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 | d1qdea_ | Initiation factor 4a | 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 <-- 1.234 --> HitDALI alignment (Z-score: 6.0 Raw score:625.10) d1tf7a1 1 ----------------------------------ehqaiakMRTMiegfddishgGLPIg 26 :::: :::: d1qdea_ 1 iqtnydkvvykfddmeldenllrgvfgygfeepsaiqqraiMPII----------EGHD- 49 d1tf7a1 27 rsTLVSGTSGTGKTLFSIQFLYNGIIEFD--ePGVFVTFE-ETPQDIIKNARsFGWD-lA 82 ::::::::::::::::::::::::::: :::::::: ::::::::::: :::: : d1qdea_ 50 --VLAQAQSGTGKTGTFSIAALQRIDTSVkapQALMLAPTrELALQIQKVVM-ALAFhmD 106 d1tf7a1 83 KLV------dEGKLFILDAspdpegqevvggfdlSALIER---inYAIQkyRARRVSIDS 133 ::: ::::::::: :::::: :::: ::::::::: d1qdea_ 107 IKVhaciglrDAQIVVGTP---------------GRVFDNiqrrrFRTD--KIKMFILDE 149 d1tf7a1 134 VTS-VFQQydassvvrrELFRLVARLKQIG--ATTVMTTErieeygpiARYGVEEFVSD- 189 ::: :::: ::::::::::::: :::::::: ::::::::::: d1qdea_ 150 ADEmLSSG---------FKEQIYQIFTLLPptTQVVLLSA--------TMPNDVLEVTTk 192 d1tf7a1 190 -----NVVIlrnvlegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 :::: d1qdea_ 193 fmrnpVRIL------------------------------------------------- 201 FAST alignment (Normalized score: 5.38 Raw score:1186.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------------------------------ 24 d1qdea_ 1 ------------------------IQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAI 36 d1tf7a1 25 ---------IGRSTLVSGTSGTGKTLFSIQFLYNG-IIEFDE--PGVFVTFEE---TPQD 69 :::::::::::::::::::::::::: ::::: ::::::: :::: d1qdea_ 37 QQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK-APQALMLAP--TRELALQ 93 d1tf7a1 70 IIKNARS--FGWDLAKLVD----------EGKLFILDASPDPEGQEVVGGFDLSALIERI 117 ::::::: :::: ::::::: ::::: d1qdea_ 94 IQKVVMALAFHMD------IKVHACIGLRDAQIVVG-------------------TPGRV 128 d1tf7a1 118 NYAIQKY-------RARRVSIDSVTSVFQQYDASSVVRRE--LFRLVARLKQ---IGATT 165 ::::: ::::::::::::::: :::::::::: ::::: d1qdea_ 129 FDNIQ--RRRFRTDKIKMFILDEADEMLS-----------SGFKEQIYQIFTLLPPTTQV 175 d1tf7a1 166 VMTTERIEEYGPIA--RYGVEEFVS-------DNVVILRNVLEGERRRRTLEILKLRGTS 216 :::: :::::::: :::: d1qdea_ 176 VLLS----------ATMPNDVLEV-TTKFMRNPVRI------------------------ 200 d1tf7a1 217 HMKGEYPFTITDHGINIFPLGAMRLT- 242 d1qdea_ 201 --------------------------L 201 TMalign alignment (TM-score: 0.45 Raw score:107.86) d1tf7a1 1 ------------EHQAIAKMRTMIE----------------------GFDDISHGGLPIG 26 ::: ::::::::::: d1qdea_ 1 IQTNYDKVVYKF----------DDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGH-- 48 d1tf7a1 27 RSTLVSGTSGTGKTLFSIQFLYNGIIEFD--EPGVFVTFE-ETPQDIIKNARSFGWD-LA 82 :::::::::::::::::::::::::::: ::::::::: :::::::::::: ::: :: d1qdea_ 49 -DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMA-LAFHMD 106 d1tf7a1 83 KLV----D--EGKLFILDASPDPEGQEVVGGFD-LSALIERINYAIQKYRARRVSIDSVT 135 ::: : :::::: ::: : :::::::::::::::::::::::: d1qdea_ 107 IKVHACIGLRDAQIVV-GTP------------GR--VFDNIQRRRFRTDKIKMFILDEAD 151 d1tf7a1 136 SVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEE-FV--SD-NV 191 ::::::: : :::::::::::::::::::::: ::::::: :: :: :: d1qdea_ 152 EMLSSGF----K--EQIYQIFTLLPPTTQVVLLSAT-------MPNDVLEVTTKFMRNPV 198 d1tf7a1 192 VILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 ::: d1qdea_ 199 RIL------------------------------------------------ 201 HHsearch alignment (Probability: 0.94 E-value:0.00) d1tf7a1 23 LPIGRSTLVSGTSGTGKTLFS-IQFLYNG-IIEFDEPGVFVT-FEETPQDIIKNARSFGW 79 ::::::::::::::::::::: ::::::: :::::::::::: ::::::::::::::::: d1qdea_ 44 IIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAF 103 d1tf7a1 80 DLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINY-AIQKYRARRVSIDSVTSVF 138 :::::::: ::::: :::::::::::::::::: ::::::::::::::::::: d1qdea_ 104 HMDIKVHA-------CIGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML 154 d1tf7a1 139 QQYDASSVVRRELFRLVARLKQIGATTVMTTERIE 173 ::: ::::::::::::::::::::::::::: d1qdea_ 155 SSG-----FKEQIYQIFTLLPPTTQVVLLSATMPN 184