NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|375813399|gb|AFA84928|]
View 

DNA repair protein RadA, partial [Aeromonas taiwanensis]

Protein Classification

DNA repair protein RadA family protein( domain architecture ID 1008227)

DNA repair protein RadA family protein is an AAA+ ATPase that may be responsible for the stabilization or processing of branched DNA molecules

EC:  3.6.4.-
Gene Ontology:  GO:0046872|GO:0005524|GO:0016887|GO:0003684|GO:0140664|GO:0006281

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Sms super family cl34087
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-135 4.17e-66

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1066:

Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 206.82  E-value: 4.17e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   1 CGECKEWNTITEVRlgVATPGKSARYTGYAGAiGSQVQTLAEIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGA 80
Cdd:COG1066   24 CPECGAWNTLVEEV--VAKAKKGRAASGAAGR-ASKPVPLSEVEAEEEPRISTGIGELDRVLGGGLVPGSVVLIGGEPGI 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  81 GKSTLLLQTMCGLAERM-KTLYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:COG1066  101 GKSTLLLQVAARLAKKGgKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEA 156
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-135 4.17e-66

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 206.82  E-value: 4.17e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   1 CGECKEWNTITEVRlgVATPGKSARYTGYAGAiGSQVQTLAEIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGA 80
Cdd:COG1066   24 CPECGAWNTLVEEV--VAKAKKGRAASGAAGR-ASKPVPLSEVEAEEEPRISTGIGELDRVLGGGLVPGSVVLIGGEPGI 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  81 GKSTLLLQTMCGLAERM-KTLYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:COG1066  101 GKSTLLLQVAARLAKKGgKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEA 156
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 1-135 1.74e-60

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: 186.97  E-value: 1.74e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   1 CGECKEWNTITEVrlgVATPGKSARYTGYAGAIGSQVQTLAEIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGA 80
Cdd:cd01121   17 CPSCGEWNTFVEE---VVSASSSASRRASASPSPSKPLPLSDVEAEEEERISTGIGELDRVLGGGLVPGSVVLIGGDPGI 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  81 GKSTLLLQTMCGLAER-MKTLYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:cd01121   94 GKSTLLLQVAARLAQRgGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEA 149
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 50-120 4.93e-10

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 56.04  E-value: 4.93e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375813399  50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLL---LQTMCGLAERmkTLYVTGEESLQQVAMRASRLGL 120
Cdd:PRK09302 254 RISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLAskfAEAACRRGER--CLLFAFEESRAQLIRNARSWGI 325
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 52-126 8.91e-09

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: 51.86  E-value: 8.91e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399   52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLAERM--KTLYVTGEESLQQVAMRASRLGLPTDKLR 126
Cdd:pfam06745   2 KTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYgePGVFVTLEEPPEDLRENARSFGWDLEKLE 78
circ_KaiC TIGR02655
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, ...
 50-125 1.03e-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: 40.70  E-value: 1.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375813399   50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLL---LQTMCGLAERmkTLYVTGEESLQQVAMRASRLGLPTDKL 125
Cdd:TIGR02655 244 RVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVskfLENACANKER--AILFAYEESRAQLLRNAYSWGIDFEEM 320
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 68-135 9.20e-03

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: 34.27  E-value: 9.20e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375813399    68 PGSAILIGGNPGAGKSTLLLQTMCGLAERMKT-LYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGvIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRL 69
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-135 4.17e-66

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 206.82  E-value: 4.17e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   1 CGECKEWNTITEVRlgVATPGKSARYTGYAGAiGSQVQTLAEIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGA 80
Cdd:COG1066   24 CPECGAWNTLVEEV--VAKAKKGRAASGAAGR-ASKPVPLSEVEAEEEPRISTGIGELDRVLGGGLVPGSVVLIGGEPGI 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  81 GKSTLLLQTMCGLAERM-KTLYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:COG1066  101 GKSTLLLQVAARLAKKGgKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEA 156
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 1-135 1.74e-60

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: 186.97  E-value: 1.74e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   1 CGECKEWNTITEVrlgVATPGKSARYTGYAGAIGSQVQTLAEIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGA 80
Cdd:cd01121   17 CPSCGEWNTFVEE---VVSASSSASRRASASPSPSKPLPLSDVEAEEEERISTGIGELDRVLGGGLVPGSVVLIGGDPGI 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  81 GKSTLLLQTMCGLAER-MKTLYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:cd01121   94 GKSTLLLQVAARLAQRgGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEA 149
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
50-125 2.12e-19

