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Conserved domains on  [gi|1958786037|ref|XP_038969210|]
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DNA repair protein RAD51 homolog 2 isoform X6 [Rattus norvegicus]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 91-267 5.30e-73

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19493:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 222  Bit Score: 223.35  E-value: 5.30e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  91 DEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYF----NT 166
Cdd:cd19493     1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAMPARKGGLDGGVLYIDTESKFSAERLAEIAEARFPEAFsgfmEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 167 EEKLLLTSSRVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPQLqGNIKERNKFLGKGASLLKYLS 246
Cdd:cd19493    81 NERAEEMLKRVAVVRVTTLAQLLERLPNLEEHILSSGVRLVVIDSIAALVRREFGGSD-GEVTERHNALAREASSLKRLA 159

                         170       180
                  ....*....|....*....|.
gi 1958786037 247 GEFSVPVILTNQITTHLSGAL 267
Cdd:cd19493   160 EEFRIAVLVTNQATTHFGDAG 180
 
Name Accession Description Interval E-value
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 91-267 5.30e-73

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: 223.35  E-value: 5.30e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  91 DEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYF----NT 166
Cdd:cd19493     1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAMPARKGGLDGGVLYIDTESKFSAERLAEIAEARFPEAFsgfmEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 167 EEKLLLTSSRVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPQLqGNIKERNKFLGKGASLLKYLS 246
Cdd:cd19493    81 NERAEEMLKRVAVVRVTTLAQLLERLPNLEEHILSSGVRLVVIDSIAALVRREFGGSD-GEVTERHNALAREASSLKRLA 159

                         170       180
                  ....*....|....*....|.
gi 1958786037 247 GEFSVPVILTNQITTHLSGAL 267
Cdd:cd19493   160 EEFRIAVLVTNQATTHFGDAG 180
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 65-276 1.07e-42

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: 146.68  E-value: 1.07e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  65 QTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTE 144
Cdd:pfam08423   4 TTATELHQRRSELIQ---ITTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 145 SAFTAERLVEIAEsRFPqyFNTEEKLL-LTSSRVHlcqelTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPq 223
Cdd:pfam08423  81 GTFRPERLVAIAE-RYG--LDPEDVLDnVAYARAY-----NSEHQMQLLQQAAAMMSESRFALLIVDSATALYRTDFSG- 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958786037 224 lQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSG-ALPSQADLVSP 276
Cdd:pfam08423 152 -RGELAERQQHLAKFLRTLQRLADEFGVAVVITNQVVAQVDGaAGMFSGDPKKP 204
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 37-277 1.84e-35

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: 129.51  E-value: 1.84e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  37 ELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQ 116
Cdd:TIGR02238  35 ALCKIKGLSEAKVDKIKEAASKIINPGFITAFEISQKRKKVLK---ITTGSQALDGILGGGIESMSITEVFGEFRCGKTQ 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 117 FCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESrfpqyFNTEEKLLLTSsrVHLCQELTCEGLLQRLESLE 196
Cdd:TIGR02238 112 LSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAER-----FGVDPDAVLDN--ILYARAYTSEHQMELLDYLA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 197 EEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:TIGR02238 185 AKFSEEPFRLLIVDSIMALFRVDFSG--RGELSERQQKLAQMLSRLNKISEEFNVAVFVTNQVQADPGATMTFIADPKKP 262


                  .
gi 1958786037 277 A 277
Cdd:TIGR02238 263 I 263
PTZ00035 PTZ00035
Rad51 protein; Provisional
 37-277 6.09e-35

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 128.58  E-value: 6.09e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  37 ELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQ 116
Cdd:PTZ00035   57 DLCNIKGISEAKVEKIKEAASKLVPMGFISATEYLEARKNIIR---ITTGSTQLDKLLGGGIETGSITELFGEFRTGKTQ 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 117 FCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAEsRFPqyFNTEEKLlltsSRVHLCQELTCEGLLQRLESLE 196
Cdd:PTZ00035  134 LCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIAE-RFG--LDPEDVL----DNIAYARAYNHEHQMQLLSQAA 206

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 197 EEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:PTZ00035  207 AKMAEERFALLIVDSATALFRVDYSG--RGELAERQQHLGKFLRALQKLADEFNVAVVITNQVMADVDGASMFVADPKKP 284


                  .
gi 1958786037 277 A 277
Cdd:PTZ00035  285 I 285
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
83-261 2.43e-12

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 64.94  E-value: 2.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCimMSVLAtlptrlgglEGA-----VLYIDTESafTAERLVEIAE 157
Cdd:COG0467     2 VPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLA--LQFLA---------EGLrrgekGLYVSFEE--SPEQLLRRAE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 158 SR---FPQYFNtEEKLLLtssrVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPQlqgnikERNKF 234
Cdd:COG0467    69 SLgldLEEYIE-SGLLRI----IDLSPEELGLDLEELLARLREAVEEFGAKRVVIDSLSGLLLALPDPE------RLREF 137

