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 | d1f2t.1 | Rad50 | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 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 <-- 1.430 --> HitDALI alignment (Z-score: 7.1 Raw score:807.80) d1tf7a1 1 ehqaiakMRTMI--------EGFDdishgGLPIgRSTLVSGTSGTGKTLFSIQFLYNGII 52 ::::: :::: :::: :::::::::::::::::::::::::: d1f2t.1 1 -----mkLERVTvknfrshsDTVV-----EFKE-GINLIIGQNGSGKSSLLDAILVGLYW 49 d1tf7a1 53 efdepgvfvtfeetpqdiikNARSFG---------------------------------- 78 :::::: d1f2t.1 50 ------------------plRIKDIKkdeftkvgardtyidlifekdgtkyritrrflkg 91 d1tf7a1 79 --------------------------wdlAKLVdEGKLFI------lDASP--------- 97 :::: :::::: :::: d1f2t.1 92 eihamkrlvgnewkhvtepsskaisafmeKLIP-YNIFLNaiyirqgQIDAilesareaa 150 d1tf7a1 98 -----------------------------------------dpegQEVVGGFDLSALIER 116 ::::::::::::::: d1f2t.1 151 lskigelaseifaeftegkysevvvraeenkvrlfvvwegkerplTFLSGGERIALGLAF 210 d1tf7a1 117 INYAIQKY--RARRVSIDSVtSVFQqydasSVVRRELFRLVA-RLKQiGATTVMTTErie 173 :::::::: :::::::::: :::: :::::::::::: :::: ::::::::: d1f2t.1 211 RLAMSLYLagEISLLILDEP-TPYL----dEERRRKLITIMErYLKK-IPQVILVSH--- 261 d1tf7a1 174 eygpiaryGVEEFVSDNVVILRNVLegerRRRTLEILKlrgtshmkgeypftitdhgini 233 ::::::::::::::::: ::::::::: d1f2t.1 262 -------dEELKDAADHVIRISLEN----GSSKVEVVS---------------------- 288 d1tf7a1 234 fplgamrlt 242 d1f2t.1 289 --------- 289 FAST alignment (Normalized score: 4.74 Raw score:1250.00) d1tf7a1 1 EHQAIAK---MRTMIEGFDDISHG------------GLPIGRSTLVSGTSGTGKTLFSIQ 45 :::: :::: ::::::::::::::::::: d1f2t.1 1 -------MKLERVT----------VKNFRSHSDTVVEFKE-GINLIIGQNGSGKSSLLDA 42 d1tf7a1 46 FLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEV- 104 ::::: d1f2t.1 43 ILVGL------------------------------------------------------Y 48 d1tf7a1 105 ------------------------------------------------------------ 105 d1f2t.1 49 WPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGEIHAMKRLVGNEWKHVT 108 d1tf7a1 105 ------------------------------------------------------------ 105 d1f2t.1 109 EPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESAREAALSKIGELASEIFAEFTEG 168 d1tf7a1 105 ------------------------------VGGFDLSALIERINYAIQK--YRARRVSID 132 ::::::::::::::::::: ::::::::: d1f2t.1 169 KYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILD 228 d1tf7a1 133 SVTSVFQQYDASSV----VRRELFRLVA----RLKQIGATTVMTTERIEEYGPIARYGVE 184 :: :::::::::: ::::: :::::: :::::: d1f2t.1 229 EP------------TPYLDEERRRKLITIMERYLKKI-PQVILV----------SHDEEL 265 d1tf7a1 185 EFVSDNVVILRNVLEGER--RRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 :::::::::::: ::::::: d1f2t.1 266 KDAADHVIRISL------ENGSSKVEV--------------------------------- 286 d1tf7a1 243 -- 243 d1f2t.1 287 VS 288 TMalign alignment (TM-score: 0.43 Raw score:104.70) d1tf7a1 1 EHQAIAKMRTMI---------EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGI 51 ::::::: :::: ::: :::::::::::::::::::::: : d1f2t.1 1 -----MKLERVTVKNFRSHSDTVVE-----FKE--GINLIIGQNGSGKSSLLDAILV--G 46 d1tf7a1 52 IEFDEPGVFVTFEETPQDIIKNARS---------FGW-----------------D--LAK 83 :::: :: :::::: ::: : :: d1f2t.1 47 -----LYWP------LR--IKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLK-GE 92 d1tf7a1 84 -L----------------VDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRA 126 : :::::: ::::::: d1f2t.1 93 IHAMKRLVGNEWKHVTEPSSKAIS-----------------------------AFMEKLI 123 d1tf7a1 127 RR--V----SIDS-VTSVFQQY-------------------------------------- 141 :: : :::: :::::::: d1f2t.1 124 PYNIFLNAIYIRQGQIDAILESAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVR 183 d1tf7a1 142 -----------D--A----S-SVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGV 183 : : : ::::::::::::::::::::::::::::::::::: ::: d1f2t.1 184 LFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERR-RKL 242 d1tf7a1 184 EEF---VS--D--NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 236 ::: :: : :::::::: ::::::: :: ::::::::: ::::: d1f2t.1 243 ITIMERYLKKIPQVILVSHDE--------ELKDAAD----HV--IRISLENGS-SKVEV- 286 d1tf7a1 237 GAMRLT 242 :: d1f2t.1 287 VS---- 288 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 121 IQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIAR 180 :::::::::::::::::: ::: ::::::::::::::::::::::::::: d1f2t.1 217 YLAGEISLLILDEPTPYL----DEE-RRRKLITIMERYLKKIPQVILVSHDEE------- 264 d1tf7a1 181 YGVEEFVSDNVVILRNVLEGERR 203 :::::::::::::::::::: d1f2t.1 265 ---LKDAADHVIRISLENGSSKV 284