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 79.96  E-value: 2.12e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399  50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQ-TMCGLAERMKTLYVTGEESLQQVAMRASRLGLPTDKL 125
Cdd:COG0467    1 RVPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQfLAEGLRRGEKGLYVSFEESPEQLLRRAESLGLDLEEY 77
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 52-120 1.24e-10

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: 56.50  E-value: 1.24e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQ-TMCGLAERMKTLYVTGEESLQQVAMRASRLGL 120
Cdd:cd01124    2 KTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLFGLQfLYAGAKNGEPGLFFTFEESPERLLRNAKSFGW 71
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 52-128 2.03e-10

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: 56.20  E-value: 2.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMC-GLAERMKTLYVTGEESLQQVAMRASRLGLPTDKLRML 128
Cdd:cd19488    2 STGIPGLDDILRGGLPPRRLYLVEGAPGTGKTTLALQFLLeGAANGETGLYITLSETEQELRAVALSHGWSLDGIHIF 79
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 50-120 4.93e-10

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 56.04  E-value: 4.93e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375813399  50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLL---LQTMCGLAERmkTLYVTGEESLQQVAMRASRLGL 120
Cdd:PRK09302 254 RISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLAskfAEAACRRGER--CLLFAFEESRAQLIRNARSWGI 325
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 52-135 2.04e-09

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: 53.46  E-value: 2.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLAER-MKTLYVTGEESLQQVAMRASRLGLPTDKLRMLSE 130
Cdd:cd19487    2 SSGVPELDELLGGGLERGTSTLLIGPAGVGKSTLALQFAKAAAARgERSVLFSFDESIGTLFERSEALGIDLRAMVEKGL 81


                 ....*
gi 375813399 131 TSVEQ 135
Cdd:cd19487   82 LSIEQ 86
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 52-126 6.25e-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: 52.13  E-value: 6.25e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375813399  52 SSGFKELDRVLGGgVVPGSAILIGGNPGAGKSTLLLQTM--CGLAERMKTLYVTGEESLQQVAMR--ASRLGLPTDKLR 126
Cdd:cd00984    3 PTGFTDLDKLTGG-LQPGDLIIIAARPSMGKTAFALNIAenIALDEGLPVLFFSLEMSAEQLAERllSSESGVSLSKLR 80
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 52-126 8.91e-09

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: 51.86  E-value: 8.91e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399   52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLAERM--KTLYVTGEESLQQVAMRASRLGLPTDKLR 126
Cdd:pfam06745   2 KTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYgePGVFVTLEEPPEDLRENARSFGWDLEKLE 78
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
50-105 1.27e-07

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 48.29  E-value: 1.27e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399  50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCG-LAERMKTLYVTGE 105
Cdd:COG2874    2 IISTGNDELDKRLGGGIPLGSLVLIEGENGTGKSVLSQQFAYGaLENGLSVTYISTE 58
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 52-112 3.89e-07

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: 46.92  E-value: 3.89e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLAER-MKTLYVTGE----ESLQQVA 112
Cdd:cd01394    2 STGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICLQLAVEAAKQgKKVVYIDTEglspERFQQIA 67
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 52-126 4.87e-07

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: 4.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   52 SSGFKELDRVLgGGVVPGSAILIGGNPGAGKSTLLL---QTMCgLAERMKTLYVTGEESLQQVAMR--ASRLGLPTDKLR 126
Cdd:pfam03796   3 PTGFTDLDRLT-GGLQPGDLIIIAARPSMGKTAFALniaRNAA-VKHKKPVAIFSLEMSAEQLVMRllASEAGVDSQKLR 80
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 52-120 7.01e-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: 46.17  E-value: 7.01e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 375813399  52 SSGFKELDRVL-GGGVVPGSAILIGGNPGAGKSTL---LLQTMCGLAERmkTLYVTGEESLQQVAMRASRLGL 120
Cdd:cd19484    2 STGIPRLDAMLgGGGFFRGSSILVSGATGTGKTLLaasFADAACRRGER--CLYFAFEESPAQLIRNAKSIGI 72
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
47-126 8.45e-07