                         170       180
                  ....*....|....*....|....*..
gi 1958786037 235 LgkgASLLKYLSgEFSVPVILTNQITT 261
Cdd:COG0467   138 L---HRLLRYLK-KRGVTTLLTSETGG 160
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 101-267 8.67e-06

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: 44.67  E-value: 8.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  101 GSLTEVTGPPGCGKTQFCIMMSVLatlptrLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYFNTEekllltssrvhlc 180
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARE------LGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS------------- 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  181 QELTCEGLLQRLESLeeeiiskGVKLVIVDSIASVVRKEFDPQLQGNIKERNKFLgkgasllkyLSGEFSVPVILTNQIT 260
Cdd:smart00382  63 GELRLRLALALARKL-------KPDVLILDEITSLLDAEQEALLLLLEELRLLLL---------LKSEKNLTVILTTNDE 126


                   ....*..
gi 1958786037  261 THLSGAL 267
Cdd:smart00382 127 KDLGPAL 133
 
Name Accession Description Interval E-value
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 91-267 5.30e-73

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: 223.35  E-value: 5.30e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  91 DEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYF----NT 166
Cdd:cd19493     1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAMPARKGGLDGGVLYIDTESKFSAERLAEIAEARFPEAFsgfmEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 167 EEKLLLTSSRVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPQLqGNIKERNKFLGKGASLLKYLS 246
Cdd:cd19493    81 NERAEEMLKRVAVVRVTTLAQLLERLPNLEEHILSSGVRLVVIDSIAALVRREFGGSD-GEVTERHNALAREASSLKRLA 159

                         170       180
                  ....*....|....*....|.
gi 1958786037 247 GEFSVPVILTNQITTHLSGAL 267
Cdd:cd19493   160 EEFRIAVLVTNQATTHFGDAG 180
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 101-277 6.47e-49

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: 160.60  E-value: 6.47e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 101 GSLTEVTGPPGCGKTQFCIMMSVLATLptrlggLEGAVLYIDTESAFTAERLVEIAEsrfpQYFNTEEKLLLTSSRVHLC 180
Cdd:cd01393     1 GKITEIYGPPGSGKTQLALQLAANALL------LGGGVVWIDTEGAFPPSRLVQILE----ASPSSELELAEALSRLLYF 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 181 QELTCEGLLQRLESLEEEIIS-KGVKLVIVDSIASVVRKEFDPQLQG--NIKERNKFLGKGASLLKYLSGEFSVPVILTN 257
Cdd:cd01393    71 RPPDTLAHLLALDSLPESLFPpPNTSLVVVDSVSALFRKAFPRGGDGdsSSSLRARLLSQLARALQKLAAQFNLAVVVTN 150

                         170       180
                  ....*....|....*....|
gi 1958786037 258 QITTHLSGAlpSQADLVSPA 277
Cdd:cd01393   151 QVTTKIRGG--SGASLVPPA 168
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 65-276 1.07e-42

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: 146.68  E-value: 1.07e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  65 QTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTE 144
Cdd:pfam08423   4 TTATELHQRRSELIQ---ITTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 145 SAFTAERLVEIAEsRFPqyFNTEEKLL-LTSSRVHlcqelTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPq 223
Cdd:pfam08423  81 GTFRPERLVAIAE-RYG--LDPEDVLDnVAYARAY-----NSEHQMQLLQQAAAMMSESRFALLIVDSATALYRTDFSG- 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958786037 224 lQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSG-ALPSQADLVSP 276
Cdd:pfam08423 152 -RGELAERQQHLAKFLRTLQRLADEFGVAVVITNQVVAQVDGaAGMFSGDPKKP 204
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 90-286 4.74e-40

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: 139.73  E-value: 4.74e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  90 LDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYFNTEEK 169
Cdd:cd19491     1 LDELLGGGIPVGGITEIAGESGAGKTQLCLQLALTVQLPRELGGLGGGAVYICTESSFPSKRLQQLASSLPKRYHLEKAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 170 LLLTSSRVHLCQEL----TCegLLQRLESLeeeIISKGVKLVIVDSIASVVRKEFDPQlQGNIKERNKFLGKGASLLKYL 245
Cdd:cd19491    81 NFLDNIFVEHVADLetleHC--LNYQLPAL---LERGPIRLVVIDSIAALFRSEFDTS-RSDLVERAKYLRRLADHLKRL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1958786037 246 SGEFSVPVILTNQITthlsgALPSQADLVSPADDLSPSEAW 286
Cdd:cd19491   155 ADKYNLAVVVVNQVT-----DRFDSSSDASGLGVLDYLSQF 190
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 37-277 1.84e-35

