|
Name |
Accession |
Description |
Interval |
E-value |
| Sms |
COG1066 |
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ... |
1-457 |
0e+00 |
|
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];
Pssm-ID: 440685 [Multi-domain] Cd Length: 453 Bit Score: 762.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 1 MAKAaKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAATSSSRnerfsGFAGDAKGASRVQKLSEISLEALPRFSTG 80
Cdd:COG1066 1 MAKT-KTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGR-----AASGAAGRASKPVPLSEVEAEEEPRISTG 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 81 FKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATEM-KTLYVTGEESLQQVAMRAHRLGLPTAELNMLSETSI 159
Cdd:COG1066 75 IGELDRVLGGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGgKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 160 EQICLIASQEKPKLMVIDSIQVMHMADIQSSPGSVAQVRETAAYLTRFAKTNDVAIIMVGHVTKDGTLAGPKVLEHCIDC 239
Cdd:COG1066 155 EAILATIEELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMVDT 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 240 SVMLDGETDSRFRTLRSHKNRFGAVNELGVFAMTEQGLREVSNPSAIFLSRGDEITSGSSVMVVWEGTRPLLVEIQALVD 319
Cdd:COG1066 235 VLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQALVS 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 320 HSMLSNPRRVAVGLEQNRLAILLAVLHRHGGLQMSDQDVFVNVVGGVKVTETSADLALLLSLVSSFRNRPLPRDLVIFGE 399
Cdd:COG1066 315 PSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAVALAIASSFRDRPLPPDTVFFGE 394
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 1391259463 400 VGLAGEIRPVPSGQERIAEAAKHGFKRAIVPSANMPKKNPPDMKVYGVKKLSDALSVL 457
Cdd:COG1066 395 VGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKKKLKPKGIEIIGVSTLEEALEAL 452
|
|
| sms |
TIGR00416 |
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ... |
1-454 |
0e+00 |
|
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273067 [Multi-domain] Cd Length: 454 Bit Score: 761.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 1 MAKAaKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAATS-SSRNERFSGFAGDAkGASRVQKLSEISLEALPRFST 79
Cdd:TIGR00416 1 MAKA-KSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLgAQKNRRNSGKAGIP-QAQKSQTISAIELEEVPRFSS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 80 GFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLAT-EMKTLYVTGEESLQQVAMRAHRLGLPTAELNMLSETS 158
Cdd:TIGR00416 79 GFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKnQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETN 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 159 IEQICLIASQEKPKLMVIDSIQVMHMADIQSSPGSVAQVRETAAYLTRFAKTNDVAIIMVGHVTKDGTLAGPKVLEHCID 238
Cdd:TIGR00416 159 WEQICANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMVD 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 239 CSVMLDGETDSRFRTLRSHKNRFGAVNELGVFAMTEQGLREVSNPSAIFLSRGDEITSGSSVMVVWEGTRPLLVEIQALV 318
Cdd:TIGR00416 239 TVLYFEGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPMSGSSITVTWEGTRPLLVEIQALV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 319 DHSMLSNPRRVAVGLEQNRLAILLAVLHRHGGLQMSDQDVFVNVVGGVKVTETSADLALLLSLVSSFRNRPLPRDLVIFG 398
Cdd:TIGR00416 319 SPTSFANPRRVATGLDQNRLALLLAVLEKRLGLPLADQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLG 398
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1391259463 399 EVGLAGEIRPVPSGQERIAEAAKHGFKRAIVPSANMPKKNPPDMKVYGVKKLSDAL 454
Cdd:TIGR00416 399 EVGLAGEIRPVPSLEERLKEAAKLGFKRAIVPKANSPKTAPEGIKVIGVKKVGDAL 454
|
|
| RadA_SMS_N |
cd01121 |
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ... |
9-280 |
5.01e-154 |
|
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.
Pssm-ID: 410866 [Multi-domain] Cd Length: 268 Bit Score: 437.73 E-value: 5.01e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 9 FVCNECGADYPRWQGQCSACHAWNTITEVRLAATSSSrnerfSGFAGDAKGASRVQKLSEISLEALPRFSTGFKEFDRVL 88
Cdd:cd01121 1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSA-----SRRASASPSPSKPLPLSDVEAEEEERISTGIGELDRVL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 89 GGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATE-MKTLYVTGEESLQQVAMRAHRLGLPTAELNMLSETSIEQICLIAS 167
Cdd:cd01121 76 GGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRgGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEAILAEIE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 168 QEKPKLMVIDSIQVMHMADIQSSPGSVAQVRETAAYLTRFAKTNDVAIIMVGHVTKDGTLAGPKVLEHCIDCSVMLDGET 247
Cdd:cd01121 156 ELKPSLVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKDGAIAGPKVLEHMVDTVLYFEGDR 235
|
250 260 270
....*....|....*....|....*....|...
