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Conserved domains on  [gi|949735726|gb|ALN12604|]
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recombinase A, partial [Burkholderia vietnamiensis]

Protein Classification

DNA recombination/repair protein RecA( domain architecture ID 1000164)

DNA recombination/repair protein RecA catalyzes an ATP-dependent DNA strand-exchange reaction, which is a critical step in the repair of DNA double-strand breaks by homologous recombination

Gene Ontology:  GO:0005524|GO:0006310|GO:0006281
PubMed:  31100988

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
recA super family cl35814
recombinase A; Provisional
 1-113 2.61e-79

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 236.61  E-value: 2.61e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:PRK09354  25 GSIMRLGD-DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 103

                         90       100       110
                 ....*....|....*....|....*....|...
gi 949735726  81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:PRK09354 104 YAKKLGVDIDNLLVSQPDTGEQALEIADTLVRS 136
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-113 2.61e-79

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 236.61  E-value: 2.61e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:PRK09354  25 GSIMRLGD-DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 103

                         90       100       110
                 ....*....|....*....|....*....|...
gi 949735726  81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:PRK09354 104 YAKKLGVDIDNLLVSQPDTGEQALEIADTLVRS 136
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-113 5.17e-77

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 230.83  E-value: 5.17e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:COG0468   28 GSIMRLGD-KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPE 106

                         90       100       110
                 ....*....|....*....|....*....|...
gi 949735726  81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:COG0468  107 YAKKLGVDIDNLLVSQPDTGEQALEIAETLVRS 139
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-113 5.77e-69

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: 207.25  E-value: 5.77e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726    1 GSIMRMGDGDvKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:pfam00154  17 GSIMKLGDEK-KLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 95

                          90       100       110
                  ....*....|....*....|....*....|...
gi 949735726   81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:pfam00154  96 YAKKLGVDIDNLLVSQPDTGEQALEIADMLVRS 128
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-113 2.15e-68

protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 162659 [Multi-domain]  Cd Length: 321  Bit Score: 207.61  E-value: 2.15e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726    1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:TIGR02012  20 GSIMRLGE-KTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 98

                          90       100       110
                  ....*....|....*....|....*....|...
gi 949735726   81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:TIGR02012  99 YARKLGVDIDNLLVSQPDTGEQALEIAETLVRS 131
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 14-113 1.84e-64

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: 195.08  E-value: 1.84e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  14 DIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQYAAKLGVNVPELL 93
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100
                 ....*....|....*....|
gi 949735726  94 ISQPDTGEQALEITDALVRS 113
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRS 100
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 36-112 1.05e-05

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: 41.98  E-value: 1.05e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 949735726    36 RGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQYAAKLGVNVPELLISqpDTGEQALEITDALVR 112
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALAR 75
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-113 2.61e-79

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 236.61  E-value: 2.61e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:PRK09354  25 GSIMRLGD-DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 103

                         90       100       110
                 ....*....|....*....|....*....|...
gi 949735726  81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:PRK09354 104 YAKKLGVDIDNLLVSQPDTGEQALEIADTLVRS 136
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-113 5.17e-77

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 230.83  E-value: 5.17e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:COG0468   28 GSIMRLGD-KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPE 106

                         90       100       110
                 ....*....|....*....|....*....|...
gi 949735726  81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:COG0468  107 YAKKLGVDIDNLLVSQPDTGEQALEIAETLVRS 139
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-113 5.77e-69

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: 207.25  E-value: 5.77e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726    1 GSIMRMGDGDvKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:pfam00154  17 GSIMKLGDEK-KLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 95

                          90       100       110
                  ....*....|....*....|....*....|...
gi 949735726   81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:pfam00154  96 YAKKLGVDIDNLLVSQPDTGEQALEIADMLVRS 128
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-113 2.15e-68

protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 162659 [Multi-domain]  Cd Length: 321  Bit Score: 207.61  E-value: 2.15e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726    1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:TIGR02012  20 GSIMRLGE-KTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV 98

                          90       100       110
                  ....*....|....*....|....*....|...
gi 949735726   81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:TIGR02012  99 YARKLGVDIDNLLVSQPDTGEQALEIAETLVRS 131
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 14-113 1.84e-64

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: 195.08  E-value: 1.84e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  14 DIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQYAAKLGVNVPELL 93
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100
                 ....*....|....*....|
gi 949735726  94 ISQPDTGEQALEITDALVRS 113
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRS 100
recA PRK09519
intein-containing recombinase RecA;
1-113 1.00e-47

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 162.18  E-value: 1.00e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   1 GSIMRMGDgDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQ 80
Cdd:PRK09519  25 GSVMRLGD-EARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPD 103

                         90       100       110
                 ....*....|....*....|....*....|...
gi 949735726  81 YAAKLGVNVPELLISQPDTGEQALEITDALVRS 113
Cdd:PRK09519 104 YAKKLGVDTDSLLVSQPDTGEQALEIADMLIRS 136
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 37-113 2.09e-18

RecA family; 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. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs RadA and RadB.