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: 129.51  E-value: 1.84e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  37 ELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQ 116
Cdd:TIGR02238  35 ALCKIKGLSEAKVDKIKEAASKIINPGFITAFEISQKRKKVLK---ITTGSQALDGILGGGIESMSITEVFGEFRCGKTQ 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 117 FCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESrfpqyFNTEEKLLLTSsrVHLCQELTCEGLLQRLESLE 196
Cdd:TIGR02238 112 LSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAER-----FGVDPDAVLDN--ILYARAYTSEHQMELLDYLA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 197 EEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:TIGR02238 185 AKFSEEPFRLLIVDSIMALFRVDFSG--RGELSERQQKLAQMLSRLNKISEEFNVAVFVTNQVQADPGATMTFIADPKKP 262


                  .
gi 1958786037 277 A 277
Cdd:TIGR02238 263 I 263
PTZ00035 PTZ00035
Rad51 protein; Provisional
 37-277 6.09e-35

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 128.58  E-value: 6.09e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  37 ELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQ 116
Cdd:PTZ00035   57 DLCNIKGISEAKVEKIKEAASKLVPMGFISATEYLEARKNIIR---ITTGSTQLDKLLGGGIETGSITELFGEFRTGKTQ 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 117 FCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAEsRFPqyFNTEEKLlltsSRVHLCQELTCEGLLQRLESLE 196
Cdd:PTZ00035  134 LCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIAE-RFG--LDPEDVL----DNIAYARAYNHEHQMQLLSQAA 206

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 197 EEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:PTZ00035  207 AKMAEERFALLIVDSATALFRVDYSG--RGELAERQQHLGKFLRALQKLADEFNVAVVITNQVMADVDGASMFVADPKKP 284


                  .
gi 1958786037 277 A 277
Cdd:PTZ00035  285 I 285
radA PRK04301
DNA repair and recombination protein RadA; Validated
 4-259 2.90e-34

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 126.15  E-value: 2.90e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037   4 KKLRRAGlsqelcdrlcryqIVNCQDFLNLSPLELMKVTGLSYRGVHELLHTVSKACA-PQMQTAYELKTRRsahLSPAF 82
Cdd:PRK04301   20 EKLREAG-------------YDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADiGGFETALEVLERR---KNVGK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESR--- 159
Cdd:PRK04301   84 ITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAEALgld 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 160 ---------FPQYFNTEEKLLLtssrvhlcqeltcegllqrLESLeEEIISKG--VKLVIVDSIASVVRKEFDPqlQGNI 228
Cdd:PRK04301  164 pdevldnihVARAYNSDHQMLL-------------------AEKA-EELIKEGenIKLVIVDSLTAHFRAEYVG--RGNL 221

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1958786037 229 KERNKFLGKGASLLKYLSGEFSVPVILTNQI 259
Cdd:PRK04301  222 AERQQKLNKHLHDLLRLADLYNAAVVVTNQV 252
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 83-276 8.34e-32

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: 117.63  E-value: 8.34e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAesrfpQ 162
Cdd:cd01123     1 ITTGSKELDKLLGGGIETGSITEMFGEFRTGKTQLCHTLAVTCQLPIDRGGGEGKAIYIDTEGTFRPERLRAIA-----Q 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 163 YFNTEEKLLLtsSRVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLL 242
Cdd:cd01123    76 RFGLDPDDVL--DNVAYARAFNSDHQTQLLDQAAAMMVESRFKLLIVDSATALYRTDYSG--RGELSARQMHLAKFLRML 151

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1958786037 243 KYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:cd01123   152 QRLADEFGVAVVVTNQVVAQVDGAMMFAADPKKP 185
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 83-276 9.56e-32

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: 117.46  E-value: 9.56e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESrfpq 162
Cdd:cd19514     1 ISTGSTELDKLLGGGIESMSITEVFGEFRTGKTQLSHTLCVTAQLPGSMGGGGGKVAYIDTEGTFRPDRIRPIAER---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 163 yFNTEEKLLLTSsrVHLCQELTCEGLLQRLESLEEEIISKGV-KLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASL 241
Cdd:cd19514    77 -FGVDHDAVLDN--ILYARAYTSEHQMELLDYVAAKFHEEAVfRLLIIDSIMALFRVDFSG--RGELAERQQKLAQMLSR 151

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1958786037 242 LKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:cd19514   152 LQKISEEYNVAVFITNQVTADPGAAMTFQADPKKP 186
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 4-265 8.15e-30

