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 | d1pvoa3 | Transcription termination factor Rho, ATPase 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 <-- 2.448 --> HitDALI alignment (Z-score: 13.1 Raw score:1336.90) d1tf7a1 1 ---------ehqaIAKMRT------mIEGFDDIShgGLPIGRSTLVSGTSGTGKTLFSIQ 45 :::::: :::::::: :::::::::::::::::::::::: d1pvoa3 1 nkilfenltplhaNSRLRMgstedltARVLDLAS--PIGRGQRGLIVAPPKAGKTMLLQN 58 d1tf7a1 46 FLYNGIIEFD-EPGVFVTFEE---TPQDIIKNArsfgwdlaklvdegKLFILDASPDpeg 101 :::::::::: :::::::::: ::::::::: :::::::::: d1pvoa3 59 IAQSIAYNHPdCVLMVLLIDErpeEVTEMQRLV--------------KGEVVASTFD--- 101 d1tf7a1 102 qevVGGFDLsALIERINYAIQKYR----aRRVSIDSVTSVFQ-----------qYDASSV 146 :::::: :::::::::::::: ::::::::::::: :::::: d1pvoa3 102 --ePASRHV-QVAEMVIEKAKRLVehkkdVIILLDSITRLARayntvvpavltgGVDANA 158 d1tf7a1 147 VrRELFRLVARLK----qiGATTVMTTERIE-eygpiaRYGVEEFVSDNVVILRNVlege 201 : ::::::::::: :::::::::::: :::::::::::::::::: d1pvoa3 159 L-HRPKRFFGAARnveeggSLTIIATALIDTgskmdevIYEEFKGTGNMELHLSRK-iae 216 d1tf7a1 202 RRRR-TLEI--LKLRGTS---------------------hmkGEYPftitdhginiFPLG 237 :::: :::: ::::::: :::: :::: d1pvoa3 217 KRVFpAIDYnrSGTRKEEllttqeelqkmwilrkiihpmgeiDAME---------fLINK 267 d1tf7a1 238 A-------MRLT--- 242 : :::: d1pvoa3 268 LamtktndDFFEmmk 282 FAST alignment (Normalized score: 8.25 Raw score:2155.00) d1tf7a1 1 EHQA-------------IAKMRTM--------IEGFDDISHGGLPIGRSTLVSGTSGTGK 39 ::::: :::::::: :::::::::::::::::: d1pvoa3 1 ----NKILFENLTPLHANSRLR--MGSTEDLTARVLDLAS--PIGRGQRGLIVAPPKAGK 52 d1tf7a1 40 TLFSIQFLYNGIIE-FDEPGVFVTFEE---TPQDIIKNARSFGWDLAKLVDEG--KLFIL 93 :::::::::::::: :::::::::::: ::::::: ::::: d1pvoa3 53 TMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQR----------------LVKGEVV 96 d1tf7a1 94 DASPDPEGQEV---VGGFDLSALIERINYAIQKYRA-------RRVSIDSVTSVFQQ--- 140 ::: ::::: ::::::::::::: ::::::::::::: d1pvoa3 97 AST--------FDEPASRH-VQVAEMVIEKAKR---LVEHKKDVIILLDSITRLAR-AYN 143 d1tf7a1 141 ---------YDASSVVRRELFRLVARLKQI-------GATTVMTTERIEEYGPIAR---- 180 :::::: ::::::::::: ::::::::: d1pvoa3 144 TVVPAVLTGGVDANA-LHRPKRFFGAA---RNVEEGGSLTIIATAL----------IDTG 189 d1tf7a1 181 -------YGVEEFVSDNVVILRNVLEGERRR---------RTLEI---LKLRGTSHMKGE 221 ::::::::::::::: :::: :::: d1pvoa3 190 SKMDEVIYEEFKGTGNMELHLS---------RKIAEKRVFPAID-YNRSGTR-------- 231 d1tf7a1 222 YPFTITDHGINIFPLGAMRLT--------------------------------------- 242 d1pvoa3 232 ---------------------KEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAM 270 d1tf7a1 243 ------------ 243 d1pvoa3 271 TKTNDDFFEMMK 282 TMalign alignment (TM-score: 0.67 Raw score:162.23) d1tf7a1 1 ---------EHQAIAKMRT----M--IEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQ 45 :::::::::: : :::::::: :::::::::::::::::::::::: d1pvoa3 1 NKILFENLTPLHANSRLRMGSTEDLTARVLDLAS--PIGRGQRGLIVAPPKAGKTMLLQN 58 d1tf7a1 46 FLYNGIIEFDE-PGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEV 104 ::::::::::: :::::::::::::::: : :::: ::::::::: : :::: d1pvoa3 59 IAQSIAYNHPDCVLMVLLIDERPEEVTE-M------QRLV----KGEVVASTF-D-EPAS 105 d1tf7a1 105 VGGFDLSALIERINYAIQK-YRARRVSIDSVTSVFQQ--Y--------DASSVVRRELFR 153 ::::::::::::::::::: :::::::::::::::: : :::::::::::: d1pvoa3 106 RHVQVAEMVIEKAKRLVEHK-KDVIILLDSITRLARAYNTVVPAVLTGGVDANALHRPKR 164 d1tf7a1 154 LVARLK-Q---IGATTVMTTERIE--EYGP-IARY--GVEEFVSDNVVILRNVLEGERRR 204 :::::: : ::::::::::::: : ::: :::::::::::::::::: :::: d1pvoa3 165 FFGAARNVEEGGSLTIIATALIDTGS---KM-DEVIYEEFKGTGNMELHLSRKIA-EKRV 219 d1tf7a1 205 --RTLE-ILKLRGTS----------HM--K---G---E--YPFTITDHGINIFPLG---- 237 :::: :::::::: :: : : : :::: ::::: d1pvoa3 220 FPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEF-------LINKLAMTK 272 d1tf7a1 238 ---AM--RLT 242 :: ::: d1pvoa3 273 TNDDFFEMMK 282 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 6 AKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE-PGVFVTFE 64 ::::::::::::::: :::::::::::::::::::::::::::::::::: :::::::: d1pvoa3 21 STEDLTARVLDLASP--IGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLID 78 d1tf7a1 65 ETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKY 124 ::::::::::::::: ::::::::::::::: ::::::::::::::::: d1pvoa3 79 ERPEEVTEMQRLVKG----------EVVASTFDEPASRHV---QVAEMVIEKAKRLVEHK 125 d1tf7a1 125 RARRVSIDSVTSVFQQYDA----------SSVVRRELFRLVAR---LKQI-GATTVMTTE 170 ::::::::::::::::::: :::::::::::::: :::: ::::::::: d1pvoa3 126 KDVIILLDSITRLARAYNTVVPAVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATAL 185 d1tf7a1 171 RI-EEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKL 212 :: :::::::::::::::::::::::::::::::::::::::: d1pvoa3 186 IDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRS 228