1bd0a2 107 -YSGPFPIHFHLKMDT----------------GMGRLGV---KDEEETKRIVALIERHPH 146 d1hkva2 160 LRLVGLHSHIGSQ----IFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQ----IATVDLG 211 :::::::::: :::::::::::::::::::: :::: d1bd0a2 147 FVLEGLYTHF---ATADEVNTDYFSYQYTRFLHMLEW------------LPSRPPLV--- 188 d1hkva2 212 GGLGISYLPSDDPPPIAE------LAAKLGTIVSDESTAVGLPTPK---LVVEPGRAIAG 262 ::::::: ::::::::: d1bd0a2 189 ------------------HCANSAASLRFPD---------------RTFNMVRFGIAM-- 213 d1hkva2 263 PGT-------------------- 265 d1bd0a2 214 ---YGLAPSPGIKPLLPYPLKEA 233 TMalign alignment (TM-score: 0.67 Raw score:178.29) d1hkva2 1 -DEDDFRSRCRETAAAFGSGANVHYAAK---AF-LCSEVARWISEEGL-CLDVCTGGELA 54 ::::::::::::::::::::::::::: :: :::::::::::::: ::::::::::: d1bd0a2 1 VDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEAL 60 d1hkva2 55 VALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVL 114 ::::::::: ::::::: :::::::::::::: ::::::::::::::::::: ::::::: d1bd0a2 61 ALREKGIEA-PILVLGA-SRPADAALAAQQRI-ALTVFRSDWLEEASALYSG-PFPIHFH 116 d1hkva2 115 VRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIF 174 :::::: : : : :::::: :::::::::::::::::::::::::::::: d1bd0a2 117 LKMDTG-M-----------G-R-LGVKDE-EETKRIVALIERHPHFVLEGLYTHFATADE 161 d1hkva2 175 DVD-GFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAK 233 ::: ::::::::::::::::: : ::::::::: :: ::: :::: d1bd0a2 162 VNTDYFSYQYTRFLHMLEWLP-------S-RPPLVHCAN-SA---------ASL-RFPD- 201 d1hkva2 234 LGTIVSDESTAVGLPTPKLVVEPGRAIAGP---------------GT 265 :: ::::::::::::: :: d1bd0a2 202 RT---------------FNMVRFGIAMYGLAPSPGIKPLLPYPLKEA 233 HHsearch alignment (Probability: 1.00 E-value:0.00) d1hkva2 1 DEDDFRSRCRETAAAFGSGANVHYAAKAFL----CSEVARWISEEG-LCLDVCTGGELAV 55 :::::::::::::::::::::::::::::: :::::::::::: ::::::::::::: d1bd0a2 2 DLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALA 61 d1hkva2 56 ALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLV 115 ::::::::::::::: :::::::::::::: :::::::::::::::::: ::::::::: d1bd0a2 62 LREKGIEAPILVLGA--SRPADAALAAQQRI-ALTVFRSDWLEEASALYS-GPFPIHFHL 117 d1hkva2 116 RLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQI-F 174 :::: :: ::::::::::::: :::::::::::::::::::::::: : d1bd0a2 118 KMDT------------GM--GRLGVKDEEETKR-IVALIERHPHFVLEGLYTHFATADEV 162 d1hkva2 175 DVDGFELAAHRVIGLLR 191 ::::::::::::::::: d1bd0a2 163 NTDYFSYQYTRFLHMLE 179