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 115.26  E-value: 8.15e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037   4 KKLRRAGlsqelcdrlcryqIVNCQDFLNLSPLELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafL 83
Cdd:PLN03187   45 KKLQDAG-------------IYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLKRKSVVR---I 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  84 STTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESrfpqy 163
Cdd:PLN03187  109 TTGSQALDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAER----- 183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 164 FNTEEKLLLTS---SRVHlcqelTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGAS 240
Cdd:PLN03187  184 FGMDADAVLDNiiyARAY-----TYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTG--RGELAERQQKLAQMLS 256

                         250       260
                  ....*....|....*....|....*
gi 1958786037 241 LLKYLSGEFSVPVILTNQITTHLSG 265
Cdd:PLN03187  257 RLTKIAEEFNVAVYMTNQVIADPGG 281
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 83-259 1.05e-29

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: 112.07  E-value: 1.05e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESR--- 159
Cdd:cd19515     1 ISTGSKELDKLLGGGIETQAITEVFGEFGSGKTQLCHQLAVNVQLPPEEGGLNGKAVYIDTENTFRPERIMQMAKALgld 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 160 ---------FPQYFNTEEKLLLtssrvhlcqeltcegllqrLESLeEEIISKG--VKLVIVDSIASVVRKEFDPqlQGNI 228
Cdd:cd19515    81 pdevldniyVARAYNSNHQMLL-------------------VEKA-EDLIKEGnnIKLLIVDSLTSHFRAEYVG--RGTL 138

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1958786037 229 KERNKFLGKGASLLKYLSGEFSVPVILTNQI 259
Cdd:cd19515   139 AERQQKLNKHLHDLHRLADLYNIAVLVTNQV 169
recomb_radA TIGR02236
DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA ...
 34-259 1.43e-29

DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 131290 [Multi-domain]  Cd Length: 310  Bit Score: 113.69  E-value: 1.43e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  34 SPLELMKVTGLSYRGVHELLHTVSKAC-APQMQTAYELKTRRSahlSPAFLSTTLGALDEALHGGVPCGSLTEVTGPPGC 112
Cdd:TIGR02236  30 SPKELSEIAGISEGTAAKIIQAARKAAdLGGFETADDVLERRK---TIGKITTGSKELDELLGGGIETQAITEVFGEFGS 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 113 GKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESR------------FPQYFNTEEKLLLTSSRVHLC 180
Cdd:TIGR02236 107 GKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMAEARgldpdevlkniyVARAYNSNHQMLLVEKAEDLI 186

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958786037 181 QELtcegllqrlesleeeiiSKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQI 259
Cdd:TIGR02236 187 KEL-----------------NNPVKLLIVDSLTSHFRAEYVG--RGALAERQQKLNKHLHDLLRLADLYNAAVVVTNQV 246
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 37-276 3.66e-29

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 113.29  E-value: 3.66e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  37 ELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQ 116
Cdd:PLN03186   62 DLLQIKGISEAKVEKILEAASKLVPLGFTTASQLHAQRQEIIQ---ITTGSRELDKILEGGIETGSITEIYGEFRTGKTQ 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 117 FCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAEsRFPqyFNTEEKLlltsSRVHLCQELTCEGLLQRLESLE 196
Cdd:PLN03186  139 LCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAE-RFG--LNGADVL----ENVAYARAYNTDHQSELLLEAA 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 197 EEIISKGVKLVIVDSIASVVRKEFDPQlqGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:PLN03186  212 SMMAETRFALMIVDSATALYRTEFSGR--GELSARQMHLGKFLRSLQRLADEFGVAVVITNQVVAQVDGSAFFAGPQLKP 289
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 96-268 4.67e-29

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: 109.65  E-value: 4.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  96 GGVPCGSLTEVTGPPGCGKTQFCimMSVLATLPTRLGgleGAVLYIDTESAFTAERLVEIAESRfpqyFNTEEKLLLTSS 175
Cdd:cd19489     2 GGLRTGEITELVGESSSGKTQLC--LTAAANVASRSG---QNVLYIDTKSSFSARRLAQILKSR----AQDAEEIDKALQ 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 176 RVHLCQELTCEGLLQRLESL------EEEIISKGVKLVIVDSIASVvrkeFDPQLQGNIK-ERNKFLGKGASLLKYLSGE 248
Cdd:cd19489    73 RIRVVRVFDPYELLDLLEELrntlsqQQENLYSRLKLVIIDSLSAL----ISPLLGGSKHsEGHALLASLARLLKKLAAE 148

                         170       180
                  ....*....|....*....|
gi 1958786037 249 FSVPVILTNQITTHLSGALP 268
Cdd:cd19489   149 YQIAVLVTNLTVRGGDGGQQ 168
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 83-276 2.06e-28

