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 | d1ct5a_ | (Hypothetical( protein ybl036c | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1kcxa2 | Dihydropyrimidinase related protein-1 | Metallo-dependent hydrolases | TIM beta/alpha-barrel | α/β |
Query <-- 1.881 --> IntermediateDALI alignment (Z-score: 13.8 Raw score:1257.60) query 1 mietpyyLIDK-AKLTRNMERIAHVREKS----GAKALLALKcFATWSVFDLMR-DYMDG 54 :::: ::::::::::::::::: ::::::::: ::::::::::: ::::: d1ct5a_ 1 --tgityDEDRkTQLIAQYESVREVVNAEaknvKILLLVVSK-LKPASDIQILYdHGVRE 57 query 55 TTSSSLFEVRLGRERFG--KETHAYSVAYGDnEIDEVVSH--ADKII-FNSISQLERFAD 109 ::::::::::::::::: :::::::::::: :::::::: ::::: :::::::::::: d1ct5a_ 58 FGENYVQELIEKAKLLPddIKWHFIGGLQTN-KCKDLAKVpnLYSVEtIDSLKKAKKLNE 116 query 110 KAA-------GIARGLRLNPQ----RLGEWDVPKVER-VMDR---------INGFMIHNN 148 ::: ::::::::::: :::::::::::: :::: ::::::::: d1ct5a_ 117 SRAkfqpdcnPILCNVQINTShedqKSGLNNEAEIFEvIDFFlseeckyikLNGLMTIGS 176 query 149 CenkdfglfDRMLGEIEERFGALI---aRVDWVSLGGGIhftgddypvdafsARLRAFSd 205 : ::::::::::::::: ::::::::::: ::::::: d1ct5a_ 177 W--------NRDFATLVEWKKKIDakfgTSLKLSMGMSA-----------dfREAIRQG- 216 query 206 rygvqIYLEPGEASITksttlevtvldtlynknlaivdssieahmldlliyretakvlpn 265 ::::::::::: d1ct5a_ 217 ----tAEVRIGTDIFG-------------------------------------------- 228 query 266 egshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiai 325 d1ct5a_ 229 ------------------------------------------------------------ 229 query 326 reldgsvrtvreftyadyeqsls 348 d1ct5a_ 229 ----------------------- 229 FAST alignment (Normalized score: 7.94 Raw score:2236.00) query 1 MIETPYYLI--------DKAKLTRNMERIAHVREK----SGAKALLALKCFATWSVFDLM 48 :::::::::::::::::: ::::::::::: ::::::::: d1ct5a_ 1 ---------TGITYDEDRKTQLIAQYESVREVVNAEAKNVKILLLVVSKL-KPASDIQIL 50 query 49 RD-YMDGTTSSSLFEVRLGRERFG---KETHAYSVAYGDNEIDEVV--SHADKI-IFNSI 101 :: :::::::::::::::::::: ::::::: ::::::::::: :::::: ::::: d1ct5a_ 51 YDHGVREFGENYVQELIEKAKLL-PDDIKWHFIG-GLQTNKCKDLAKVPNLYSVETIDSL 108 query 102 SQLERFADKAA--------GIARGLRLNP-----QRLGEWDVPKVERVMD---------- 138 :::::::::: ::::::::: :::::::::::::::: d1ct5a_ 109 KKAKKLNESR-AKFQPDCNPILCNVQIN-TSHEDQKSGLNNEAEIFEVIDFFLSEECKYI 166 query 139 RINGFMIHNNCENKDFGL-FDRMLGEIEERFGALIARVDWV---------SLGGGIHFTG 188 ::::::::: ::::::::::::::::: :::: d1ct5a_ 167 KLNGLMTIG---------SWNRDFATLVEWKKKIDA-----KFGTSLKLSMGMS------ 206 query 189 DDYPVDAFSA-RLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIE 247 ::::::: ::: :::::::::: d1ct5a_ 207 ----------ADFREAIR-QGT-AEVRIGTDIF--------------------------- 227 query 248 AHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGY 307 d1ct5a_ 228 ------------------------------------------------------------ 228 query 308 TMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d1ct5a_ 228 -----------------------------------------G 228 TMalign alignment (TM-score: 0.46 Raw score:159.99) query 1 -----MIETPYYLIDKAKLTRNMERIAHVREK-S---GAKALLALKCFATWSVFDLMR-D 50 ::::::::::::::::::::: : ::::::::::: ::::::::: : d1ct5a_ 1 TGITY------DEDRKTQLIAQYESVREVVNAEAKNVKILLLVVSKLK-PASDIQILYDH 53 query 51 YMDGTTSS-SLFEVRLGRERF-GKETHAY-SVAY-GDNEIDEVVSHADKII-FNSISQLE 105 :::::::: :::::::::::: ::::::: :::: :::::::: ::::::: :::::::: d1ct5a_ 54 GVREFGENYVQELIEKAKLLPDDIKWHFIGGLQTNKCKDLAKV-PNLYSVETIDSLKKAK 112 query 106 RFADKAA-------GIARGLRLNPQ----RLGEWDVPKVERVMD-R---------INGFM 144 ::::::: ::::::::::: ::::::::::::::: : ::::: d1ct5a_ 113 KLNESRAKFQPDCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLM 172 query 145 IHNNCENKDFGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLR 201 ::::: :::::::::::::::: ::::::::::::: :: ::: d1ct5a_ 173 TIGSW--------NRDFATLVEWKKKIDAKFGTSLKLSMGMSADF---------RE-AIR 214 query 202 AFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAK 261 ::: ::::::::::: d1ct5a_ 215 QGT------AEVRIGTDIFG---------------------------------------- 228 query 262 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMP 321 d1ct5a_ 229 ------------------------------------------------------------ 229 query 322 AIAIRELDGSVRTVREFTYADYEQSLS 348 d1ct5a_ 229 --------------------------- 229 HHsearch alignment (Probability: 0.69 E-value:0.00) query 11 KAKLTRNMERIAHVRE----KSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLG 66 :::::::::::::::: :::::::::::::::::::::::::::::::::::::::: d1ct5a_ 10 KTQLIAQYESVREVVNAEAKNVKILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEK 69 query 67 RERFGKETHAYSVA----YGDNEIDEVVSHADKIIFNSISQLERFADKAAGIA------- 115 :::::::::::::: ::::::::::::::::::::::::::::::::::: d1ct5a_ 70 AKLLPDDIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNPIL 129 query 116 RGLRLN----PQRLGEWDVPKVERVM-----DRINGFMIHNNCENKDFGLFDRMLGEIEE 166 :::::: :::::::::::::::: ::::::::::::::::::::::::::::: d1ct5a_ 130 CNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLMTIGSWNRDFATLVEWKK 189 query 167 RFGALIARVDWVSLG 181 ::::::::::::::: d1ct5a_ 190 KIDAKFGTSLKLSMG 204
Intermediate <-- 1.150 --> HitDALI alignment (Z-score: 9.3 Raw score:1029.40) d1ct5a_ 1 -------------------------------------tgitydedrktQLIAQYESVREV 23 :::::::::::: d1kcxa2 1 pggidvntylqkpsqgmtsaddffqgtkaalaggttmiidhvvpepgsSLLTSFEKWHEA 60 d1ct5a_ 24 VNAEAKnVKILLLVVSKLK---PASDIQILYD-HGVREFGENY---------vQELIEKA 70 :::::: :::::::::::: :::::::::: :::::::::: ::::::: d1kcxa2 61 ADTKSC-CDYSLHVDITSWydgVREELEVLVQdKGVNSFQVYMaykdlyqmsdSQLYEAF 119 d1ct5a_ 71 KLL-PDDIKWHFIGG------------------------------lQTNKCKDLAKVP-- 97 ::: ::::::::::: :::::::::::: d1kcxa2 120 TFLkGLGAVILVHAEngdliaqeqkrilemgitgpeghalsrpeelEAEAVFRAIAIAgr 179 d1ct5a_ 98 --NLYSVETIDSLKKAKKLNESRAkfqPDCNpILCNVQIN---------------tshED 140 :::::::::::::::::::::: :::: :::::::: :: d1kcxa2 180 inCPVYITKVMSKSAADIIALARK---KGPL-VFGEPIAAslgtdgthywsknwakaaAF 235 d1ct5a_ 141 QK--SGLNNEAEIFEVIDFFLSeeckyiKLNGLMTIGSW-------------------nr 179 :: :::::::::::::::::: ::::::::::: d1kcxa2 236 VTspPLSPDPTTPDYLTSLLAC-----gDLQVTGSGHCPystaqkavgkdnftlipegvn 290 d1ct5a_ 180 DFATLVEWKKKID--AKFG-----TSLKlsmgmsadfreairqgtaevrigtdifg 228 ::::::::::::: :::: :::: d1kcxa2 291 GIEERMTVVWDKAvaTGKMdenqfVAVT------------stnaakifnlyprkgr 334 FAST alignment (Normalized score: 5.72 Raw score:1579.00) d1ct5a_ 1 TGITYDEDRKTQLIA--------------------------------------------- 15 d1kcxa2 1 ---------------PGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPE 45 d1ct5a_ 16 ---QYESVREVVNAEAKN---VKILLLVVSKLK-----PASDIQILYD-HGVREFGE--- 60 ::::::::::::::: :::::::::: :::::::::: :::::::: d1kcxa2 46 PGSSLLTSFEKWHEAADTKSCCDYSLHVDIT--SWYDGVREELEVLVQDKGVNSFQVYMA 103 d1ct5a_ 61 ------NYVQELIEKAKLLP---DDIKWHFIGGL-------------------------- 85 :::::::::::: :::::::: d1kcxa2 104 YKDLYQMSDSQLYEAFTF--LKGLGAVILVH---AENGDLIAQEQKRILEMGITGPEGHA 158 d1ct5a_ 86 -------QTNKCKDLAKVPNL--------YSVETIDSLKKAKKLNESRAKFQPDCN--PI 128 :::::::::: ::::::::::::::::::::: :: d1kcxa2 159 LSRPEELEAEAVFRAIA----IAGRINCPVYITKVMSKSAADIIALARKK------GPLV 208 d1ct5a_ 129 LCNVQINTSHEDQK--------------------------SGLNNEAEIFEVIDFFLSEE 162 ::::: :::::::::::::::: d1kcxa2 209 FGEPI---------AASLGTDGTHYWSKNWAKAAAFVTSPPLSPDPTTPDYLTSLL---- 255 d1ct5a_ 163 CKYI---KLNGLMTIGSWNR-----------------------DFATLVEWKKKIDAKFG 196 ::::::::: :::::::::::: d1kcxa2 256 ----ACGDLQVTGSGH----CPYSTAQKAVGKDNFTLIPEGVNGIEERMTVVWDK----- 302 d1ct5a_ 197 TSLKLSMGMSADFREAIRQGTAEVRIGTDIFG---------------------------- 228 d1kcxa2 303 --------------------------------AVATGKMDENQFVAVTSTNAAKIFNLYP 330 d1ct5a_ 229 ---- 229 d1kcxa2 331 RKGR 334 TMalign alignment (TM-score: 0.62 Raw score:141.89) d1ct5a_ 1 ------------------------------------------------TGITYDEDRKTQ 12 : d1kcxa2 1 PGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPEPGS-----------S 49 d1ct5a_ 13 LIAQYESVREVVNAEAKNVKILLLVVSKLKPASDIQILYDHG----VREFGENY------ 62 :::::::::::::::: ::::::::::::::::::::::::: :::::::: d1kcxa2 50 LLTSFEKWHEAADTKS-CCDYSLHVDITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLY 108 d1ct5a_ 63 -V-Q-ELIEKAKLL-PDDIKWHFIGG------------------------------LQTN 88 : : ::::::::: ::::::::::: :::: d1kcxa2 109 QMSDSQLYEAFTFLKGLGAVILVHAENGDLIAQEQKRILEMGITGPEGHALSRPEELEAE 168 d1ct5a_ 89 KCKDLAK-V---PNLYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQI-----N-T-- 136 ::::::: : :::::::::::::::::::::::::: : :::::::: : : d1kcxa2 169 AVFRAIAIAGRINCPVYITKVMSKSAADIIALARKKGP--L-VFGEPIAASLGTDGTHYW 225 d1ct5a_ 137 -----SHE-DQ-KSGLNN-EAEIFEVIDFFLSEECKYIKLNGLMTIGS------------ 176 ::: :: :::::: :::::::::::::: : ::::::::::: d1kcxa2 226 SKNWAKAAAFVTSPPLSPDPTTPDYLTSLLACG-D--LQVTGSGHCPYSTAQKAVGKDNF 282 d1ct5a_ 177 ---W-NRDFATLVEWKKKIDAKFG---------TS-LKL---------------SMGMSA 207 : ::: :::::::::::::: :: ::: d1kcxa2 283 TLIPE-GVN-GIEERMTVVWDKAVATGKMDENQFVAVTSTNAAKIFNLYPRKGR------ 334 d1ct5a_ 208 DFREAIRQGTAEVRIGTDIFG 228 d1kcxa2 335 --------------------- 335 HHsearch alignment (Probability: 0.03 E-value:0.06) d1ct5a_ 36 LVVSKLKP---ASDIQILYDHGVREF 58 :::::::: ::::::::::::::: d1kcxa2 73 VDITSWYDGVREELEVLVQDKGVNSF 98