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 | d1ny5a2 | Transcriptional activator sigm54 (NtrC1), C-terminal domain | 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 <-- 2.149 --> HitDALI alignment (Z-score: 6.6 Raw score:669.50) d1tf7a1 1 -ehqaiakmrtmIEGFDDishgGLPIgrSTLVSGTSGTGKTLFSIQFLYNGiiefDEPGV 59 :::::: :::: ::::::::::::::::::::::: ::::: d1ny5a2 1 eyvfespkmkeiLEKIKK--isCAEC--PVLITGESGVGKEVVARLIHKLS-drsKEPFV 55 d1tf7a1 60 FVTFEEtpqdiiknarsfgwdlaklvdegklfildaspdpegqevVGGFDLSALIE---- 115 :::::: ::::::::::: d1ny5a2 56 ALNVAS--------------------------------------iPRDIFEAELFGyekg 77 d1tf7a1 116 ----------RINYAIQkyrARRVSIDSVTSVFqqydassvvRRELFRLVARLKQI---- 161 ::::::: ::::::::::::: :::::::::::::: d1ny5a2 78 aftgavsskeGFFELAD---GGTLFLDEIGELS---------LEAQAKLLRVIESGkfyr 125 d1tf7a1 162 ---------GATTVMTTERieeygpiARYGV---------eEFVS-DNVVILRNVLegER 202 :::::::::: ::::: :::: :::::::::: :: d1ny5a2 126 lggrkeievNVRILAATNR-------NIKELvkegkfredlYYRLgVIEIEIPPLRerKE 178 d1tf7a1 203 RR-----------------------------rtleilklrgtshmkgeypftitdhgini 233 :: d1ny5a2 179 DIiplanhflkkfsrkyakevegftksaqelllsypwygnvrelknvieravlfsegkfi 238 d1tf7a1 234 fplgamrlt 242 d1ny5a2 239 drgelsclv 247 FAST alignment (Normalized score: 4.57 Raw score:1116.00) d1tf7a1 1 EHQAIAKMRTM--------IEGFDDISHGGLP------IGRSTLVSGTSGTGKTLFSIQF 46 ::::::: :::::::::::::::::::::: d1ny5a2 1 -----------EYVFESPKMKEILEK------IKKISCAECPVLITGESGVGKEVVARLI 43 d1tf7a1 47 LYNGIIE---FDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQE 103 ::: ::::::::::: d1ny5a2 44 HKL----SDRSKEPFVALNVA--------------------------------------- 60 d1tf7a1 104 V--VGGFDLS------------------ALIERINYAIQKYRA---RRVSIDSVTSVFQQ 140 ::::::: ::::: :::::::::: d1ny5a2 61 -SIPRDIFEAELFGYEKGAFTGAVSSKEGFFEL----------ADGGTLFLDEIGE---- 105 d1tf7a1 141 YDA-SSVVRRELFRLVARLK-------------QIGATTVMTTERIEEYGPIA------- 179 ::::::::::::: :::::::::: d1ny5a2 106 ---LSLEAQAKLLRVIE---SGKFYRLGGRKEIEVNVRILAAT----------NRNIKEL 149 d1tf7a1 180 -----RYGVEEFV-SDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINI 233 :::::::: ::::::::: d1ny5a2 150 VKEGKFREDLYYRLGVIEIEIPP------------------------------------- 172 d1tf7a1 234 FPLGAMRLT--------------------------------------------------- 242 d1ny5a2 173 ---------LRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELK 223 d1tf7a1 243 ------------------------ 243 d1ny5a2 224 NVIERAVLFSEGKFIDRGELSCLV 247 TMalign alignment (TM-score: 0.36 Raw score:87.98) d1tf7a1 1 ---EHQAIAKMRTMI----EGFDDISHGGL-PIGRSTLVSGTSGTGKTLFSIQFLYNGII 52 : ::::::::::: ::::::::::::::::::::::::::::: d1ny5a2 1 EYV-----------FESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDR 49 d1tf7a1 53 EFDEPGVFVTFEET----------------------------PQDIIKNARSFGWDLAKL 84 : :::::::::::: d1ny5a2 50 S-KEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFF------------------ 90 d1tf7a1 85 VDEGKLFILDASP-DPEGQEVVGGFDLSALIERI--NYA--------IQKYRARRVSIDS 133 ::::::::::::: :::::::::::::: ::: ::::: :::::: d1ny5a2 91 ELADGGTLFLDEIG------ELSLEAQAKLLRVIESGKFYRLGGRKE-IEVNV-RILAAT 142 d1tf7a1 134 VTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVI 193 ::: : ::::::::::::::::: ::::::: d1ny5a2 143 NRN-I---KELVKEGKFREDLYYRL----------------------------GVIEIEI 170 d1tf7a1 194 LRNVL-E------------------------------GERRR----------RTLEILKL 212 ::::: : ::::: d1ny5a2 171 PPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVREL-------- 222 d1tf7a1 213 RGTSHMKGEYPFTI------------------------TDHGINIFPLGAMRLT 242 : d1ny5a2 223 -------------KNVIERAVLFSEGKFIDRGELSCLV---------------- 247 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tf7a1 12 IEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETP 67 ::::::::::::::::::::::::::::::::::::: :::::::::::::::::: d1ny5a2 9 MKEILEKIKKISCAECPVLITGESGVGKEVVARLIHK-LSDRSKEPFVALNVASIP 63