gi 1391259463 248 DSRFRTLRSHKNRFGAVNELGVFAMTEQGLREV 280
Cdd:cd01121 236 GSSYRILRSVKNRFGPTNEIGVFEMTENGLREV 268
|
|
| RAD55 |
COG0467 |
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms]; |
76-278 |
1.05e-23 |
|
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
Pssm-ID: 440235 [Multi-domain] Cd Length: 221 Bit Score: 98.83 E-value: 1.05e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATE-MKTLYVTGEESLQQVAMRAHRLGLPTAElnML 154
Cdd:COG0467 1 RVPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRgEKGLYVSFEESPEQLLRRAESLGLDLEE--YI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 155 SETSIEQICL------------------IASQEKPKLMVIDSIqvmhmADIQSSPGSVAQVRETAAYLTRFAKTNDVAII 216
Cdd:COG0467 79 ESGLLRIIDLspeelgldleellarlreAVEEFGAKRVVIDSL-----SGLLLALPDPERLREFLHRLLRYLKKRGVTTL 153
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1391259463 217 MVGHVTKDGTLAGPKVLEHCIDCSVMLD--GETDSRFRTLRSHKNRFGAV-NELGVFAMTEQGLR 278
Cdd:COG0467 154 LTSETGGLEDEATEGGLSYLADGVILLRyvELGGELRRALSVLKMRGSAHdRTIREFEITDGGIE 218
|
|
| RepA |
COG3598 |
RecA-family ATPase [Replication, recombination and repair]; |
91-334 |
5.53e-17 |
|
RecA-family ATPase [Replication, recombination and repair];
Pssm-ID: 442817 [Multi-domain] Cd Length: 313 Bit Score: 81.49 E-value: 5.53e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 91 GVVP-GSAILIGGSPGAGKSTLLLQTMCRLATEM----------KTLYVTGEESLQQV-----AMRAH----------RL 144
Cdd:COG3598 8 GLLPeGGVTLLAGPPGTGKSFLALQLAAAVAAGGpwlgrrvppgKVLYLAAEDDRGELrrrlkALGADlglpfadldgRL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 145 GLPTAELNMLSETSIEQICLIASQEKPKLMVIDSIQVMHMADIQSSpgsvAQVRETAAYLTRFAKTNDVAIIMVGHVTKD 224
Cdd:COG3598 88 RLLSLAGDLDDTDDLEALERAIEEEGPDLVVIDPLARVFGGDENDA----EEMRAFLNPLDRLAERTGAAVLLVHHTGKG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 225 G-------TLAGPKVLEHCIDCSVMLDGETDSRFRTLRSHKNRFGAVNELGVfaMTEQGLREVSNPSAIFLSRGDEITSG 297
Cdd:COG3598 164 GagkdsgdRARGSSALRGAARSVLVLSREKGEDLRVLTRAKSNYGPEIALRW--DNGGRLALEEVAALTAGAGEVELKEL 241
|
250 260 270
....*....|....*....|....*....|....*..
gi 1391259463 298 SSVMVVWeGTRPLLVEIQALVDHSMLSNPRRVAVGLE 334
Cdd:COG3598 242 VGGVART-GTDSELEEGLLEVPLAEAESAGEDAELAA 277
|
|
| KaiC-like |
cd01124 |
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ... |
78-262 |
5.67e-16 |
|
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.
Pssm-ID: 410869 [Multi-domain] Cd Length: 222 Bit Score: 76.92 E-value: 5.67e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCR-LATEMKTLYVTGEESLQQVAMRAHRLGL---------- 146
Cdd:cd01124 2 KTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLFGLQFLYAgAKNGEPGLFFTFEESPERLLRNAKSFGWdfdemedegk 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 147 -------PTAELNMLSETSIEQICLIASQEKPKLMVIDSIQVMHMADIQSSpgsvaQVRETAAYLTRFAKTNDVAIIMVG 219
Cdd:cd01124 82 liivdapPTEAGRFSLDELLSRILSIIKSFKAKRVVIDSLSGLRRAKEDQM-----RARRIVIALLNELRAAGVTTIFTS 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1391259463 220 --HVTKDGTLAGPKVLEHCIDCSVMLD--GETDSRFRTLRSHKNRFG 262
Cdd:cd01124 157 emRSFLSSESAGGGDVSFIVDGVILLRyvEIEGELRRTIRVLKMRGT 203
|
|
| ATPase |
pfam06745 |
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ... |
78-260 |
1.12e-12 |
|
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.
Pssm-ID: 429095 [Multi-domain] Cd Length: 231 Bit Score: 67.27 E-value: 1.12e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATEM--KTLYVTGEESLQQVAMRAHRLG---------- 145
Cdd:pfam06745 2 KTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYgePGVFVTLEEPPEDLRENARSFGwdlekleeeg 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 146 -------------LPTAELNMLSETSIEQICLIASQEKPKLMVIDSIQVMhmadIQSSpgSVAQVRETAAYLTRFAKTND 212
Cdd:pfam06745 82 klaiidastsgigIAEVEDRFDLEELIERLREAIREIGAKRVVIDSITTL----FYLL--KPAVAREILRRLKRVLKGLG 155
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1391259463 213 VAIIMVGHVTKD-GTLAGPKVLEHCIDCSVMLDGET--DSRFRTLRSHKNR 260
Cdd:pfam06745 156 VTAIFTSEKPSGeGGIGGYGVEEFIVDGVIRLDLKEieEERVRTIEIVKMR 206
|
|
| archRadB |
cd01394 |
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ... |
78-260 |
2.55e-12 |
|
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional homologue to the bacterial RecA. The precise function of RadB is unclear.