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: 108.94  E-value: 2.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAEsRFPq 162
Cdd:cd19513     1 ITTGSKELDKLLGGGIETGSITELFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERLLAIAE-RYG- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 163 yFNTEEKL-LLTSSRVHLCQELTceGLLQRLESLEEEiiSKgVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASL 241
Cdd:cd19513    79 -LNGEDVLdNVAYARAYNTDHQM--QLLIQASAMMAE--SR-YALLIVDSATALYRTDYSG--RGELSARQMHLAKFLRM 150

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1958786037 242 LKYLSGEFSVPVILTNQITTHLSGALPSQADLVSP 276
Cdd:cd19513   151 LQRLADEFGVAVVITNQVVAQVDGAAMFAGDPKKP 185
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 37-266 2.26e-28

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: 110.58  E-value: 2.26e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  37 ELMKVTGLSYRGVHELLHTVSKACAPQMQTAYELKTRRSAHLSpafLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQ 116
Cdd:TIGR02239  35 QLLEIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRQEVIQ---LTTGSKELDKLLGGGIETGSITEIFGEFRTGKTQ 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 117 FCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAEsRFPqyFNTEEKLL-LTSSRVHLCQELTceGLLQRLESL 195
Cdd:TIGR02239 112 LCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERLLAIAE-RYG--LNPEDVLDnVAYARAYNTDHQL--QLLQQAAAM 186

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958786037 196 EEEiiSKgVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLLKYLSGEFSVPVILTNQITTHLSGA 266
Cdd:TIGR02239 187 MSE--SR-FALLIVDSATALYRTDFSG--RGELSARQMHLARFLRSLQRLADEFGVAVVITNQVVAQVDGA 252
Rad51C cd19492
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 101-270 2.55e-26

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: 101.53  E-value: 2.55e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 101 GSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLEGAVLYIDTESAFTAerlveiaesrfpQYFnteekllltssRVHLC 180
Cdd:cd19492     1 GKITEICGVPGVGKTQLCMQLAVNVQIPKCFGGLAGEAIYIDTEGSFNI------------HYF-----------RVHDY 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 181 QELTceGLLQRLES-LEEEiisKGVKLVIVDSIASVVRKEFDpqlqgNIKERNKFLGKGASLLKYLSGEFSVPVILTNQI 259
Cdd:cd19492    58 VELL--ALINSLPKfLEDH---PKVKLIVVDSIAFPFRHDFD-----DLAQRTRLLNGLAQLLHSLARQHNLAVVLTNQV 127

                         170
                  ....*....|.
gi 1958786037 260 TTHLSGALPSQ 270
Cdd:cd19492   128 TTKISEDGQSQ 138
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 83-261 3.22e-26

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 102.63  E-value: 3.22e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLptrlggLEGAVLYIDTESaFTAERLVEIAESRFpq 162
Cdd:PRK09361    5 LPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAK------NGKKVIYIDTEG-LSPERFKQIAGEDF-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 163 yfnteEKLLltsSRVHLCQELTCEGLLQRLESLeEEIISKGVKLVIVDSIASVVRKEFDPqlQGNIKERNKFLGKGASLL 242
Cdd:PRK09361   76 -----EELL---SNIIIFEPSSFEEQSEAIRKA-EKLAKENVGLIVLDSATSLYRLELED--EEDNSKLNRELGRQLTHL 144

                         170
                  ....*....|....*....
gi 1958786037 243 KYLSGEFSVPVILTNQITT 261
Cdd:PRK09361  145 LKLARKHDLAVVITNQVYS 163
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 83-261 1.16e-25

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: 100.85  E-value: 1.16e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLAtlpTRLGGLegaVLYIDTEsAFTAERLVEIAESRFPQ 162
Cdd:cd01394     1 LSTGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICLQLAVEA---AKQGKK---VVYIDTE-GLSPERFQQIAGERFES 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 163 YFNTeekllLTSSRVHLCQELtcEGLLQRLESLEEeiiSKGVKLVIVDSIASVVRKEfdpqlQGNIKERNKFLGKGASLL 242
Cdd:cd01394    74 IASN-----IIVFEPYSFDEQ--GVAIQEAEKLLK---SDKVDLVVVDSATALYRLE-----LGDDSEANRELSRQMSKL 138

                         170
                  ....*....|....*....
gi 1958786037 243 KYLSGEFSVPVILTNQITT 261
Cdd:cd01394   139 LSIARKYDIPVVITNQVYS 157
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 90-261 2.53e-23