Pssm-ID: 410881 [Multi-domain]  Cd Length: 185  Bit Score: 75.85  E-value: 2.09e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  37 GRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQYAAKLGVNVPE-----------LLISQPDTGEQALE 105
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVQILEASPSselelaealsrLLYFRPPDTLAHLL 80


                 ....*...
gi 949735726 106 ITDALVRS 113
Cdd:cd01393   81 ALDSLPES 88
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 18-74 3.27e-11

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: 57.32  E-value: 3.27e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAE 74
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE 56
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
7-104 2.28e-10

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 55.32  E-value: 2.28e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726   7 GDGDVKEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYGPE-SSGKTTLTLQVIAELQKLGGTAAFIDAEHALdvqYA--- 82
Cdd:COG4544   18 GEGLAAAARAVLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDL---YApgl 94

                         90       100
                 ....*....|....*....|..
gi 949735726  83 AKLGVNVPELLISQPDTGEQAL 104
Cdd:COG4544   95 AAAGLDPERLLLVRARRPADAL 116
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
18-93 2.50e-10

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 54.92  E-value: 2.50e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALD--VQYAAKLGVNVPELL 93
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEqlLRRAESLGLDLEEYI 78
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 15-74 6.74e-10

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 54.10  E-value: 6.74e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  15 IQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAE 74
Cdd:PRK09361   2 DERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE 60
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 25-74 1.92e-07

DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).


Pssm-ID: 274047 [Multi-domain]  Cd Length: 209  Bit Score: 47.03  E-value: 1.92e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 949735726   25 LDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAE 74
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE 49
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 18-71 6.84e-07

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: 45.72  E-value: 6.84e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFI 71
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFF 53
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 37-79 1.44e-06

XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells 2) 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. XRCC2, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC3, helps recruit RAD51 to the break site.


Pssm-ID: 410898 [Multi-domain]  Cd Length: 226  Bit Score: 44.65  E-value: 1.44e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 949735726  37 GRVVEIYGPESSGKTTLTLQVIA-----------ELQKLGGTAAFIDAEHALDV 79
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAArcilpsswggvPLGGLEAAVVFIDTDGRFDI 54
radA PRK04301
DNA repair and recombination protein RadA; Validated
 12-74 1.53e-06

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 44.87  E-value: 1.53e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 949735726  12 KEDIQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQK------LGGTAAFIDAE 74
Cdd:PRK04301  78 RKNVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQLpeekggLEGKAVYIDTE 145
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 12-74 1.63e-06

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: 44.60  E-value: 1.63e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 949735726   12 KEDIQVvSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAELQK-LGGT---AAFIDAE 74
Cdd:pfam08423  14 SELIQI-TTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLchTLCVTCQLPLeMGGGegkALYIDTE 80
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 18-71 2.16e-06

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: 44.26  E-value: 2.16e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFI 71
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYI 53
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 18-92 3.20e-06

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: 43.77  E-value: 3.20e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 949735726   18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAE-LQKLGGTAAFIDA-EHALDV-QYAAKLGVNVPEL 92
Cdd:pfam06745   1 VKTGIPGLDEILK-GGFPEGRVVLITGGPGTGKTIFGLQFLYNgALKYGEPGVFVTLeEPPEDLrENARSFGWDLEKL 77
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 11-74 6.16e-06

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 43.18  E-value: 6.16e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  11 VKEDIQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAEL--QKLGGT--AAFIDAE 74
Cdd:PLN03186  98 QRQEIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLchTLCVTCQLplDQGGGEgkAMYIDTE 166
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 36-112 1.05e-05

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: 41.98  E-value: 1.05e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 949735726    36 RGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDVQYAAKLGVNVPELLISqpDTGEQALEITDALVR 112
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALAR 75
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 26-76 1.08e-05

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: 42.31  E-value: 1.08e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 949735726  26 DIALGvGGLPRGRVVEIYGPESSGKT----TLTLQVIAELQKLGGTAA--FIDAEHA 76
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTqfalTLASSAAMPARKGGLDGGvlYIDTESK 56
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 18-93 1.51e-05

archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a homolog of Rad51. RAD51 recombinase plays an essential role in DNA repair by homologous recombination (HR)


Pssm-ID: 410923 [Multi-domain]  Cd Length: 233  Bit Score: 41.97  E-value: 1.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQK------LGGTAAFIDAEHALD----VQYAAKLGV 87
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeeggLNGKAVYIDTENTFRperiMQMAKALGL 79


                 ....*.
gi 949735726  88 NVPELL 93
Cdd:cd19515   80 DPDEVL 85
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 42-73 7.33e-05

ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family.


