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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1tf7a1 | Circadian clock protein KaiC | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
| Hit | d1t64a_ | Histone deacetylase 8, HDAC8 | Arginase/deacetylase | Arginase/deacetylase | α/β |
Query <-- 1.007 --> IntermediateDALI alignment (Z-score: 2.3 Raw score:411.50) query 1 ----------------------------------------------------sLQLRLAL 8 ::::::: d1tf7a1 1 ehqaiakmrtmiegfddishgglpigrstlvsgtsgtgktlfsiqflyngiieFDEPGVF 60 query 9 NQID------------------------------------stvgDIAGNAEAILRWTRHS 32 :::: :::::::::::::::: d1tf7a1 61 VTFEetpqdiiknarsfgwdlaklvdegklfildaspdpegqevVGGFDLSALIERINYA 120 query 33 A-EQGAHLVAFPemALTGypvedlalrssFVEASRTALRELAARLAEEgfgELPVLVGYl 91 : :::::::::: :::: ::::::::::::::::::: :::::::: d1tf7a1 121 IqKYRARRVSID--SVTS-----vfqqydASSVVRRELFRLVARLKQI---GATTVMTT- 169 query 92 drsesaqpkygqpagAPRNaaavlhrgrVALTFAKHHLPNygvfdefryfvpgdtmpivr 151 :::: :::::::::::: d1tf7a1 170 ---------erieeyGPIA-rygveefvSDNVVILRNVLE---------------gerrr 204 query 152 lhgvdialaicedlwqdgGRVPaarsagaglllsvnaspyerdkddtrlelvrkRAQEAg 211 :::: ::::: d1tf7a1 205 rtleilklrgtshmkgeyPFTI--------------------------------TDHGI- 231 query 212 cttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaaeaePPTGvv 271 :::: d1tf7a1 232 ---------------------------------------------------nifPLGA-- 238 query 272 ddglridrlviseeplpayeaelaggyadrl 302 d1tf7a1 239 ---------------------------mrlt 242 FAST alignment (Normalized score: 2.60 Raw score:703.80) query 1 ----------------------------------------------------SLQLRLAL 8 :::::::: d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 query 9 NQIDST-----------------------------------------VGDIAGNAEAILR 27 : ::::::::::::: d1tf7a1 61 V-----TFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIE 115 query 28 WTRHSA-EQGAHLVAFPEMALTGYPVEDLALRSS----------FVEASRTALRELAARL 76 :::::: :::::::::: :::::::::::::::: d1tf7a1 116 RINYAIQKYRARRVSID-----------------SVTSVFQQYDASSVVRRELFRLVARL 158 query 77 AEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG---------------RVA 121 ::: :::::::::: ::: d1tf7a1 159 KQI---GATTVMTTER--------------------------IEEYGPIARYGVEEFVSD 189 query 122 LTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAG 181 :::::::: d1tf7a1 190 NVVILRNV---------------------------------------------------- 197 query 182 LLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEV 241 d1tf7a1 198 ------------------------------------------------------------ 198 query 242 VARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADR 301 d1tf7a1 198 ------------------------------------------------------------ 198 query 302 L--------------------------------------------- 302 d1tf7a1 198 -LEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 TMalign alignment (TM-score: 0.33 Raw score:100.58) query 1 -----SLQL------------RL-----ALNQIDSTVGDIAGNAEAILRWTRHSAEQGAH 38 :::: :: ::::::: : :: :: d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTS-------G--TG--KT--------- 40 query 39 