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 | d1nn5a_ | Thymidylate kinase | 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 <-- 0.869 --> HitDALI alignment (Z-score: 4.0 Raw score:488.00) d1tf7a1 1 ehqaiakmrtmiegfddishgglpiGRSTLVSGTSGTGKTLFSIQFLYNGIieFDEPgvf 60 :::::::::::::::::::::::::: :::: d1nn5a_ 1 -----------------------rrGALIVLEGVDRAGKSTQSRKLVEALC--AAGH--- 32 d1tf7a1 61 vtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvggfdlsalierinya 120 d1nn5a_ 33 ------------------------------------------------------------ 33 d1tf7a1 121 iqkyraRRVSIDsVTSV---FQQY-----------------DASSVVRRELFRLVARLKQ 160 :::::: :::: :::: ::::::::::::::::::: d1nn5a_ 33 ------RAELLR-FPERsteIGKLlssylqkksdvedhsvhLLFSANRWEQVPLIKEKLS 85 d1tf7a1 161 IGATTVMTTerieeygpIARYG---------------veeFVSDN--VVILRNVLE---- 199 ::::::::: ::::: ::::: ::::::::: d1nn5a_ 86 QGVTLVVDR------yaFSGVAftgakenfsldwckqpdvGLPKPdlVLFLQLQLAdaak 139 d1tf7a1 200 -----------------gerrrrtlEILKlrgtshmkgeyPFTITdHGINI--------- 233 :::: ::::: ::::: d1nn5a_ 140 reryengafqeralrcfhqlmkdttLNWK-------mvdaSKSIE-AVHEDirvlsedai 191 d1tf7a1 234 ----fplgamrlt 242 d1nn5a_ 192 atatekplgelwk 204 FAST alignment (Normalized score: 3.97 Raw score:882.30) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI--GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPG 58 ::::::::::::::::::::::::::: ::::: d1nn5a_ 1 -------------------------RRGALIVLEGVDRAGKSTQSRKLVEALCA-AGHRA 34 d1tf7a1 59 VFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASP----------------DPEGQ 102 ::::: ::::: d1nn5a_ 35 ELLRF----------------------------------PERSTEIGKLLSSYLQKKSDV 60 d1tf7a1 103 EVV-------GGFDLSALIERINYAIQKYRA--RRVSID-SVTSVFQ------QYDASSV 146 : ::::::::::::::::: :::::: :::::: ::::::: d1nn5a_ 61 E--DHSVHLLFSANRWEQVPLIKEKLS----QGVTLVVDRYAFSGV-AFTGAKENFSLDW 113 d1tf7a1 147 VRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEF--VSDNVVILRNVLEGERRR 204 ::::::: ::::::::: d1nn5a_ 114 CKQPDVG---------------------------------LPKPDLVLFLQ--------- 131 d1tf7a1 205 RTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT---------------------- 242 d1nn5a_ 132 --------------------------------------LQLADAAKRERYENGAFQERAL 153 d1tf7a1 243 --------------------------------------------------- 243 d1nn5a_ 154 RCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK 204 TMalign alignment (TM-score: 0.43 Raw score:104.44) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 : : :::::::: ::::::::::::::::::::::::::: d1nn5a_ 1 -----R-R----------------GALIVLEG-VDRAGKSTQSRKLVEALCAAGHRAELL 37 d1tf7a1 61 VTFEETP--QDIIKNARSFGWDLAKLVDEGKLFILDA-SPD----PEGQE--VVGGFDLS 111 :::: :: ::: ::: ::::: ::::::: d1nn5a_ 38 RFPE-RSTE-------------------------IGKLLSSYLQKKSDVEDHSVHLLFS- 70 d1tf7a1 112 ALIERINYAI-QKY-R-ARRVSIDSVTSVF-QQ--Y--DASSVVRRELFRLVARLKQIGA 163 :::::::::: ::: : ::::::::::::: :: : :::::::::: : :::: : d1nn5a_ 71 ANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPD-V--GLPK---P 124 d1tf7a1 164 TTVMTTERIEE--------------YGPIARY-GVEEFV-SDNVVILRNVLEGERRRRTL 207 ::::::::::: :::::: :::::: ::::::::: : d1nn5a_ 125 DLVLFLQLQLADAAKRERYENGAFQ-ERALRCFHQLMKDTTLNWKMVDA--------S-- 173 d1tf7a1 208 EILKLRGTSHMKGEYPFTITDHGINI----------------------FPLGAMRLT 242 :::: ::::: d1nn5a_ 174 ----------------KSIE-AVHEDIRVLSEDAIATATEKPLGELWK--------- 204 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDII 71 :::::::::::::::::::::::: ::::::::::::::::::::::: d1nn5a_ 1 RRGALIVLEGVDRAGKSTQSRKLV-EALCAAGHRAELLRFPERSTEIG 47