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: 94.79  E-value: 2.53e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  90 LDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLAtlpTRLGGLegaVLYIDTEsAFTAERLVEIAESRFPQYFnteEK 169
Cdd:TIGR02237   1 IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNA---ARQGKK---VVYIDTE-GLSPERFKQIAEDRPERAL---SN 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 170 LLLtsSRVHLCQELtcEGLLQRLESLeeeIISKGVKLVIVDSIASVVRKEfdpqLQGNIKERNKFLGKGASLLKYLSGEF 249
Cdd:TIGR02237  71 FIV--FEVFDFDEQ--GVAIQKTSKF---IDRDSASLVVVDSFTALYRLE----LSDDRISRNRELARQLTLLLSLARKK 139

                         170
                  ....*....|..
gi 1958786037 250 SVPVILTNQITT 261
Cdd:TIGR02237 140 NLAVVITNQVYT 151
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 101-284 2.25e-22

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: 92.41  E-value: 2.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 101 GSLTEVTGPPGCGKTQFCIMMSVLATLPT-----RLGGLEGAVLYIDTESAFTAERLVEIAESRFPQ----------YFN 165
Cdd:cd19490     1 GDVIEITGPSGSGKTELLYHLAARCILPSswggvPLGGLEAAVVFIDTDGRFDILRLRSILEARIRAaiqaanssddEED 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 166 TEEKLLLTSSRVHL--CQELtcEGLLQRLESLEEEIIS----KGVKLVIVDSIAS---VVRKEFDPQLQGNIKERNkFLG 236
Cdd:cd19490    81 VEEIARECLQRLHIfrCHSS--LQLLATLLSLENYLLSlsanPELGLLLIDSISAfywQDRFSAELARAAPLLQEA-ALR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1958786037 237 KGASLLKYLSGEFSVPVILTNQITTHLSGALPSQADLVSPADDLSPSE 284
Cdd:cd19490   158 AILRELRRLRRRFQLVVIATKQALFPGKSASTDNPAANNAVSKASAPS 205
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
83-261 2.43e-12

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 64.94  E-value: 2.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCimMSVLAtlptrlgglEGA-----VLYIDTESafTAERLVEIAE 157
Cdd:COG0467     2 VPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLA--LQFLA---------EGLrrgekGLYVSFEE--SPEQLLRRAE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 158 SR---FPQYFNtEEKLLLtssrVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPQlqgnikERNKF 234
Cdd:COG0467    69 SLgldLEEYIE-SGLLRI----IDLSPEELGLDLEELLARLREAVEEFGAKRVVIDSLSGLLLALPDPE------RLREF 137

                         170       180
                  ....*....|....*....|....*..
gi 1958786037 235 LgkgASLLKYLSgEFSVPVILTNQITT 261
Cdd:COG0467   138 L---HRLLRYLK-KRGVTTLLTSETGG 160
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
89-219 2.75e-11

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 63.27  E-value: 2.75e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  89 ALDEAL-HGGVPCGSLTEVTGPPGCGKTQFCimMSVLATLpTRLGGLegaVLYIDTESAFT---AERL-VEIaesrfpqy 163
Cdd:COG0468    50 ALDIALgVGGLPRGRIVEIYGPESSGKTTLA--LHAIAEA-QKAGGI---AAFIDAEHALDpeyAKKLgVDI-------- 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958786037 164 fnteEKLLLTssrvhlcQELTCEgllQRLESLEEEIISKGVKLVIVDSIASVVRKE 219
Cdd:COG0468   116 ----DNLLVS-------QPDTGE---QALEIAETLVRSGAVDLIVVDSVAALVPKA 157
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 83-258 9.45e-11

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: 60.36  E-value: 9.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCimMSVLATlptrlGGLEGA-VLYIDTESafTAERLVEIAESrfp 161
Cdd:cd01124     1 VKTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLFG--LQFLYA-----GAKNGEpGLFFTFEE--SPERLLRNAKS--- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 162 qyFNTEEKLLLTSSRVHLCQELTCEGLLQRLESL----EEEIISKGVKLVIVDSIASvvrkefdpqLQGNIKERNKFLGK 237
Cdd:cd01124    69 --FGWDFDEMEDEGKLIIVDAPPTEAGRFSLDELlsriLSIIKSFKAKRVVIDSLSG---------LRRAKEDQMRARRI 137

                         170       180
                  ....*....|....*....|.
gi 1958786037 238 GASLLKYLSGEFsVPVILTNQ 258
Cdd:cd01124   138 VIALLNELRAAG-VTTIFTSE 157
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
94-219 2.51e-10