LVAF--------PEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGE------L 84 :::: : d1tf7a1 41 LFSIQFLYNGII----------------------------------------EFDEPGV- 59 query 85 PVL-VG-YLDRSESAQPKYGQPAGAPRNAAA-VLHRGRVALT--------FAKHHLPNYG 133 : : ::: ::::: :::::::::: :::::: d1tf7a1 60 --FV-TFEET----------------PQDIIKNARSFGWDLAKLVDEGKLFILDAS---- 96 query 134 VFDEFRYF-------VPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSV 186 ::::: :::::::::::::::::::::::: d1tf7a1 97 ---PDPEGQEVVGGF---------------------DLSALIERINYAIQKYRARRVSID 132 query 187 N-AS--P-YERDKD-DT-RLELVRKRAQEAGCTTAYLAMIGG-----QDELVFDGDSIVV 235 : :: : :::::: :: :::::::::: ::::::::::::: ::::::::: d1tf7a1 133 SVTSVFQQYDASSVVRRELFRLVARLKQ-IGATTVMTTERIEEYGPI----ARYGVEEFV 187 query 236 DRDGEVVARAP--QFSE--------GCVV-LDLDLPAAEAEPPTGVVDDGLRIDRLVISE 284 :::::: :: :::: :::: d1tf7a1 188 -----SDNVVILR--NVLEGERRRRTLEILKLRG-------------------------- 214 query 285 EPLPAYEAELAGG----------------------YADRL 302 :::::: d1tf7a1 215 -------TSHMKGEYPFTITDHGINIFPLGAMRLT----- 242 HHsearch alignment (Probability: 0.01 E-value:0.33) query 203 VRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGC 252 :::::::::::::::::::::::::::::::::::::::::::::::::: d1tf7a1 154 LVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERR 203
Intermediate <-- 1.146 --> HitDALI alignment (Z-score: 6.0 Raw score:772.20) d1tf7a1 1 ------------------------------------------------------------ 1 d1t64a_ 1 lvpvyiyspeyvsmcdslakipkrasmvhslieayalhkqmrivkpkvasmeematfhtd 60 d1tf7a1 1 --------------------------------------------ehqaiakMRTMiegfd 16 :::: d1t64a_ 61 aylqhlqkvsqegdddhpdsieyglgydcpategifdyaaaiggatitaaqCLID----- 115 d1tf7a1 17 dishgGLPIgrSTLVSG-------------tSGTGKTLFSIQFLYNGIiefdEPGVFVTF 63 :::: :::::: ::::::::::::::::: :::::::: d1t64a_ 116 -----GMCK--VAINWSggwhhakkdeasgfCYLNDAVLGILRLRRKF----ERILYVDL 164 d1tf7a1 64 --EETPqDIIKNarsfgwdLAKLvdeGKLFILDASPDPE--------------------- 100 :::: ::::: :::: ::::::::::::: d1t64a_ 165 dlHHGD-GVEDA-------FSFT---SKVMTVSLHKFSPgffpgtgdvsdvglgkgryys 213 d1tf7a1 101 ----gQEVVG-GFDLSALIERINYAIQKYRARRVSIDSVTSvFQQYD---assvVRRELF 152 ::::: :::::::::::::::::::::::::::::: ::::: :::::: d1t64a_ 214 vnvpiQDGIQdEKYYQICESVLKEVYQAFNPKAVVLQLGAD-TIAGDpmcsfnmTPVGIG 272 d1tf7a1 153 RLVARLKQIGATTVMTTErieeygpiaRYGVE---EFVSD-nvvilrnvlegerrrrtle 208 :::::::::::::::::: ::::: ::::: d1t64a_ 273 KCLKYILQWQLATLILGG--ggynlanTARCWtylTGVILgktlsseipdhefftaygpd 330 d1tf7a1 209 ilklrgtshmkgeypftitdhginifplgamrlt 242 d1t64a_ 331 yvleitpscrpdrnephriqqilnyikgnlkhvv 364 FAST alignment (Normalized score: 4.69 Raw score:1392.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIG---------------------------------- 26 d1t64a_ 1 --------------------------LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEA 34 d1tf7a1 27 ------------------------------------------------------------ 27 d1t64a_ 35 YALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEG 94 d1tf7a1 27 ------------------------RSTLVSGTSGTGKT-------------------LFS 43 ::::: ::: d1t64a_ 95 IFDYAAAIGGATITAAQCLIDGMCKVAIN---------WSGGWHHAKKDEASGFCYLNDA 