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 46.61  E-value: 8.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  47 EIPRFSSGFKELDRVLgGGVVPGSAILIGGNPGAGKSTLLLQTMCGLA--ERMKTLYVTGEESLQQVAMR--ASRLGLPT 122
Cdd:COG0305  170 GITGVPTGFTDLDKLT-GGLQPGDLIILAARPSMGKTAFALNIARNAAikEGKPVAIFSLEMSAEQLVMRllSSEARIDS 248


                 ....
gi 375813399 123 DKLR 126
Cdd:COG0305  249 SKLR 252
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 41-135 8.59e-07

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: 45.83  E-value: 8.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   41 AEIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLA------------ERMKTLYVTGEESL 108
Cdd:pfam13481   5 LELLDVLADGLAAPPPPRRWLIKGLLPAGGLGLLAGAPGTGKTTLALDLAAAVAtgkpwlggprvpEQGKVLYVSAEGPA 84

                          90       100
                  ....*....|....*....|....*..
gi 375813399  109 QQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:pfam13481  85 DELRRRLRAAGADLDLPARLLFLSLVE 111
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 52-107 2.26e-06

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 44.96  E-value: 2.26e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCG-LAERMKTLYVTGEES 107
Cdd:PRK06067   8 STGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGaLKQGKKVYVITTENT 64
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 50-112 4.27e-06

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 44.08  E-value: 4.27e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 375813399  50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLAER-MKTLYVTGE----ESLQQVA 112
Cdd:PRK09361   4 RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNgKKVIYIDTEglspERFKQIA 71
PRK07773 PRK07773
replicative DNA helicase; Validated
 48-126 1.03e-05

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 43.59  E-value: 1.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  48 IPRFSSGFKELDRvLGGGVVPGSAILIGGNPGAGKSTLLLQTMCGLAERMKTLYV--TGEESLQQVAMR--ASRLGLPTD 123
Cdd:PRK07773 197 ARGVPTGFTELDA-MTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAifSLEMSKEQLVMRllSAEAKIKLS 275


                 ...
gi 375813399 124 KLR 126
Cdd:PRK07773 276 DMR 278
PRK05636 PRK05636
replicative DNA helicase; Provisional
 17-114 1.69e-05

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 42.90  E-value: 1.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  17 VATPGKSARYTGYAGAIGSQVQTLAEIAT-----TEIPrfsSGFKELDRvLGGGVVPGSAILIGGNPGAGKSTLLLQTM- 90
Cdd:PRK05636 212 VSQKNQSEDYAVLADILDPTMDELEMLSSqggiaTGIP---TGFKDLDD-LTNGLRGGQMIIVAARPGVGKSTLALDFMr 287

                         90       100
                 ....*....|....*....|....*
gi 375813399  91 -CGLAERMKTLYVTGEESLQQVAMR 114
Cdd:PRK05636 288 sASIKHNKASVIFSLEMSKSEIVMR 312
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
65-119 2.20e-05

RecA-family ATPase [Replication, recombination and repair];


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 42.58  E-value: 2.20e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  65 GVVP-GSAILIGGNPGAGKSTLLLQTMCGLA----------ERMKTLYVTGEESLQQVAMRASRLG 119
Cdd:COG3598    8 GLLPeGGVTLLAGPPGTGKSFLALQLAAAVAaggpwlgrrvPPGKVLYLAAEDDRGELRRRLKALG 73
circ_KaiC TIGR02655
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, ...
 50-125 1.03e-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: 40.70  E-value: 1.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375813399   50 RFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLL---LQTMCGLAERmkTLYVTGEESLQQVAMRASRLGLPTDKL 125
Cdd:TIGR02655 244 RVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVskfLENACANKER--AILFAYEESRAQLLRNAYSWGIDFEEM 320
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 58-131 1.19e-04

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: 39.97  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  58 LDRVLGGGVVPGSAILIGGNPGAGKSTLLLQ---------TMCGLAErmKTLYVTGEESlqqvamrasrlgLPTDKLRML 128
Cdd:cd19491    1 LDELLGGGIPVGGITEIAGESGAGKTQLCLQlaltvqlprELGGLGG--GAVYICTESS------------FPSKRLQQL 66