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 59.91  E-value: 2.51e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  94 LHGGVPCGSLTEVTGPPGCGKTQFCIMMSVLATLPTRLGGLE---GAVLYIDTE--SAFTAERLVEIAESRFPQYFNTEE 168
Cdd:COG3598     6 VPGLLPEGGVTLLAGPPGTGKSFLALQLAAAVAAGGPWLGRRvppGKVLYLAAEddRGELRRRLKALGADLGLPFADLDG 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958786037 169 KLLLTSSRvhlcQELTCEGLLQRlesLEEEIISKGVKLVIVDSIASVVRKE 219
Cdd:COG3598    86 RLRLLSLA----GDLDDTDDLEA---LERAIEEEGPDLVVIDPLARVFGGD 129
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 90-232 8.73e-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: 54.56  E-value: 8.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  90 LDEALHGGVPCGSLTEVTGPPGCGKTQFCIMMSVlatlptrlgglEGAV------LYIDTESafTAERLVEIAES---RF 160
Cdd:pfam06745   8 LDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLY-----------NGALkygepgVFVTLEE--PPEDLRENARSfgwDL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 161 PQYFNtEEKLL---LTSSRVHLCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIAS--------VVRKEFDpQLQGNIK 229
Cdd:pfam06745  75 EKLEE-EGKLAiidASTSGIGIAEVEDRFDLEELIERLREAIREIGAKRVVIDSITTlfyllkpaVAREILR-RLKRVLK 152


                  ...
gi 1958786037 230 ERN 232
Cdd:pfam06745 153 GLG 155
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 82-259 1.13e-08

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: 54.48  E-value: 1.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  82 FLSTTLGALDEAL-HGGVPCGSLTEVTGPPGCGKTQfcIMMSVLATLpTRLGGLegaVLYIDTESAFT---AERL-VEIa 156
Cdd:cd00983     4 VIPTGSLSLDIALgIGGLPRGRIIEIYGPESSGKTT--LALHAIAEA-QKLGGT---AAFIDAEHALDpeyAKKLgVDI- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 157 esrfpqyfnteEKLLltssrvhLCQELTCEgllQRLESLEEEIISKGVKLVIVDSIASVVRKEfdpQLQGNIKErnKFLG 236
Cdd:cd00983    77 -----------DNLL-------VSQPDTGE---QALEIADTLIRSGAVDLIVVDSVAALVPKA---EIEGEMGD--SHVG 130

                         170       180       190
                  ....*....|....*....|....*....|
gi 1958786037 237 KGASL----LKYLSGEFS---VPVILTNQI 259
Cdd:cd00983   131 LQARLmsqaLRKLTGSLSkskTTVIFINQL 160
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 89-259 4.54e-07

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: 50.09  E-value: 4.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  89 ALDEALH-GGVPCGSLTEVTGPPGCGKTQfcIMMSVLATLpTRLGGLegaVLYIDTESAFTaerlveiaesrfPQY---- 163
Cdd:pfam00154  39 ALDIALGiGGYPKGRIIEIYGPESSGKTT--LALHAIAEA-QKAGGT---AAFIDAEHALD------------PVYakkl 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 164 -FNTEEklLLTSsrvhlcQELTCEgllQRLESLEEEIISKGVKLVIVDSIASVVRKEfdpQLQGNIKERNkfLGKGASL- 241
Cdd:pfam00154 101 gVDIDN--LLVS------QPDTGE---QALEIADMLVRSGAIDLIVVDSVAALVPKA---EIEGEMGDSH--VGLQARLm 164

                         170       180
                  ....*....|....*....|....
gi 1958786037 242 ---LKYLSGEFS---VPVILTNQI 259
Cdd:pfam00154 165 sqaLRKLTGSISksnTTVIFINQI 188
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 83-226 1.38e-06

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: 48.68  E-value: 1.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQfcIMMSVLAtlptRLGGLEGAVLYIDTEsaftaERLVEIAeSRFpq 162
Cdd:cd01121    64 ISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKST--LLLQVAA----RLAQRGGKVLYVSGE-----ESLSQIK-LRA-- 129

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958786037 163 yfnteEKLLLTSSRVHlcqeLTCEgllQRLESLEEEIISKGVKLVIVDSIASVvrkeFDPQLQG 226
Cdd:cd01121   130 -----ERLGLGSDNLY----LLAE---TNLEAILAEIEELKPSLVVIDSIQTV----YSPELTS 177
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 78-217 6.65e-06

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: 6.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  78 LSPAFLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCI-----MMSVLATLPTRLGGLEGAVLYIDTE-SAFTAER 151
Cdd:pfam13481  10 VLADGLAAPPPPRRWLIKGLLPAGGLGLLAGAPGTGKTTLALdlaaaVATGKPWLGGPRVPEQGKVLYVSAEgPADELRR 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 152 LVEIAESRFPQyfntEEKLLLTS--SRVHLCQELTCEGLLQR-LESLEEEII-SKGVKLVIVDSIASVVR 217
Cdd:pfam13481  90 RLRAAGADLDL----PARLLFLSlvESLPLFFLDRGGPLLDAdVDALEAALEeVEDPDLVVIDPLARALG 155
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 101-267 8.67e-06