145 d1tf7a1 44 IQFLYNGIIEFDEPGVFVT-FEETPQDIIKNARSFGWDLAKL--VDEGKLFILDASPDPE 100 ::::::::::: ::::::: :::::::::: ::::::::::::: d1t64a_ 146 VLGILRLRRKF-ERILYVDLDLHHGDGVED------------AFSFTSKVMTVSLHK--- 189 d1tf7a1 101 ----------------------------GQEV-VGGFDLSALIERINYAIQKYRARRVSI 131 :::: ::::::::::::::::::::::::::: d1t64a_ 190 FSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVL 249 d1tf7a1 132 DSVTSVFQQYDASSV-----------------VRRELFRLVARLKQIGATTVMT-TERIE 173 :::::::::::::::::::::: ::::: d1t64a_ 250 ---------------QLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYN 294 d1tf7a1 174 EYGPIAR------YGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTIT 227 : ::::::: d1t64a_ 295 L------ANTARCWTYLTGV---------------------------------------- 308 d1tf7a1 228 DHGINIFPLGAMRLT--------------------------------------------- 242 d1t64a_ 309 ---------------ILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQIL 353 d1tf7a1 243 ----------- 243 d1t64a_ 354 NYIKGNLKHVV 364 TMalign alignment (TM-score: 0.51 Raw score:123.30) d1tf7a1 1 EHQAIAK------------------------------------------------MRTM- 11 :::: : d1t64a_ 1 ---LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASME---EM 54 d1tf7a1 12 ------------------------------------------------IE--GFDDISH- 20 :: ::::::: d1t64a_ 55 ATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLI 114 d1tf7a1 21 GGLPIGRSTLVSGTSG----------TGKTLFSIQFLYNGIIEFDEPGVFVT-FEETPQD 69 ::::: : :::::::: ::::::::::::::: :::::::::: ::::::: d1t64a_ 115 DGMCK-V-AINWSGGWHHAKKDEASGFCYLNDAVLGILRLR-RKFERILYVDLDLHHGDG 171 d1tf7a1 70 IIKNARSFGWDLAKLVDEGKLFILDASPDPE--------------------------GQE 103 ::: : :::: ::::::::::::: ::: d1t64a_ 172 VED-A------FSFT---SKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDG 221 d1tf7a1 104 VVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQ------QYDASSVVRRELFRLVAR 157 :::::::::::::::::::::::::::::::::::: ::: :: ::::::::: d1t64a_ 222 IQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNM---TP-VGIGKCLKY 277 d1tf7a1 158 LKQIGATTVMTTE-RIEEYGPIARY--GVEEFVSDN------------------------ 190 ::::::::::::: ::: :::::: ::::::::: d1t64a_ 278 ILQWQLATLILGGGGYN--LANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEI 335 d1tf7a1 191 -----------------------------VVILRNVLEGERRRRTLEILKLRGTSHMKGE 221 d1t64a_ 336 TPSCRPDRNEPHRIQQILNYIKGNLKHVV------------------------------- 364 d1tf7a1 222 YPFTITDHGINIFPLGAMRLT 242 d1t64a_ 365 --------------------- 365 HHsearch alignment (Probability: 0.43 E-value:0.01) d1tf7a1 46 FLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDL---AKLVDEGKLFILDASP----- 97 :::::::::::::::::::::::::::::::::::: :::::::::::::::: d1t64a_ 147 LGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGL 206 d1tf7a1 98 -----DPE---GQEVVGGFDLSALIER-INYAIQKYRARRVSIDSVTSVF--QQYDASSV 146 ::: :::::::::::::::: :::::::::::::::::::::: :::::::: d1t64a_ 207 GKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNM 266 d1tf7a1 147 VRRELFRLVARLKQIGATTVMTTERIEEYGPIA 179 ::::::::::::::::::::::::::::::::: d1t64a_ 267 TPVGIGKCLKYILQWQLATLILGGGGYNLANTA 299