Pssm-ID: 410882 [Multi-domain] Cd Length: 216 Bit Score: 65.80 E-value: 2.55e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATE-MKTLYVTGE----ESLQQVAMRAhrlglPTAELN 152
Cdd:cd01394 2 STGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICLQLAVEAAKQgKKVVYIDTEglspERFQQIAGER-----FESIAS 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 153 ML----------SETSIEQICLIASQEKPKLMVIDSIQVMHMADIQSSPGSVAQVRETAAYLTRFAKTNDVAIIMVGHV- 221
Cdd:cd01394 77 NIivfepysfdeQGVAIQEAEKLLKSDKVDLVVVDSATALYRLELGDDSEANRELSRQMSKLLSIARKYDIPVVITNQVy 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 1391259463 222 --TKDGTLA--GPKVLEHCIDCSVMLD-GETDSRFRTLRSHKNR 260
Cdd:cd01394 157 sdIDDDRLKpvGGTLLEHWSKAIIRLEkSPPGLRRATLEKHRSR 200
|
|
| AAA_25 |
pfam13481 |
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins. |
88-225 |
2.10e-11 |
|
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
Pssm-ID: 463892 [Multi-domain] Cd Length: 193 Bit Score: 62.78 E-value: 2.10e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 88 LGGGVVP-GSAILIGGSPGAGKSTLLLQTMCRLAT------------EMKTLYVTGEESLQQVAMRAHRLG--------- 145
Cdd:pfam13481 25 LIKGLLPaGGLGLLAGAPGTGKTTLALDLAAAVATgkpwlggprvpeQGKVLYVSAEGPADELRRRLRAAGadldlparl 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 146 --LPTAELNMLSETS---------IEQIC-LIASQEKPKLMVIDSIQVMHMADIQSSpgsvAQVRETAAYLTRFAKTNDV 213
Cdd:pfam13481 105 lfLSLVESLPLFFLDrggplldadVDALEaALEEVEDPDLVVIDPLARALGGDENSN----SDVGRLVKALDRLARRTGA 180
|
170
....*....|..
gi 1391259463 214 AIIMVGHVTKDG 225
Cdd:pfam13481 181 TVLLVHHVGKDG 192
|
|
| Rubredoxin_2 |
pfam18073 |
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ... |
9-36 |
2.61e-11 |
|
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.
Pssm-ID: 436248 [Multi-domain] Cd Length: 28 Bit Score: 57.94 E-value: 2.61e-11
10 20
....*....|....*....|....*...
gi 1391259463 9 FVCNECGADYPRWQGQCSACHAWNTITE 36
Cdd:pfam18073 1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
94-244 |
1.23e-10 |
|
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 59.69 E-value: 1.23e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 94 PGSAILIGGSPGAGKSTLLLQTMCRL-ATEMKTLYVTGEESLQQVAMRAHRLGLPTAELNMLSETSIEQICLIASQEKPK 172
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELgPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPD 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1391259463 173 LMVIDSIQVMHMADIQSSpgsvAQVRETAAYLTRFAKTNDVAIIMVGHVTKDgtlAGPKVLEHCIDCSVMLD 244
Cdd:smart00382 81 VLILDEITSLLDAEQEAL----LLLLEELRLLLLLKSEKNLTVILTTNDEKD---LGPALLRRRFDRRIVLL 145
|
|
| KaiC-like_C |
cd19487 |
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ... |
78-278 |
3.44e-10 |
|
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.
Pssm-ID: 410895 [Multi-domain] Cd Length: 219 Bit Score: 59.62 E-value: 3.44e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLAT--EMKTLYVTgEESLQQVAMRAHRLGLPTAELNMLS 155
Cdd:cd19487 2 SSGVPELDELLGGGLERGTSTLLIGPAGVGKSTLALQFAKAAAArgERSVLFSF-DESIGTLFERSEALGIDLRAMVEKG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 156 ETSIEQI-----------CLIAS---QEKPKLMVIDSI----QVMHMADIqsspgSVAQVRETAAYLTRFAktndVAIIM 217
Cdd:cd19487 81 LLSIEQIdpaelspgefaQRVRTsveQEDARVVVIDSLngylNAMPDERF-----LILQMHELLSYLNNQG----VTTLL 151
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1391259463 218 VghVTKDGTLAGPKVLEhcIDCSVMLDG-------ETDSRFRTLRS-HKNRFGAvNELGV--FAMTEQGLR 278
Cdd:cd19487 152 I--VAQHGLLGGDMGTP--VDISYLADTvvllryfEAEGEVRKAISvLKKRTGD-HERTIreFRITRSGLK 217
|
|
| KaiC-like_N |
cd19488 |
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ... |
78-179 |
1.19e-09 |
|
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.
Pssm-ID: 410896 [Multi-domain] Cd Length: 225 Bit Score: 58.13 E-value: 1.19e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATEMKT-LYVTGEESLQQVAMRAHRLGL---------- 146
Cdd:cd19488 2 STGIPGLDDILRGGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETgLYITLSETEQELRAVALSHGWsldgihifel 81
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1391259463 147 --------PTAELNMLSETSIE------QICLIASQEKPKLMVIDSI 179
Cdd:cd19488 82 spsesaldAAQQYTILHPSELElsettrLIFERVERLKPSRVVIDSL 128
|
|
| KaiC-N |
cd19485 |
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most ... |
79-260 |
1.70e-09 |
|
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.