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: 44.67  E-value: 8.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  101 GSLTEVTGPPGCGKTQFCIMMSVLatlptrLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYFNTEekllltssrvhlc 180
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARE------LGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS------------- 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  181 QELTCEGLLQRLESLeeeiiskGVKLVIVDSIASVVRKEFDPQLQGNIKERNKFLgkgasllkyLSGEFSVPVILTNQIT 260
Cdd:smart00382  63 GELRLRLALALARKL-------KPDVLILDEITSLLDAEQEALLLLLEELRLLLL---------LKSEKNLTVILTTNDE 126


                   ....*..
gi 1958786037  261 THLSGAL 267
Cdd:smart00382 127 KDLGPAL 133
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 83-278 1.95e-05

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: 44.60  E-value: 1.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQfciMMSVLATLPTRLGglEGAVLYIDTESAFTaerlveiaesrfpq 162
Cdd:cd19487     1 VSSGVPELDELLGGGLERGTSTLLIGPAGVGKST---LALQFAKAAAARG--ERSVLFSFDESIGT-------------- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 163 YFNTEEKLLLTSSRVHLCQELTceglLQRLESLE-----------EEIISKGVKLVIVDSIASvvrkefdpqLQGNIKER 231
Cdd:cd19487    62 LFERSEALGIDLRAMVEKGLLS----IEQIDPAElspgefaqrvrTSVEQEDARVVVIDSLNG---------YLNAMPDE 128

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1958786037 232 NKFLGKGASLLKYLSGEfSVPVILTNQITTHLSGALPSQADLVSPAD 278
Cdd:cd19487   129 RFLILQMHELLSYLNNQ-GVTTLLIVAQHGLLGGDMGTPVDISYLAD 174
KaiC-N cd19485
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most ...
 83-219 1.58e-04

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: 41.97  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFCimMSVLATLPTRLGglEGAVLYIDTESaftAERLVEIAESrFP- 161
Cdd:cd19485     1 LPTGIEGFDDITHGGLPKGRPTLICGTAGTGKTLFA--AQFLVNGIKEFG--EPGVFVTFEES---PEDIIKNMAS-FGw 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958786037 162 --QYFNTEEKLLLTSSRVHLCQ-----ELTCEGLLQRLESLEEEIiskGVKLVIVDSI---------ASVVRKE 219
Cdd:cd19485    73 dlPKLVAEGKLLILDASPEPSEeevtgEYDLEALLIRIEYAIRKI---GAKRVSLDSLeavfsglsdSAVVRAE 143
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 90-117 3.59e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 38.71  E-value: 3.59e-03
                          10        20
                  ....*....|....*....|....*...
gi 1958786037  90 LDEALHGGVPCGSLTEVTGPPGCGKTQF 117
Cdd:PRK09302   20 FDDITHGGLPKGRPTLVSGTAGTGKTLF 47
KaiC_arch cd19486
KaiC family protein; uncharacterized subfamily similar to Pyrococcus horikoshii PH0284; KaiC ...
 83-118 3.90e-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: 37.84  E-value: 3.90e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958786037  83 LSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFC 118
Cdd:cd19486     1 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFS 36
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 101-215 4.68e-03

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: 37.75  E-value: 4.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037 101 GSLTEVTGPPGCGKTQFCIMMSV-LATLPTRLGGLE---GAVLYIDTESAFTA--ERLVEIAESRFPQYFNTEEKLLLTS 174
Cdd:cd01125     1 GTLGMLVGPPGSGKSFLALDLAVaVATGRDWLGERRvkqGRVVYLAAEDPRDGlrRRLKAIGAHLGDEDAALAENLVIEN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1958786037 175 SRVHLCqeltcegLLQRLESLEEEIIS--KGVKLVIVDSIASV 215
Cdd:cd01125    81 LRGKPV-------SIDAEAPELERIIEelEGVRLIIIDTLARV 116
recA PRK09519
intein-containing recombinase RecA;
89-224 5.70e-03

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 38.15  E-value: 5.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958786037  89 ALDEALH-GGVPCGSLTEVTGPPGCGKTqfciMMSVLATLPTRLGGleGAVLYIDTESAFTaerlveiaesrfPQYfntE 167
Cdd:PRK09519   47 ALDVALGiGGLPRGRVIEIYGPESSGKT----TVALHAVANAQAAG--GVAAFIDAEHALD------------PDY---A 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958786037 168 EKLLLTSSRVHLCQELTCEgllQRLESLEEEIISKGVKLVIVDSIASVV-RKEFDPQL 224
Cdd:PRK09519  106 KKLGVDTDSLLVSQPDTGE---QALEIADMLIRSGALDIVVIDSVAALVpRAELEGEM 160
 
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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