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 | d1dxea_ | 2-dehydro-3-deoxy-galactarate aldolase | Phosphoenolpyruvate/pyruvate domain | 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 <-- 0.914 --> HitDALI alignment (Z-score: 9.3 Raw score:993.70) d1hkva2 1 deddfrsrcretaaafgsgaNVHYAAKaFLCSEVARWISEEGL-CLDVCT------GGEL 53 ::::::: ::::::::::::::: :::::: :::: d1dxea_ 1 ----dvfpnkfkaalaakqvQIGCWSA-LSNPISTEVLGLAGFdWLVLDGehapndISTF 55 d1hkva2 54 AVALHASF-ppeRITLHGNNKSVSELTAAVKAGVGHIVVD----sMTEIERLDaIAGE-- 106 :::::::: :::::::::::::::::::::::::::: :::::::: :::: d1dxea_ 56 IPQLMALKgsasAPVVRVPTNEPVIIKRLLDIGFYNFLIPfvetkEEAELAVA-STRYpp 114 d1hkva2 107 -----------------------AGIV-QDVLVRLTVGveahthefistahedqkfgLSV 142 :::: :::::::::: ::: d1dxea_ 115 egirgvsvshranmfgtvadyfaQSNKnITILVQIESQ-------------------QGV 155 d1hkva2 143 AsgAAMAAVRRVfatdhlRLVGLHSHIG------sqiFDVDG--FELAAHRVIGLLRDVV 194 : ::::::::: :::::::::: ::::: :::::::::::::::: d1dxea_ 156 D--NVDAIAATE------GVDGIFVGPSdlaaalghlGNASHpdVQKAIQHIFNRASAHG 207 d1hkva2 195 gefgpektaqiATVDLGGGlgisylpsddpppIAELAAKLGTIVsdestavglptpkLVV 254 :::::::: :::::::::::: ::: d1dxea_ 208 -----------KPSGILAP-------------VEADARRYLEWG------------aTFV 231 d1hkva2 255 EPG--RAIAGPGT--------- 265 ::: :::::::: d1dxea_ 232 AVGsdLGVFRSATqkladtfkk 253 FAST alignment (Normalized score: 6.69 Raw score:1733.00) d1hkva2 1 DEDDFRSRCRETAAAFGSGA----------------NVHYAAKAFLCSEVARWISEEG-L 43 :::::: ::::::::::::::: : d1dxea_ 1 --------------------DVFPNKFKAALAAKQVQIGCWS-ALSNPISTEVLGLAGFD 39 d1hkva2 44 CLDV------CTGGELAVALHASFPPE-------RITLHGN--NKSVSELTAAVKAGVGH 88 :::: ::::::::::: ::::: ::::::::::::::::: d1dxea_ 40 WLVLDGEHAPNDISTFIPQLM------ALKGSASAPVVR--VPTNEPVIIKRLLDIGFYN 91 d1hkva2 89 IVV---DSMTEIERLDAIAGEAGI-------------------------------VQDVL 114 ::: ::::::::::::: ::::: d1dxea_ 92 FLIPFVETKEEAELAVAST-----RYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITIL 146 d1hkva2 115 VRLTVGVEAHTHEFISTAHEDQKFGLSVAS-------GAAMAAVRRVFATDHL--RLVGL 165 :: :::::::: ::::: d1dxea_ 147 VQ----------------------------IESQQGVDNVDAIAA--------TEGVDGI 170 d1hkva2 166 HSHIGSQIFD---------------VDGFELAAHRVIGLLRDVVGEFGPEKTAQI--ATV 208 ::: ::::::::::::::::: ::: d1dxea_ 171 FVG-------PSDLAAALGHLGNASHPDVQKAIQHIFNRASA-------------HGKPS 210 d1hkva2 209 DLGGGLGISYLPSDDPPP---IAELAAKLGTIVSDESTAVGLPTPK---LVVE--PGRAI 260 :: :::::::::: :::: ::::: d1dxea_ 211 GI----------------LAPVEADARRYLE---------------WGATFVAVGSDLGV 239 d1hkva2 261 AGPGT---------- 265 :::: d1dxea_ 240 FRSA-TQKLADTFKK 253 TMalign alignment (TM-score: 0.54 Raw score:143.46) d1hkva2 1 ---------------DEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGL-C 44 : ::::::: ::::::::::::::: : d1dxea_ 1 DVFPNKFKAALAAKQ-----------------V-QIGCWSA--LSNPISTEVLGLAGFDW 40 d1hkva2 45 LDVCT-----GG-ELAVALHASF-PPERITLHGNNKSVSELTAAVK-AGVGHIVVDS-M- 94 ::::: :: :::::::::: :::::::::::::::::::::: :::::::::: : d1dxea_ 41 LVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETK 100 d1hkva2 95 TEIERLDAIAGE--------------------------AGIVQDVLVRLTVGVEAHTHEF 128 :::::::::::: :::::::::::: d1dxea_ 101 EEAELAVASTRYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQIE---------- 150 d1hkva2 129 ISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIG---------SQIFDVDGF 179 :: : :::::::::::: ::::::::::: ::: d1dxea_ 151 -----------SQ--Q-GVDNVDAIAATE--GVDGIFVGPSDLAAALGHLG------NAS 188 d1hkva2 180 EL-AAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIV 238 :: ::::::::::::: : :: :: ::::: : :: :::::: d1dxea_ 189 HPDVQKAIQHIFNRAS---A--HG-KP-SGILA--P---------------VE-ADARRY 223 d1hkva2 239 SDESTAVGLPTPK-LVVEPGRAIAG-PGT-------- 265 :: : ::: ::::::::::: ::: d1dxea_ 224 LE-W------GATFVAVGSDLGVFRSATQKLADTFKK 253 HHsearch alignment (Probability: 0.92 E-value:0.00) d1hkva2 11 ETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVC-------TGGE---LAVALHAS 60 :::::::::::::::::::::::::::::::::::::: :::: ::::::: d1dxea_ 6 KFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG- 64 d1hkva2 61 FPPERITLHGNNKSVSELTAAVKAGVGHIV---VDSMTEIERLDAIAGEAGIVQDVLVRL 117 ::::::::::::::::::::::::::::: :::::::::::::::: ::::::: d1dxea_ 65 -SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRY----PPEGIRG 119 d1hkva2 118 TV-----GVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRL 162 :: ::::::::::::::::::::::::::::::::::::::::::: d1dxea_ 120 VSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDG 169