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 | d1gg4a1 | UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain | 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 <-- 1.485 --> HitDALI alignment (Z-score: 3.4 Raw score:361.40) d1tf7a1 1 ehqaiakmrtmiegfddishggLPIGR-----stlvsgtsgtGKTLFSIQFLYNGIiefd 55 ::::: :::::::::::::: d1gg4a1 1 -----------------vpgrlFPIQLaenqlllddsynanvGSMTAAVQVLAEMP---- 39 d1tf7a1 56 EPGVFVTFE---------etpQDIIKNArsfgWDLAklvdegkLFILDASP-----dpeg 101 ::::::::: ::::::: :::: :::::::: d1gg4a1 40 GYRVLVVGDmaelgaeseachVQVGEAA----KAAG------iDRVLSVGKqshaistas 89 d1tf7a1 102 qevvggfDLSALIERINYAIQKYRaRRVSIDSVTSVFqqydassvvrrelfRLVARLKqi 161 ::::::::::::::::: :::::::::::: ::::::: d1gg4a1 90 gvgehfaDKTALITRLKLLIAEQQvITILVKGSRSAA------------meEVVRALQ-- 135 d1tf7a1 162 gattvmtterieeygpiarygveefvsdnvvilrnvlegerrrrtleilklrgtshmkge 221 d1gg4a1 136 ------------------------------------------------------------ 136 d1tf7a1 222 ypftitdhginifplgamrlt 242 d1gg4a1 136 --------------------- 136 FAST alignment (Normalized score: 1.74 Raw score:315.30) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------IGRSTLVSGTSGTG---KTLFSIQ 45 :::::::: ::::::: d1gg4a1 1 ------------------------VPGRLFPIQLAENQLLLDDS------YNANVGSMTA 30 d1tf7a1 46 F--------------------------------LYNGIIEFDEPGVFVTFEETPQDIIKN 73 : ::::: :::: :::::: d1gg4a1 31 AVQVLAEMPGYRVLVVGDMAELGAESEACHVQVGEAAK-AAGI-DRVLSV---------- 78 d1tf7a1 74 ARSFGWDLAKLVDEGK-----------LFILDASPDPEGQEVVGGF--DLSALIERINYA 120 ::::: :::::::::::: d1gg4a1 79 ----------------GKQSHAISTASGVGEH--------------FADKTALITRLKLL 108 d1tf7a1 121 IQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQ-IGATTVMTTERIEEYGPIA 179 ::: :::::::::: d1gg4a1 109 IAE-------------------------------------QQVITILVKGS--------- 122 d1tf7a1 180 RYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAM 239 d1gg4a1 123 ------------------------------------------------------------ 123 d1tf7a1 240 RLT------------- 242 d1gg4a1 123 ---RSAAMEEVVRALQ 135 TMalign alignment (TM-score: 0.33 Raw score:78.65) d1tf7a1 1 ----EHQAIAKMRTMIEGFDDISHGGLPIG-----RSTLVSGTSGTGKTLFSIQFLYNGI 51 : ::::: :::::::::: ::::::::::::: d1gg4a1 1 VPGR------------------L--FPIQLAENQLLLDDSYNANV-GSMTAAVQVLAEM- 38 d1tf7a1 52 IEFDEPGVFVTFE-----------ETPQDIIKNARSFGWDLAKLVDEGKLFILDASPD-- 98 : ::::::::: :: :::: :: ::: :: ::::::::: d1gg4a1 39 --P-GYRVLVVGDMAELGAESEACHV--QVGE-AA---KAA--GI----DRVLSVGKQSH 83 d1tf7a1 99 ------------PEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSV 146 ::::::::::::::::::::::::::::::: d1gg4a1 84 AISTASGVGEHF---------ADKTALITRLKLLIAEQQVITILVKGSRSAA-------- 126 d1tf7a1 147 VRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRT 206 :: ::::::: d1gg4a1 127 ---ME-EVVRALQ----------------------------------------------- 135 d1tf7a1 207 LEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 d1gg4a1 136 ------------------------------------ 136 HHsearch alignment (Probability: 0.02 E-value:0.19) d1tf7a1 112 ALIERINYAIQKYRARRVS 130 ::::::::::::::::::: d1gg4a1 58 ACHVQVGEAAKAAGIDRVL 76