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 | d1in4a2 | Holliday junction helicase RuvB | 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 <-- 1.554 --> HitDALI alignment (Z-score: 6.2 Raw score:619.80) d1tf7a1 1 ehqaiakmrtMIEG-------FDDISHGG------lpIGRSTLVSGTSGTGKTLFSIQFL 47 :::: :::::::: ::::::::::::::::::::::: d1in4a2 1 ----qflrpkSLDEfigqenvKKKLSLALeaakmrgeVLDHVLLAGPPGLGKTTLAHIIA 56 d1tf7a1 48 YNGIiefdEPGVFVTFEetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvgg 107 :::: ::::::::: d1in4a2 57 SELQ----TNIHVTSGP------------------------------------------v 70 d1tf7a1 108 fDLSALIERINYAIqkYRARRVSIDSVTSVFqqydassvvrrELFRLVARLKQI-----G 162 ::::::::::::: ::::::::::::::: :::::::::::: : d1in4a2 71 lVKQGDMAAILTSL--ERGDVLFIDEIHRLN---------kaVEELLYSAIEDFqidiqP 119 d1tf7a1 163 ATTVMTTERieeygpiARYGV--EEFVSDNVVILRNVLE--------------------- 199 ::::::::: ::::: :::::::::::::::: d1in4a2 120 FTLVGATTR-------SGLLSspLRSRFGIILELDFYTVkelkeiikraaslmdveieda 172 d1tf7a1 200 ------GERRRR--tleilklrgtshmkgeypftitdhginifplgamrlt 242 :::::: d1in4a2 173 aaemiaKRSRGTpriairltkrvrdmltvvkadrintdivlktmevlnidd 223 FAST alignment (Normalized score: 4.89 Raw score:1137.00) d1tf7a1 1 EHQAIAKMRTM-------------IEGFDDISHGGLPI--------------GRSTLVSG 33 ::::::: :::::::: d1in4a2 1 -----------QFLRPKSLDEFIGQENVKKK-------LSLALEAAKMRGEVLDHVLLAG 42 d1tf7a1 34 TSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFIL 93 :::::::::::::::: :::::::::: d1in4a2 43 PPGLGKTTLAHIIASE----LQTNIHVTSG------------------------------ 68 d1tf7a1 94 DASPDPEGQEVV----GGFDLSALIERINYAIQKYRA----RRVSIDSVTSVFQQYDA-S 144 ::::::::::: :::::::::: : d1in4a2 69 ------------PVLVKQGDMAAILTS----------LERGDVLFIDEIHR-------LN 99 d1tf7a1 145 SVVRRELFRLVARLK-----QIGATTVMTTERIEEYGPIA-----RYGVEEFVSDNVVIL 194 :::::::::::: :::::::::: ::::::::::::::: d1in4a2 100 KAVEELLYSAIE---DFQIDIQPFTLVGAT----------TRSGLLSSPLRSRFGIILEL 146 d1tf7a1 195 RNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT------------ 242 : d1in4a2 147 D-----------------------------------------------FYTVKELKEIIK 159 d1tf7a1 243 ------------------------------------------------------------ 243 d1in4a2 160 RAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTMEVL 219 d1tf7a1 243 ---- 243 d1in4a2 220 NIDD 223 TMalign alignment (TM-score: 0.43 Raw score:102.99) d1tf7a1 1 -----EHQAIAKMRTMIE-----G-FDDIS-HGG-LP-----IGRSTLVSGTSGTGKTLF 42 :::: : ::::: ::: :: :::::::::::::::::: d1in4a2 1 QFLRP---------KSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTL 51 d1tf7a1 43 SIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQ 102 ::::::::: : ::::::: ::: d1in4a2 52 AHIIASELQ----T-NIHVTSG------------------------------PVL----- 71 d1tf7a1 103 EVVGGFDLSALIERINYAIQKYRARRV-SIDSVTSVFQQYDASSVVRRELFRLVARLK-Q 160 : :: :::::::::: ::::: ::::::::: :: :: :::::::: : d1in4a2 72 --V--KQ--GDMAAILTSL---ERGDVLFIDEIHRLN-------KA-VE-ELLYSAIEDF 113 d1tf7a1 161 ----IGATTVMTTERIEEYGPIARYGV-EEFVSDNVVILRNVLEGERRRR-TLEILKLRG 214 ::::::::::: :::::: ::::::::::::::: :::: d1in4a2 114 QIDIQPFTLVGATTR------SGLLSSPLRSRFGIILELDFYT---VKELK--------- 155 d1tf7a1 215 TSHMKGEYPFTI-TD--H--------------------GI-------------------- 231 ::: :: : : d1in4a2 156 ---------EIIKRAASLMDVEIEDAAAEMIAKRSRGT-PRIAIRLTKRVRDMLTVVKAD 205 d1tf7a1 232 ------------------NIFPLGAMRLT 242 d1in4a2 206 RINTDIVLKTMEVLNIDD----------- 223 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tf7a1 14 GFDDISHGGLPIG---RSTLVSGTSGTGKTLFSIQFLY 48 ::::::::::::: :::::::::::::::::::::: d1in4a2 20 KLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS 57