Pssm-ID: 376582 [Multi-domain]  Cd Length: 222  Bit Score: 40.00  E-value: 7.33e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 949735726   42 IYGPESSGKTTLTLQVIAELQKLGGTAAFIDA 73
Cdd:pfam01637  25 IYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 25-77 1.11e-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: 39.58  E-value: 1.11e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 949735726  25 LDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIA------ELQKLGGTAAFIDAEHAL 77
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALtvqlprELGGLGGGAVYICTESSF 58
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 13-94 2.33e-04

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: 38.67  E-value: 2.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949735726  13 EDIQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVIAELQKLGGTAAFIDAEHALDvQY---AAKLGVNV 89
Cdd:cd01121   59 EEEERISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLS-QIklrAERLGLGS 136


                 ....*
gi 949735726  90 PELLI 94
Cdd:cd01121  137 DNLYL 141
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 12-74 2.67e-04

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: 38.55  E-value: 2.67e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 949735726   12 KEDIQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAEL---QKLG-GTAAFIDAE 74
Cdd:TIGR02239  72 RQEVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLchTLAVTCQLpidQGGGeGKALYIDTE 139
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 18-74 3.14e-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: 38.07  E-value: 3.14e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAEL---QKLG-GTAAFIDAE 74
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTQLchTLAVTCQLpidQGGGeGKALYIDTE 62
PTZ00035 PTZ00035
Rad51 protein; Provisional
 18-74 3.19e-04

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 38.44  E-value: 3.19e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAEL---QKLG-GTAAFIDAE 74
Cdd:PTZ00035 100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLchTLCVTCQLpieQGGGeGKVLYIDTE 161
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 18-74 3.38e-04

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: 38.28  E-value: 3.38e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAELQ----KLGGTAAFIDAE 74
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTQLchTLAVTCQLPidrgGGEGKAIYIDTE 62
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 32-72 3.70e-04

RAD51D recombinase; RAD51D 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. RAD51D, together with the other RAD51 paralogs, RAD51B, RAD51C, XRCC3, and XRCC2, helps recruit RAD51 to the break site.


Pssm-ID: 410897 [Multi-domain]  Cd Length: 209  Bit Score: 38.00  E-value: 3.70e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 949735726  32 GGLPRGRVVEIYGPESSGKTTLTLQVIAEL-QKLGGTAAFID 72
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTQLCLTAAANVaSRSGQNVLYID 43
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 12-58 4.80e-04

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 37.64  E-value: 4.80e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 949735726  12 KEDIQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQVI 58
Cdd:PRK06067   1 EGKKEIISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFV 46
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 12-74 8.71e-04

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 37.06  E-value: 8.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 949735726  12 KEDIQVVSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTL--TLQVIAEL-QKLGG---TAAFIDAE 74
Cdd:PLN03187 102 RKSVVRITTGSQALDELLG-GGIETRCITEAFGEFRSGKTQLahTLCVTTQLpTEMGGgngKVAYIDTE 169
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
18-56 1.34e-03

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 36.35  E-value: 1.34e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 949735726  18 VSTGSLGLDIALGvGGLPRGRVVEIYGPESSGKTTLTLQ 56
Cdd:COG2874    3 ISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQ 40
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 38-56 2.02e-03

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 35.57  E-value: 2.02e-03
                         10
                 ....*....|....*....
gi 949735726  38 RVVeIYGPESSGKTTLTLQ 56
Cdd:COG3172   10 KIV-LLGAESTGKTTLARA 27
fbpC PRK11432
ferric ABC transporter ATP-binding protein;
34-74 3.49e-03

ferric ABC transporter ATP-binding protein;


Pssm-ID: 183133 [Multi-domain]  Cd Length: 351  Bit Score: 35.47  E-value: 3.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 949735726  34 LPRGRVVEIYGPESSGKTTLtLQVIAELQKLGGTAAFIDAE 74
Cdd:PRK11432  29 IKQGTMVTLLGPSGCGKTTV-LRLVAGLEKPTEGQIFIDGE 68
Rad51C cd19492
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 37-81 3.84e-03

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: 34.89  E-value: 3.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 949735726  37 GRVVEIYGPESSGKTTLTLQVIAELQ------KLGGTAAFIDAEHALDVQY 81
Cdd:cd19492    1 GKITEICGVPGVGKTQLCMQLAVNVQipkcfgGLAGEAIYIDTEGSFNIHY 51
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
26-62 3.90e-03

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 35.44  E-value: 3.90e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 949735726  26 DIALGVgglPRGRVVEIYGPESSGKTTLtLQVIAELQ 62
Cdd:PRK10851  20 DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAGLE 52
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 36-84 6.51e-03

AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.


Pssm-ID: 433243  Cd Length: 199  Bit Score: 34.22  E-value: 6.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 949735726   36 RGRVVEIYGPESSGKTTLTLQViaelqklgGTAAFIDAEHALDVQYAAK 84
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFAKTL--------PKPLFLDTEKGSKALDGDR 41
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
34-84 9.26e-03

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 34.15  E-value: 9.26e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 949735726  34 LPRGRVVEIYGPESSGKTTLTLQVIAELQKlggtAAFIDAEHALDVQYAAK 84
Cdd:COG1373   17 LDNRKAVVITGPRQVGKTTLLKQLAKELEN----ILYINLDDPRLRALAEE 63
 
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.
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