Pssm-ID: 410893 [Multi-domain] Cd Length: 226 Bit Score: 57.76 E-value: 1.70e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 79 TGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATEMKT--LYVTGEESLQQVAMRAHRLGLPTAELNMLSE 156
Cdd:cd19485 3 TGIEGFDDITHGGLPKGRPTLICGTAGTGKTLFAAQFLVNGIKEFGEpgVFVTFEESPEDIIKNMASFGWDLPKLVAEGK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 157 TSIEQICLIASQE----------------------KPKLMVIDSIQV--MHMADiqsspgsVAQVRETAAYLTRFAKTND 212
Cdd:cd19485 83 LLILDASPEPSEEevtgeydleallirieyairkiGAKRVSLDSLEAvfSGLSD-------SAVVRAELLRLFAWLKQKG 155
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1391259463 213 VAIIMVGHVTKDGTLAGPKVLEHCIDCSVMLDG--ETDSRFRTLRSHKNR 260
Cdd:cd19485 156 VTAIMTGERGEDGPLTRYGVEEYVSDCVVILRNvlEGERRRRTLEILKYR 205
|
|
| DnaB_C |
cd00984 |
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ... |
78-216 |
5.11e-09 |
|
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Pssm-ID: 410864 [Multi-domain] Cd Length: 256 Bit Score: 56.75 E-value: 5.11e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGgVVPGSAILIGGSPGAGKSTLLLQTMCRLATEMK--TLYVTGEESLQQVAMR---------AHRLGL 146
Cdd:cd00984 3 PTGFTDLDKLTGG-LQPGDLIIIAARPSMGKTAFALNIAENIALDEGlpVLFFSLEMSAEQLAERllssesgvsLSKLRT 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 147 P----------TAELNMLSE----------TSIEQIC-----LIASQEKPKLMVIDSIQVMHMADIQSSPgsVAQVRETA 201
Cdd:cd00984 82 GrlddedwerlTAAMGELSElplyiddtpgLTVDEIRakarrLKREHGGLGLIVIDYLQLIRGSKRAENR--QQEVAEIS 159
|
170
....*....|....*
gi 1391259463 202 AYLTRFAKTNDVAII 216
Cdd:cd00984 160 RSLKALAKELNVPVI 174
|
|
| PRK09302 |
PRK09302 |
circadian clock protein KaiC; Reviewed |
76-217 |
6.93e-09 |
|
circadian clock protein KaiC; Reviewed
Pssm-ID: 236461 [Multi-domain] Cd Length: 509 Bit Score: 57.97 E-value: 6.93e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLL---LQTMCRlaTEMKTLYVTGEESLQQVAMRAHRLGLPTAE-- 150
Cdd:PRK09302 254 RISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLAskfAEAACR--RGERCLLFAFEESRAQLIRNARSWGIDLEKme 331
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1391259463 151 ----LNMLS--------ETSIEQICLIASQEKPKLMVIDSIQVMHmadiqsSPGSVAQVRETAAYLTRFAKTNDVAIIM 217
Cdd:PRK09302 332 ekglLKIICarpesyglEDHLIIIKREIEEFKPSRVAIDPLSALA------RGGSLNEFRQFVIRLTDYLKSEEITGLF 404
|
|
| KaiC_C |
cd19484 |
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ... |
78-217 |
1.64e-07 |
|
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.
Pssm-ID: 410892 [Multi-domain] Cd Length: 218 Bit Score: 51.94 E-value: 1.64e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVL-GGGVVPGSAILIGGSPGAGKSTL---LLQTMCRlATEmKTLYVTGEESLQQVAMRAHRLGLPTAEL-- 151
Cdd:cd19484 2 STGIPRLDAMLgGGGFFRGSSILVSGATGTGKTLLaasFADAACR-RGE-RCLYFAFEESPAQLIRNAKSIGIDLEQMer 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1391259463 152 -NML-------SETSIEQICLIASQE----KPKLMVIDSIQVMhmadiqSSPGSVAQVRETAAYLTRFAKTNDVAIIM 217
Cdd:cd19484 80 kGLLkiicarpELYGLEDHLIIIKSEinefKPSRVIVDPLSAL------ARGGSLNEVKEFVIRLIDYLKSQEITGLF 151
|
|
| PRK09302 |
PRK09302 |
circadian clock protein KaiC; Reviewed |
67-277 |
4.79e-07 |
|
circadian clock protein KaiC; Reviewed
Pssm-ID: 236461 [Multi-domain] Cd Length: 509 Bit Score: 52.19 E-value: 4.79e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 67 SEISLEALPRFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATEMKT--LYVTGEESLQQVAMRAHRL 144
Cdd:PRK09302 3 QPSASPGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEpgVFVTFEESPEDIIRNVASF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 145 GLPTAELNMLSETSIEQICLIASQE----------------------KPKLMVIDSIQVmhmadIQSSPGSVAQVRETAA 202
Cdd:PRK09302 83 GWDLQKLIDEGKLFILDASPDPSEQeeageydlealfirieyaidkiGAKRVVLDSIEA-----LFSGFSNEAVVRRELR 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 203 YLTRFAKTNDVAIIMVGHVTKD-GTLAGPKVLEHCIDCSVMLDG--ETDSRFRTLRSHKNRfGAVNELG--VFAMTEQGL 277
Cdd:PRK09302 158 RLFAWLKQKGVTAVITGERGDEyGPLTRYGVEEFVSDCVIILRNrlEGEKRTRTLRILKYR-GTTHGKNeyPFTITEDGI 236
|
|
| Rad51 |
pfam08423 |
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ... |
76-224 |
5.05e-07 |
|
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ATPase RecA protein.
Pssm-ID: 462471 [Multi-domain] Cd Length: 255 Bit Score: 50.76 E-value: 5.05e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTL--LLQTMCRLATEM-----KTLYVTGE-----ESLQQVamrAHR 143
Cdd:pfam08423 18 QITTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLchTLCVTCQLPLEMgggegKALYIDTEgtfrpERLVAI---AER 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 144 LGL-PTAELNMLS----------ETSIEQICLIASQEKPKLMVIDSIQVMHMADIqSSPGSVA----QVRETAAYLTRFA 208
Cdd:pfam08423 95 YGLdPEDVLDNVAyaraynsehqMQLLQQAAAMMSESRFALLIVDSATALYRTDF-SGRGELAerqqHLAKFLRTLQRLA 173
|
170
....*....|....*.
gi 1391259463 209 KTNDVAIIMVGHVTKD 224
Cdd:pfam08423 174 DEFGVAVVITNQVVAQ 189
|
|
| RepA_RSF1010_like |
cd01125 |
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ... |
99-227 |
5.14e-07 |
|
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent).
Pssm-ID: 410870 Cd Length: 238 Bit Score: 50.46 E-value: 5.14e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 99 LIGGSPGAGKSTLLLQTMCRLATEM-----------KTLYVTGEESLQQVAMRAHRLGL-----PTAELNMLS------- 155
Cdd:cd01125 5 MLVGPPGSGKSFLALDLAVAVATGRdwlgerrvkqgRVVYLAAEDPRDGLRRRLKAIGAhlgdeDAALAENLVienlrgk 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 156 -------ETSIEQIclIASQEKPKLMVIDSIQ-VMHMADiQSSPGSVAQVretAAYLTRFAKTNDVAIIMVGHVTKDGTL 227
Cdd:cd01125 85 pvsidaeAPELERI--IEELEGVRLIIIDTLArVLHGGD-ENDAADMGAF---VAGLDRIARETGAAVLLVHHTGKDAAG 158
|
|
| radB |
PRK09361 |
DNA repair and recombination protein RadB; Provisional |
76-281 |
5.53e-07 |
|
DNA repair and recombination protein RadB; Provisional
Pssm-ID: 236482 [Multi-domain] Cd Length: 225 Bit Score: 50.25 E-value: 5.53e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCR-LATEMKTLYVTGE----ESLQQVAmrahrlGLPTAE 150
Cdd:PRK09361 4 RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEaAKNGKKVIYIDTEglspERFKQIA------GEDFEE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 151 L--NML---------SETSIEQICLIASqEKPKLMVIDSI------QVMHMADIQSSPGSVA-QVretaAYLTRFAKTND 212
Cdd:PRK09361 78 LlsNIIifepssfeeQSEAIRKAEKLAK-ENVGLIVLDSAtslyrlELEDEEDNSKLNRELGrQL----THLLKLARKHD 152
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1391259463 213 VAIIMVGHVT----KDGTLA-GPKVLEHCIDCSVMLDGETDS-RFRTLRSHknRFGAVNELGVFAMTEQGLREVS 281
Cdd:PRK09361 153 LAVVITNQVYsdidSDGLRPlGGHTLEHWSKTILRLEKFRNGkRRATLEKH--RSRPEGESAEFRITDRGIEIID 225
|
|
| XRCC3 |
cd19491 |
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ... |
84-222 |
7.04e-07 |
|
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells 3) recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. XRCC3, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC2, helps recruit RAD51 to the break site.
Pssm-ID: 410899 [Multi-domain] Cd Length: 250 Bit Score: 50.37 E-value: 7.04e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 84 FDRVLGGGVVPGSAILIGGSPGAGKSTLLLQ--TMCRLATEM-----KTLYVTGEES-----LQQVAMRAHRLGLPTAEL 151
Cdd:cd19491 1 LDELLGGGIPVGGITEIAGESGAGKTQLCLQlaLTVQLPRELgglggGAVYICTESSfpskrLQQLASSLPKRYHLEKAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 152 NMLSETSIEQICLIASQEK------P--------KLMVIDSIQVMHMADIQSSPGSVAQ----VRETAAYLTRFAKTNDV 213
Cdd:cd19491 81 NFLDNIFVEHVADLETLEHclnyqlPallergpiRLVVIDSIAALFRSEFDTSRSDLVErakyLRRLADHLKRLADKYNL 160
|
....*....
gi 1391259463 214 AIIMVGHVT 222
Cdd:cd19491 161 AVVVVNQVT 169
|
|
| DnaB |
COG0305 |
Replicative DNA helicase [Replication, recombination and repair]; |
61-218 |
1.31e-06 |
|
Replicative DNA helicase [Replication, recombination and repair];
Pssm-ID: 440074 [Multi-domain] Cd Length: 429 Bit Score: 50.46 E-value: 1.31e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 61 SRVQKLSEISlEALPRFSTGFKEFDRVLGGgVVPGSAILIGGSPGAGKSTLLLQTMCRLATEMK--TLYVTGEESLQQVA 138
Cdd:COG0305 159 ERIEELYKNG-GGITGVPTGFTDLDKLTGG-LQPGDLIILAARPSMGKTAFALNIARNAAIKEGkpVAIFSLEMSAEQLV 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 139 MRahrlglptaelnMLS-ETSIEQICL----IASQEKPKLMviDSIQVMHMAD--IQSSPG-SVAQVRETAaylTRFAKT 210
Cdd:COG0305 237 MR------------LLSsEARIDSSKLrtgkLSDEDWERLS--SAAGELSEAPiyIDDTPGlTIAEIRAKA---RRLKRE 299
|
....*...
gi 1391259463 211 NDVAIIMV 218
Cdd:COG0305 300 HGLGLIVI 307
|
|
| YifB |
COG0606 |
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ... |
393-457 |
1.34e-06 |
|
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational modification, protein turnover, chaperones];
Pssm-ID: 440371 [Multi-domain] Cd Length: 502 Bit Score: 50.42 E-value: 1.34e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 393 DLVIFGEVGLAGEIRPV----PSgqerIAEAAKHGFKRAIVPSANMPKKN-PPDMKVYGVKKLSDALSVL 457
Cdd:COG0606 102 DYVFLGELSLDGSLRPVrgvlPA----ALAAREAGIRRLIVPAANAAEAAlVPGIEVYGASSLLEVVAFL 167
|
|
| ChlI |
pfam13541 |
Subunit ChlI of Mg-chelatase; |
387-433 |
2.92e-06 |
|
Subunit ChlI of Mg-chelatase;
Pssm-ID: 433293 [Multi-domain] Cd Length: 121 Bit Score: 46.29 E-value: 2.92e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1391259463 387 NRPLPRDLVIFGEVGLAGEIRPVPSGQERIAEAAKHGFKRAIVPSAN 433
Cdd:pfam13541 75 QIPVLEETIFLGELSLDGSLRPVRGALPIALAARKHGFRGLIVPKEN 121
|
|
| Rad51_DMC1_archRadA |
cd01123 |
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ... |
78-224 |
2.95e-06 |
|
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal protein RadA. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Pssm-ID: 410868 [Multi-domain] Cd Length: 234 Bit Score: 48.30 E-value: 2.95e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTL--LLQTMCRLATEM-----KTLYVTGEESLQQVAMR--AHRLGL-P 147
Cdd:cd01123 2 TTGSKELDKLLGGGIETGSITEMFGEFRTGKTQLchTLAVTCQLPIDRgggegKAIYIDTEGTFRPERLRaiAQRFGLdP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 148 TAELNML----SETSIEQICLI------ASQEKPKLMVIDSIQVMHMADIqSSPGSVAQVRETAAY----LTRFAKTNDV 213
Cdd:cd01123 82 DDVLDNVayarAFNSDHQTQLLdqaaamMVESRFKLLIVDSATALYRTDY-SGRGELSARQMHLAKflrmLQRLADEFGV 160
|
170
....*....|.
gi 1391259463 214 AIIMVGHVTKD 224
Cdd:cd01123 161 AVVVTNQVVAQ 171
|
|
| DnaB_C |
pfam03796 |
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ... |
78-218 |
7.86e-06 |
|
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Pssm-ID: 427509 [Multi-domain] Cd Length: 254 Bit Score: 47.03 E-value: 7.86e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGgVVPGSAILIGGSPGAGKSTLLLqTMCR---LATEMKTLYVTGEESLQQVAMRahrlglptaelnML 154
Cdd:pfam03796 3 PTGFTDLDRLTGG-LQPGDLIIIAARPSMGKTAFAL-NIARnaaVKHKKPVAIFSLEMSAEQLVMR------------LL 68
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1391259463 155 S-ETSIEQICL----IASQEKPKLMviDSIQVMHMAD--IQSSPG-SVAQVRetaAYLTRFAKTNDVAIIMV 218
Cdd:pfam03796 69 AsEAGVDSQKLrtgqLTDEDWEKLA--KAAGRLSEAPlyIDDTPGlSIAEIR---AKARRLKREHGLGLIVI 135
|
|
| DMC1 |
cd19514 |
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ... |
78-224 |
2.08e-05 |
|
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in meiosis. It assembles at the sites of programmed DNA double-strand breaks and carries out a search for allelic DNA sequences located on homologous chromatids. It forms octameric rings.
Pssm-ID: 410922 [Multi-domain] Cd Length: 236 Bit Score: 45.81 E-value: 2.08e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKsTLLLQTMC---RLATEM-----KTLYVTGE-----ESLQQVamrAHRL 144
Cdd:cd19514 2 STGSTELDKLLGGGIESMSITEVFGEFRTGK-TQLSHTLCvtaQLPGSMgggggKVAYIDTEgtfrpDRIRPI---AERF 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 145 GL-PTAEL-NML------SETSIEQICLIASQ--EKP--KLMVIDSIQVMHMADIqSSPGSVAQVRET-AAYLTRFAKTN 211
Cdd:cd19514 78 GVdHDAVLdNILyaraytSEHQMELLDYVAAKfhEEAvfRLLIIDSIMALFRVDF-SGRGELAERQQKlAQMLSRLQKIS 156
|
170
....*....|....*.
gi 1391259463 212 D---VAIIMVGHVTKD 224
Cdd:cd19514 157 EeynVAVFITNQVTAD 172
|
|
| RecA-like_superfamily |
cd01120 |
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ... |
98-224 |
3.73e-05 |
|
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Pssm-ID: 410865 [Multi-domain] Cd Length: 119 Bit Score: 42.88 E-value: 3.73e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 98 ILIGGSPGAGKSTLLLQTmcrlatemktlyvtgeeSLQQVAMRAHRLGLPTAElnmlseTSIEQICLIASQEKPKLMVID 177
Cdd:cd01120 1 ILITGPPGSGKTTLLLQF-----------------AEQALLSDEPVIFISFLD------TILEAIEDLIEEKKLDIIIID 57
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1391259463 178 SIQVMHMAdiqSSPGSVAQVRETAAYLTRFAKTNDVAIIMVGHVTKD 224
Cdd:cd01120 58 SLSSLARA---SQGDRSSELLEDLAKLLRAARNTGITVIATIHSDKF 101
|
|
| FlaH |
COG2874 |
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility]; |
76-131 |
4.98e-05 |
|
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
Pssm-ID: 442121 Cd Length: 230 Bit Score: 44.44 E-value: 4.98e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATE-MKTLYVTGE 131
Cdd:COG2874 2 IISTGNDELDKRLGGGIPLGSLVLIEGENGTGKSVLSQQFAYGALENgLSVTYISTE 58
|
|
| Rad51C |
cd19492 |
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair ... |
100-222 |
7.81e-05 |
|
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51C, together with the other RAD51 paralogs, RAD51B, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site. Additionally, RAD51C acts as a mediator in the early steps of DNA damage signaling.