                 ...
gi 375813399 129 SET 131
Cdd:cd19491   67 ASS 69
PRK04328 PRK04328
hypothetical protein; Provisional
 48-111 1.73e-04

hypothetical protein; Provisional


Pssm-ID: 235281  Cd Length: 249  Bit Score: 39.67  E-value: 1.73e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 375813399  48 IPRFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTMC-GLAERMKTLYVTGEESLQQV 111
Cdd:PRK04328   2 VKRVKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWnGLQMGEPGVYVALEEHPVQV 66
PRK08533 PRK08533
flagellar accessory protein FlaH; Reviewed
 42-85 4.25e-04

flagellar accessory protein FlaH; Reviewed


Pssm-ID: 181459  Cd Length: 230  Bit Score: 38.51  E-value: 4.25e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 375813399  42 EIATTEIPRfssgfKELDRVLGGGVVPGSAILIGGNPGAGKSTL 85
Cdd:PRK08533   2 ELAKIELSR-----DELHKRLGGGIPAGSLILIEGDESTGKSIL 40
FlaH cd19475
flagellar accessory protein FlaH; Flagellar accessory protein FlaH is part of the motor of the ...
 52-107 1.77e-03

flagellar accessory protein FlaH; Flagellar accessory protein FlaH is part of the motor of the archaellum membrane-anchored archaeal motility structure, together with FlaX and FlaI. FlaH forms a hexameric ring, and binds ATP which is essential for its interaction with FlaI and for archaellum assembly.


Pssm-ID: 410883  Cd Length: 220  Bit Score: 36.81  E-value: 1.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQ-TMCGLAERMKTLYVTGEES 107
Cdd:cd19475    2 SLGRDDLDKRLGGGIPYPSSIMIEGEESTGKSVLSQRlVYGFLQNDYSGYYISTQQT 58
YddA COG4178
ABC-type uncharacterized transport system, permease and ATPase components [General function ...
 68-93 2.74e-03

ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only];


Pssm-ID: 443337 [Multi-domain]  Cd Length: 571  Bit Score: 36.32  E-value: 2.74e-03
                         10        20
                 ....*....|....*....|....*.
gi 375813399  68 PGSAILIGGNPGAGKSTlLLQTMCGL 93
Cdd:COG4178  388 PGERLLITGPSGSGKST-LLRAIAGL 412
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
40-125 2.80e-03

RecA/RadA recombinase [Replication, recombination and repair];


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 36.30  E-value: 2.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  40 LAEIATTEIPRFSSGFKELDRVLGGGVVP-GSAILIGGNPGAGKSTLLLQTMcglAERMKT----LYVTGEESLQQVamR 114
Cdd:COG0468   33 LGDKARQDVEVISTGSLALDIALGVGGLPrGRIVEIYGPESSGKTTLALHAI---AEAQKAggiaAFIDAEHALDPE--Y 107

                         90
                 ....*....|.
gi 375813399 115 ASRLGLPTDKL 125
Cdd:COG0468  108 AKKLGVDIDNL 118
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 47-114 2.87e-03

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: 36.13  E-value: 2.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   47 EIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTL--LLQTMCGLAERM-----KTLYVTGE-----ESLQQVAMR 114
Cdd:pfam08423  15 ELIQITTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLchTLCVTCQLPLEMgggegKALYIDTEgtfrpERLVAIAER 94
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 37-125 3.04e-03

recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyzes an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.


Pssm-ID: 425488 [Multi-domain]  Cd Length: 262  Bit Score: 36.22  E-value: 3.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   37 VQTLAEIATTEIPRFSSGFKELDRVLG-GGVVPGSAILIGGNPGAGKSTLLLQTMCGLAERMKTL-YVTGEESLQQVamR 114
Cdd:pfam00154  19 IMKLGDEKKLDVETISTGSLALDIALGiGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAaFIDAEHALDPV--Y 96

                          90
                  ....*....|.
gi 375813399  115 ASRLGLPTDKL 125
Cdd:pfam00154  97 AKKLGVDIDNL 107
KaiC-N cd19485
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most ...
 53-125 3.30e-03

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: 35.81  E-value: 3.30e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 375813399  53 SGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQ-TMCGLAERMKT-LYVTGEESLQQVAMRASRLGLPTDKL 125
Cdd:cd19485    3 TGIEGFDDITHGGLPKGRPTLICGTAGTGKTLFAAQfLVNGIKEFGEPgVFVTFEESPEDIIKNMASFGWDLPKL 77
KaiC_arch cd19486
KaiC family protein; uncharacterized subfamily similar to Pyrococcus horikoshii PH0284; KaiC ...
 52-111 3.31e-03