Pssm-ID: 410900 [Multi-domain] Cd Length: 172 Bit Score: 42.98 E-value: 7.81e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 100 IGGSPGAGKSTLLLQTM--CRLATEM-----KTLYVTGEESLQQVAMRAHRLGLPTAELNMLSEtsieqicLIASQEKPK 172
Cdd:cd19492 6 ICGVPGVGKTQLCMQLAvnVQIPKCFgglagEAIYIDTEGSFNIHYFRVHDYVELLALINSLPK-------FLEDHPKVK 78
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 1391259463 173 LMVIDSIQVMHMADIQSSPGSVAQVRETAAYLTRFAKTNDVAIIMVGHVT 222
Cdd:cd19492 79 LIVVDSIAFPFRHDFDDLAQRTRLLNGLAQLLHSLARQHNLAVVLTNQVT 128
|
|
| recomb_DMC1 |
TIGR02238 |
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ... |
78-224 |
1.26e-04 |
|
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Pssm-ID: 131292 [Multi-domain] Cd Length: 313 Bit Score: 44.00 E-value: 1.26e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKsTLLLQTMC---RLATEM-----KTLYVTGEESLQQVAMR--AHRLGL- 146
Cdd:TIGR02238 79 TTGSQALDGILGGGIESMSITEVFGEFRCGK-TQLSHTLCvtaQLPREMgggngKVAYIDTEGTFRPDRIRaiAERFGVd 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 147 PTAEL-NML---SETSIEQICLIA------SQEKPKLMVIDSIQVMHMADIqSSPGSVAQ----VRETAAYLTRFAKTND 212
Cdd:TIGR02238 158 PDAVLdNILyarAYTSEHQMELLDylaakfSEEPFRLLIVDSIMALFRVDF-SGRGELSErqqkLAQMLSRLNKISEEFN 236
|
170
....*....|..
gi 1391259463 213 VAIIMVGHVTKD 224
Cdd:TIGR02238 237 VAVFVTNQVQAD 248
|
|
| PTZ00035 |
PTZ00035 |
Rad51 protein; Provisional |
76-224 |
1.45e-04 |
|
Rad51 protein; Provisional
Pssm-ID: 185407 [Multi-domain] Cd Length: 337 Bit Score: 43.83 E-value: 1.45e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTL--LLQTMCRLATEM-----KTLYVTGE-----ESLQQVamrAHR 143
Cdd:PTZ00035 99 RITTGSTQLDKLLGGGIETGSITELFGEFRTGKTQLchTLCVTCQLPIEQgggegKVLYIDTEgtfrpERIVQI---AER 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 144 LGL-PTAEL-NML---SETSIEQICLIA------SQEKPKLMVIDSIQVMHMADIqSSPGSVAQvRETA-----AYLTRF 207
Cdd:PTZ00035 176 FGLdPEDVLdNIAyarAYNHEHQMQLLSqaaakmAEERFALLIVDSATALFRVDY-SGRGELAE-RQQHlgkflRALQKL 253
|
170
....*....|....*..
gi 1391259463 208 AKTNDVAIIMVGHVTKD 224
Cdd:PTZ00035 254 ADEFNVAVVITNQVMAD 270
|
|
| Rad51 |
cd19513 |
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ... |
77-222 |
2.16e-04 |
|
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51 is recruited to the break site with the help of its paralogs, RAD51D, RAD51B, RAD51C, XRCC3, and XRCC2, where it forms long helical polymers which wrap around the ssDNA tail at the break which leads to pairing and strand invasion.
Pssm-ID: 410921 [Multi-domain] Cd Length: 235 Bit Score: 42.69 E-value: 2.16e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 77 FSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLL--LQTMCRLATEM-----KTLYVTGE-----ESLQQVamrAHRL 144
Cdd:cd19513 1 ITTGSKELDKLLGGGIETGSITELFGEFRTGKTQLChtLAVTCQLPIDQgggegKALYIDTEgtfrpERLLAI---AERY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 145 GL-PTAELNMLSETS----------IEQICLIASQEKPKLMVIDSIQVMHMADIqSSPGSVAQvRET--AAYL---TRFA 208
Cdd:cd19513 78 GLnGEDVLDNVAYARayntdhqmqlLIQASAMMAESRYALLIVDSATALYRTDY-SGRGELSA-RQMhlAKFLrmlQRLA 155
|
170
....*....|....
gi 1391259463 209 KTNDVAIIMVGHVT 222
Cdd:cd19513 156 DEFGVAVVITNQVV 169
|
|
| circ_KaiC |
TIGR02655 |
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, ... |
76-182 |
3.52e-04 |
|
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. [Cellular processes, Other]
Pssm-ID: 131703 [Multi-domain] Cd Length: 484 Bit Score: 43.01 E-value: 3.52e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 76 RFSTGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLL---LQTMCRlaTEMKTLYVTGEESLQQVAMRAHRLGLPTAEL- 151
Cdd:TIGR02655 244 RVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVskfLENACA--NKERAILFAYEESRAQLLRNAYSWGIDFEEMe 321
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1391259463 152 --NMLS-----------ETSIEQICLIASQEKPKLMVIDSIQVM 182
Cdd:TIGR02655 322 qqGLLKiicaypesaglEDHLQIIKSEIADFKPARIAIDSLSAL 365
|
|
| Rad51B |
cd19493 |
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ... |
85-222 |
5.66e-04 |
|
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51B, together with the other RAD51 paralogs, RAD51C, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site.
Pssm-ID: 410901 [Multi-domain] Cd Length: 222 Bit Score: 41.15 E-value: 5.66e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 85 DRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMCRLATEMK-------TLYVTGE-----ESLQQVAMRAHRL------GL 146
Cdd:cd19493 1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAMPARkggldggVLYIDTEskfsaERLAEIAEARFPEafsgfmEE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 147 PTAELNMLSETSIEQICLIA-------------SQEKPKLMVIDSIQVMHMADIQSSPGSVAQ----VRETAAYLTRFAK 209
Cdd:cd19493 81 NERAEEMLKRVAVVRVTTLAqllerlpnleehiLSSGVRLVVIDSIAALVRREFGGSDGEVTErhnaLAREASSLKRLAE 160
|
170
....*....|...
gi 1391259463 210 TNDVAIIMVGHVT 222
Cdd:cd19493 161 EFRIAVLVTNQAT 173
|
|
| PRK06067 |
PRK06067 |
flagellar accessory protein FlaH; Validated |
78-133 |
6.21e-04 |
|
flagellar accessory protein FlaH; Validated
Pssm-ID: 180381 Cd Length: 234 Bit Score: 41.11 E-value: 6.21e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTLLLQTMC-RLATEMKTLYVTGEES 133
Cdd:PRK06067 8 STGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYgALKQGKKVYVITTENT 64
|
|
| GvpD_P-loop |
pfam07088 |
GvpD gas vesicle protein, P-loop domain; This family consists of several archaeal GvpD gas ... |
94-256 |
8.93e-04 |
|
GvpD gas vesicle protein, P-loop domain; This family consists of several archaeal GvpD gas vesicle regulatory proteins. GvpD is involved in the regulation of gas vesicle formation and functions as a repressor through the interaction and the breakdown induction of the transcriptional activator GvpE. This domain includes the P-loop and the basic region 1 (bR1, an arginine-rich region) which are essential for GvpD repressive function.
Pssm-ID: 462087 Cd Length: 189 Bit Score: 40.33 E-value: 8.93e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 94 PGSAILIGGSPGAGKSTLLLQTMCRLATEMKTLYVT--------------GEESLQQVA---MRAHRLGLP--------T 148
Cdd:pfam07088 9 FGKTLLINGAPGTGKTLFTIRGLDVLRRHHDVLYVStrvdqetvsemyfsGHGELDKTAfldLLQDPFGLPidvdvpfeK 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 149 AELNMLSETsIEQICLIASQekpKLMVIDSIQVM--HMADIQSSPGSVAQVRETAAYLTRFAKTNDVAIIMVghvtkdgt 226
Cdd:pfam07088 89 LDLHSLLEW-VDAINAIGTR---LTIAFDSWDLIyeYLALRHDDPPDIETVTNQLAALARGSGARLVLVLET-------- 156
|
170 180 190
....*....|....*....|....*....|
gi 1391259463 227 lAGPKVLEHCIDCSVMLDGETDSRFRTLRS 256
Cdd:pfam07088 157 -AQNSRLEYIVDGVVTLNVKNDDRGRTRRS 185
|
|
| HypB |
COG0378 |
Hydrogenase/urease maturation factor HypB, Ni2+-binding GTPase [Posttranslational modification, ... |
97-130 |
1.68e-03 |
|
Hydrogenase/urease maturation factor HypB, Ni2+-binding GTPase [Posttranslational modification, protein turnover, chaperones];
Pssm-ID: 440147 [Multi-domain] Cd Length: 200 Bit Score: 39.66 E-value: 1.68e-03
10 20 30
....*....|....*....|....*....|....
gi 1391259463 97 AILIGGSPGAGKSTLLLQTMCRLATEMKTLYVTG 130
Cdd:COG0378 15 AVNLMGSPGSGKTTLLEKTIRALKDRLRIAVIEG 48
|
|
| recomb_RAD51 |
TIGR02239 |
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ... |
78-186 |
3.66e-03 |
|
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Pssm-ID: 274048 [Multi-domain] Cd Length: 316 Bit Score: 39.32 E-value: 3.66e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 78 STGFKEFDRVLGGGVVPGSAILIGGSPGAGKSTL--LLQTMCRLATEM-----KTLYVTGE-----ESLQQVamrAHRLG 145
Cdd:TIGR02239 79 TTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLchTLAVTCQLPIDQgggegKALYIDTEgtfrpERLLAI---AERYG 155
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 1391259463 146 L-PTAELNMLSETS----------IEQICLIASQEKPKLMVIDSIQVMHMAD 186
Cdd:TIGR02239 156 LnPEDVLDNVAYARayntdhqlqlLQQAAAMMSESRFALLIVDSATALYRTD 207
|
|
| PRK05636 |
PRK05636 |
replicative DNA helicase; Provisional |
79-140 |
3.74e-03 |
|
replicative DNA helicase; Provisional
Pssm-ID: 180177 [Multi-domain] Cd Length: 505 Bit Score: 39.82 E-value: 3.74e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1391259463 79 TGFKEFDRvLGGGVVPGSAILIGGSPGAGKSTLLLQTM--CRLATEMKTLYVTGEESLQQVAMR 140
Cdd:PRK05636 250 TGFKDLDD-LTNGLRGGQMIIVAARPGVGKSTLALDFMrsASIKHNKASVIFSLEMSKSEIVMR 312
|
|
| AAA_14 |
pfam13173 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
97-180 |
6.63e-03 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.
Pssm-ID: 463799 [Multi-domain] Cd Length: 128 Bit Score: 36.80 E-value: 6.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391259463 97 AILIGGSPGAGKSTLLLQTMCRLATEMKTLYVTGEESlqqvamrahrlglptaELNMLSETSIEQICLIASQEKPKLMVI 176
Cdd:pfam13173 4 ILVITGPRQVGKTTLLLQLIKELLPPENILYINLDDP----------------RLLKLADFELLELFLELLYPGKTYLFL 67
|
....
gi 1391259463 177 DSIQ 180
Cdd:pfam13173 68 DEIQ 71
|
|
| |