KaiC family protein; uncharacterized subfamily similar to Pyrococcus horikoshii PH0284; 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: 410894  Cd Length: 230  Bit Score: 35.91  E-value: 3.31e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTM-CGLAERMKTLYVTGEESLQQV 111
Cdd:cd19486    2 KTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLwNGLKEGEPGVFVALEEHPVQV 62
CcmA COG4133
ABC-type transport system involved in cytochrome c biogenesis, ATPase component ...
 68-119 3.74e-03

ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443308 [Multi-domain]  Cd Length: 206  Bit Score: 35.53  E-value: 3.74e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 375813399  68 PGSAILIGGNPGAGKSTlLLQTMCGLAERMK-TLYVTGEESLQQVAMRASRLG 119
Cdd:COG4133   27 AGEALALTGPNGSGKTT-LLRILAGLLPPSAgEVLWNGEPIRDAREDYRRRLA 78
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 42-125 3.97e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 36.01  E-value: 3.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  42 EIATTEIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLLQTmcgLAERMKT-----LYVTGEESLQQVAMRAS 116
Cdd:PRK09302   4 PSASPGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQF---LVNGIKRfdepgVFVTFEESPEDIIRNVA 80


                 ....*....
gi 375813399 117 RLGLPTDKL 125
Cdd:PRK09302  81 SFGWDLQKL 89
Elp4 cd19494
Elongator subcomplex subunit Elp4; Elongator is a highly conserved multiprotein complex ...
 52-87 5.46e-03

Elongator subcomplex subunit Elp4; Elongator is a highly conserved multiprotein complex involved in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. It is composed of two subcomplexes, Elp1-3 and Elp4-6. Elp4-6 forms a heterohexameric RecA-like ring structure, although they lack the key sequence signatures of ATPases.


Pssm-ID: 410902  Cd Length: 259  Bit Score: 35.36  E-value: 5.46e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 375813399  52 SSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLLL 87
Cdd:cd19494   14 STGIASLDDLLGGGLPLGSLLLIEEDSHSSYAKLLL 49
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 51-114 6.43e-03

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: 34.99  E-value: 6.43e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375813399  51 FSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTLL--LQTMCGLAERM-----KTLYVTGE-----ESLQQVAMR 114
Cdd:cd19513    1 ITTGSKELDKLLGGGIETGSITELFGEFRTGKTQLChtLAVTCQLPIDQgggegKALYIDTEgtfrpERLLAIAER 76
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 47-125 7.33e-03

recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange.


Pssm-ID: 410863 [Multi-domain]  Cd Length: 235  Bit Score: 34.84  E-value: 7.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399  47 EIPRFSSGFKELDRVLGGGVVP-GSAILIGGNPGAGKSTLLLQTMcglAERMKT----LYVTGEESLQQVAmrASRLGLP 121
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPrGRIIEIYGPESSGKTTLALHAI---AEAQKLggtaAFIDAEHALDPEY--AKKLGVD 75


                 ....
gi 375813399 122 TDKL 125
Cdd:cd00983   76 IDNL 79
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 47-114 8.85e-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: 34.70  E-value: 8.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813399   47 EIPRFSSGFKELDRVLGGGVVPGSAILIGGNPGAGKSTL--LLQTMCGLAERM-----KTLYVTGE-----ESLQQVAMR 114
Cdd:TIGR02239  74 EVIQLTTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLchTLAVTCQLPIDQgggegKALYIDTEgtfrpERLLAIAER 153
Herpes_Helicase pfam02689
Helicase; This family consists of Helicases from the Herpes viruses. Helicases are responsible ...
 32-84 9.00e-03

Helicase; This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle.


Pssm-ID: 280797  Cd Length: 809  Bit Score: 35.07  E-value: 9.00e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 375813399   32 AIGSQVQTLAEIATTEIPRFSSGFKELDRVLGGG----VVPGSAILIGGNPGAGKST 84
Cdd:pfam02689  19 PIVDKIRSLSRERTAQPPEMQWFRSEFDPEDPEGpnfsELPFSAYLITGTAGAGKST 75
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 68-135 9.20e-03

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: 34.27  E-value: 9.20e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375813399    68 PGSAILIGGNPGAGKSTLLLQTMCGLAERMKT-LYVTGEESLQQVAMRASRLGLPTDKLRMLSETSVEQ 135
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGvIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRL 69
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH