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Conserved domains on  [gi|818624219|gb|KKS72232|]
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replication and repair protein RecF protein [candidate division WWE3 bacterium GW2011_GWD1_42_70]

Protein Classification

DNA replication/repair protein RecF( domain architecture ID 11439814)

DNA replication/repair protein RecF is required for DNA replication and normal SOS inducibility; it binds preferentially to single-stranded, linear DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-349 6.23e-118

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


:

Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 344.83  E-value: 6.23e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   2 KILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGKY 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  82 LLEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYL 160
Cdd:COG1195   81 RLGLGLSRG------GKKRVRINGKPvRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 161 KAVRQRNKILEKIAEENRGWdeIGYWTKKCLEHGTYIQEQRKKLFDYFNNKLPGAVEKLNGKDTEVEIKYLMNEISE--- 237
Cdd:COG1195  155 RALKQRNALLKQGREADLAL--LDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYEsae 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 238 ------ERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDIF 311
Cdd:COG1195  233 leeallEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 818624219 312 SELDENHRSSVFNILEQQ--QTIITSTEPPDFLASKSNAH 349
Cdd:COG1195  313 AELDEERREALLELLADLggQVFITTTDPEDFPALLERAK 352
 
Name Accession Description Interval E-value
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-349 6.23e-118

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 344.83  E-value: 6.23e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   2 KILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGKY 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  82 LLEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYL 160
Cdd:COG1195   81 RLGLGLSRG------GKKRVRINGKPvRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 161 KAVRQRNKILEKIAEENRGWdeIGYWTKKCLEHGTYIQEQRKKLFDYFNNKLPGAVEKLNGKDTEVEIKYLMNEISE--- 237
Cdd:COG1195  155 RALKQRNALLKQGREADLAL--LDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYEsae 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 238 ------ERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDIF 311
Cdd:COG1195  233 leeallEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 818624219 312 SELDENHRSSVFNILEQQ--QTIITSTEPPDFLASKSNAH 349
Cdd:COG1195  313 AELDEERREALLELLADLggQVFITTTDPEDFPALLERAK 352
recF PRK00064
recombination protein F; Reviewed
 1-353 5.26e-99

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 297.07  E-value: 5.26e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGK 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  81 YLLEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAY 159
Cdd:PRK00064  81 LPLGLEIDKK------GGRKVRINGEPqRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQY 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 160 LKAVRQRNKILEkiaEENRGWdeIGYWTKKCLEHGTYIQEQRKKLFDYFNNKLPGAVEKLNGKDTEVEIKYL------MN 233
Cdd:PRK00064 155 ERALKQRNALLK---QADYAW--LDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQssveddAE 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 234 EISE---ERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDI 310
Cdd:PRK00064 230 KIEEdllEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 818624219 311 FSELDENHRSSVFNILE--QQQTIITSTEPPDFLASKSNAHEIKV 353
Cdd:PRK00064 310 ASELDDGRRAALLERLKglGAQVFITTTDLEDLADLLENAKIFHV 354
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-336 1.00e-70

recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273173 [Multi-domain]  Cd Length: 365  Bit Score: 224.93  E-value: 1.00e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGK 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   81 YLLEMQVIKEPdasniSSKKTKVNKVSK-SLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAY 159
Cdd:TIGR00611  81 VTIPLEGLLKK-----KGKKAKVNIDGQdKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDY 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  160 LKAVRQRNKILEKIAEENRGWDEIGYWTKKCLEHGTYIQEQR-----------KKLFDYFNNKLPGAVEKLNGKDTEVEI 228
Cdd:TIGR00611 156 QRVLKQRNAALKQAQRQYGDRTTLEVWDSQLAELGAKVSAWRaefieklepeaQKAHQLLLPELESLSLFYRGELWDKET 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  229 KYLmneiseERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLD 308
Cdd:TIGR00611 236 DYA------EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLD 309

                         330       340       350
                  ....*....|....*....|....*....|
gi 818624219  309 DIFSELDENHRSSVFNILE--QQQTIITST 336
Cdd:TIGR00611 310 DVASELDDQRRRLLAELLQslGVQVFVTAI 339
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-351 4.08e-66

ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213209 [Multi-domain]  Cd Length: 270  Bit Score: 209.85  E-value: 4.08e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   3 ILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGKYL 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  83 LEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYLK 161
Cdd:cd03242   81 LELTIRSG------GGRKARLNGIKvRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQK 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 162 AVRQRNKIlekiaeenrgwdeigywtkkclehgtyiqeqrkklfdyfnnklpgaveklngkdteveikylmneiseerlk 241
Cdd:cd03242  155 ALRQRNAL------------------------------------------------------------------------ 162

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 242 kheehevhakttLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDIFSELDENHRSS 321
Cdd:cd03242  163 ------------LKGPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAA 230

                        330       340       350
                 ....*....|....*....|....*....|.
gi 818624219 322 VFNILEQ-QQTIITSTEPPDFLASKSNAHEI 351
Cdd:cd03242  231 LLDAIEGrVQTFVTTTDLADFDALWLRRAQI 261
AAA_23 pfam13476
AAA domain;
6-175 3.13e-06

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 47.11  E-value: 3.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    6 LRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAI-YALsTGKSIKAKYDR-------DMINYSAQFSAASADIENS 77
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIkLAL-YGKTSRLKRKSgggfvkgDIRIGLEGKGKAYVEITFE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   78 SGKYLLEMQVIKEPDASNISSKKTKVNK------------VSKSLASFSGIFNSVMFSPEDLNvvtgSPSERRKYMDAIL 145
Cdd:pfam13476  80 NNDGRYTYAIERSRELSKKKGKTKKKEIleileidelqqfISELLKSDKIILPLLVFLGQERE----EEFERKEKKERLE 155

                         170       180       190
                  ....*....|....*....|....*....|.
gi 818624219  146 VQTNK-NYKRNTAAYLKAVRQRNKILEKIAE 175
Cdd:pfam13476 156 ELEKAlEEKEDEKKLLEKLLQLKEKKKELEE 186
 
Name Accession Description Interval E-value
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-349 6.23e-118

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 344.83  E-value: 6.23e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   2 KILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGKY 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  82 LLEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYL 160
Cdd:COG1195   81 RLGLGLSRG------GKKRVRINGKPvRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 161 KAVRQRNKILEKIAEENRGWdeIGYWTKKCLEHGTYIQEQRKKLFDYFNNKLPGAVEKLNGKDTEVEIKYLMNEISE--- 237
Cdd:COG1195  155 RALKQRNALLKQGREADLAL--LDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYEsae 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 238 ------ERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDIF 311
Cdd:COG1195  233 leeallEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 818624219 312 SELDENHRSSVFNILEQQ--QTIITSTEPPDFLASKSNAH 349
Cdd:COG1195  313 AELDEERREALLELLADLggQVFITTTDPEDFPALLERAK 352
recF PRK00064
recombination protein F; Reviewed
 1-353 5.26e-99

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 297.07  E-value: 5.26e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGK 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  81 YLLEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAY 159
Cdd:PRK00064  81 LPLGLEIDKK------GGRKVRINGEPqRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQY 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 160 LKAVRQRNKILEkiaEENRGWdeIGYWTKKCLEHGTYIQEQRKKLFDYFNNKLPGAVEKLNGKDTEVEIKYL------MN 233
Cdd:PRK00064 155 ERALKQRNALLK---QADYAW--LDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQssveddAE 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 234 EISE---ERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDI 310
Cdd:PRK00064 230 KIEEdllEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 818624219 311 FSELDENHRSSVFNILE--QQQTIITSTEPPDFLASKSNAHEIKV 353
Cdd:PRK00064 310 ASELDDGRRAALLERLKglGAQVFITTTDLEDLADLLENAKIFHV 354
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-336 1.00e-70

recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273173 [Multi-domain]  Cd Length: 365  Bit Score: 224.93  E-value: 1.00e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGK 80
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   81 YLLEMQVIKEPdasniSSKKTKVNKVSK-SLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAY 159
Cdd:TIGR00611  81 VTIPLEGLLKK-----KGKKAKVNIDGQdKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDY 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  160 LKAVRQRNKILEKIAEENRGWDEIGYWTKKCLEHGTYIQEQR-----------KKLFDYFNNKLPGAVEKLNGKDTEVEI 228
Cdd:TIGR00611 156 QRVLKQRNAALKQAQRQYGDRTTLEVWDSQLAELGAKVSAWRaefieklepeaQKAHQLLLPELESLSLFYRGELWDKET 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  229 KYLmneiseERLKKHEEHEVHAKTTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLD 308
Cdd:TIGR00611 236 DYA------EALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLD 309

                         330       340       350
                  ....*....|....*....|....*....|
gi 818624219  309 DIFSELDENHRSSVFNILE--QQQTIITST 336
Cdd:TIGR00611 310 DVASELDDQRRRLLAELLQslGVQVFVTAI 339
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-351 4.08e-66

ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213209 [Multi-domain]  Cd Length: 270  Bit Score: 209.85  E-value: 4.08e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   3 ILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIENSSGKYL 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  83 LEMQVIKEpdasniSSKKTKVNKVS-KSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYLK 161
Cdd:cd03242   81 LELTIRSG------GGRKARLNGIKvRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQK 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 162 AVRQRNKIlekiaeenrgwdeigywtkkclehgtyiqeqrkklfdyfnnklpgaveklngkdteveikylmneiseerlk 241
Cdd:cd03242  155 ALRQRNAL------------------------------------------------------------------------ 162

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 242 kheehevhakttLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDIFSELDENHRSS 321
Cdd:cd03242  163 ------------LKGPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAA 230

                        330       340       350
                 ....*....|....*....|....*....|.
gi 818624219 322 VFNILEQ-QQTIITSTEPPDFLASKSNAHEI 351
Cdd:cd03242  231 LLDAIEGrVQTFVTTTDLADFDALWLRRAQI 261
recF PRK14079
recombination protein F; Provisional
 1-349 3.63e-52

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 176.13  E-value: 3.63e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYaLSTGKSIKAKYDRDMINYSAQFSAASADIENSSGK 80
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIY-LALTGELPNGRLADLVRFGEGEAWVHAEVETGGGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  81 YLLEMQVIKEpdasnisSKKTKVNKVSKSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYL 160
Cdd:PRK14079  80 SRLEVGLGPG-------RRELKLDGVRVSLRELARLPGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 161 KAVRQRNKILEKIAEENrgwdeIGYWTKKCLEHGTYIQEQRKKLFDYFNNKLPGAVEKLnGKDTEVEIKyLMNEISEERL 240
Cdd:PRK14079 153 RAVQQRNAALKSGGGWG-----LHVWDDELVKLGDEIMALRRRALTRLSELAREAYAEL-GSRKPLRLE-LSESTAPEGY 225

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 241 ------KKHEEHEVHAktTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDERPVLLLDDIFSEL 314
Cdd:PRK14079 226 laaleaRRAEELARGA--TVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDFTAEL 303

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 818624219 315 DENHRSSVFNILEQ-QQTIITSTEPPDFLASKSNAH 349
Cdd:PRK14079 304 DPRRRGALLALAASlPQAIVAGTEAPPGAALTLRIE 339
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-84 1.96e-11

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 62.72  E-value: 1.96e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   2 KILELRLTNFRNHK-KLKLGLDYGIVLLTGKNGAGKTNILEAI-YALsTGKSIK-AKYDRDMINYSAQFSAASADIENSS 78
Cdd:COG0419    1 KLLRLRLENFRSYRdTETIDFDDGLNLIVGPNGAGKSTILEAIrYAL-YGKARSrSKLRSDLINVGSEEASVELEFEHGG 79


                 ....*.
gi 818624219  79 GKYLLE 84
Cdd:COG0419   80 KRYRIE 85
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-119 5.22e-10

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 60.02  E-value: 5.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSiKAKYDRDMINYSAQFSAASADIE---NS 77
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRLLLGPSS-SRKFDEEDFYLGDDPDLPEIEIEltfGS 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 818624219  78 SGKYLLEmQVIKEPDASNISSKKTKVNK-VSKSLASFSGIFNS 119
Cdd:COG3593   80 LLSRLLR-LLLKEEDKEELEEALEELNEeLKEALKALNELLSE 121
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-49 2.30e-09

Predicted ATP-binding protein involved in virulence [General function prediction only];


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 57.70  E-value: 2.30e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDY--GIVLLTGKNGAGKTNILEAIYALSTG 49
Cdd:COG3950    1 MRIKSLTIENFRGFEDLEIDFDNppRLTVLVGENGSGKTTLLEAIALALSG 51
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 1-345 2.55e-07

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 52.66  E-value: 2.55e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219     1 MKILELRLTNFRNHKKLKL---GLDYGIVLLTGKNGAGKTNILEAI-YAL-----STGKSIKAKYDrdmiNYSAQFSAAS 71
Cdd:TIGR00618    1 MKPLRLTLKNFGSYKGTHTidfTALGPIFLICGKTGAGKTTLLDAItYALygklpRRSEVIRSLNS----LYAAPSEAAF 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    72 ADIENSSG-----------------KYLLEMQVIKEPDASNISSKKTKVNKVSKSLASFSGI----FNSVMFSP--EDLN 128
Cdd:TIGR00618   77 AELEFSLGtkiyrvhrtlrctrshrKTEQPEQLYLEQKKGRGRILAAKKSETEEVIHDLLKLdyktFTRVVLLPqgEFAQ 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   129 VVTGSPSERR----------KY-MDAILVQTNKNYKRNTAAYLKAvrqRNKILEKIAEEN-RGWDEIGYWTKKCLEHGTY 196
Cdd:TIGR00618  157 FLKAKSKEKKellmnlfpldQYtQLALMEFAKKKSLHGKAELLTL---RSQLLTLCTPCMpDTYHERKQVLEKELKHLRE 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   197 IQEQRKKLFDYFNNKLPGAVEKLN----GKDTEVEIKYLMNEISE--------------ERLKKHEEHEVHAK------- 251
Cdd:TIGR00618  234 ALQQTQQSHAYLTQKREAQEEQLKkqqlLKQLRARIEELRAQEAVleetqerinrarkaAPLAAHIKAVTQIEqqaqrih 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   252 TTLVGPHRDDFCIFQKNHNLAEFGSRGEQRSAMLALKLCEINFIEQENDErPVLLLDDIFSELDENHRssvfnILEQQQT 331
Cdd:TIGR00618  314 TELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEV-ATSIREISCQQHTLTQH-----IHTLQQQ 387

                          410
                   ....*....|....
gi 818624219   332 IITSTEPPDFLASK 345
Cdd:TIGR00618  388 KTTLTQKLQSLCKE 401
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-61 5.05e-07

ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 49.53  E-value: 5.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818624219   3 ILELRLTNFR-NHKKLKLGLDYGIVLLTGKNGAGKTNILEAI-YALsTG----KSIKAKYDRDMI 61
Cdd:cd03240    1 IDKLSIRNIRsFHERSEIEFFSPLTLIVGQNGAGKTTIIEALkYAL-TGelppNSKGGAHDPKLI 64
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-43 8.87e-07

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 50.31  E-value: 8.87e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 818624219   2 KILELRLTNFRNHKKLKLGLDyGIVLLTGKNGAGKTNILEAI 43
Cdd:COG4637    1 MITRIRIKNFKSLRDLELPLG-PLTVLIGANGSGKSNLLDAL 41
ABC_sbcCD cd03279
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ...
 1-91 1.20e-06

ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.


Pssm-ID: 213246 [Multi-domain]  Cd Length: 213  Bit Score: 48.80  E-value: 1.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   1 MKILELRLTNFRNHKKLKL----GLDY-GIVLLTGKNGAGKTNILEAI-YALsTGKSI---KAKYDRDMINYSAQFSAAS 71
Cdd:cd03279    1 MKPLKLELKNFGPFREEQVidftGLDNnGLFLICGPTGAGKSTILDAItYAL-YGKTPrygRQENLRSVFAPGEDTAEVS 79

                         90       100
                 ....*....|....*....|
gi 818624219  72 ADIENSSGKYllemQVIKEP 91
Cdd:cd03279   80 FTFQLGGKKY----RVERSR 95
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-45 2.63e-06

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 49.29  E-value: 2.63e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYA 45
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILV 45
AAA_23 pfam13476
AAA domain;
6-175 3.13e-06

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 47.11  E-value: 3.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    6 LRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAI-YALsTGKSIKAKYDR-------DMINYSAQFSAASADIENS 77
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIkLAL-YGKTSRLKRKSgggfvkgDIRIGLEGKGKAYVEITFE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   78 SGKYLLEMQVIKEPDASNISSKKTKVNK------------VSKSLASFSGIFNSVMFSPEDLNvvtgSPSERRKYMDAIL 145
Cdd:pfam13476  80 NNDGRYTYAIERSRELSKKKGKTKKKEIleileidelqqfISELLKSDKIILPLLVFLGQERE----EEFERKEKKERLE 155

                         170       180       190
                  ....*....|....*....|....*....|.
gi 818624219  146 VQTNK-NYKRNTAAYLKAVRQRNKILEKIAE 175
Cdd:pfam13476 156 ELEKAlEEKEDEKKLLEKLLQLKEKKKELEE 186
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-76 6.82e-06

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433011 [Multi-domain]  Cd Length: 392  Bit Score: 47.59  E-value: 6.82e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818624219    1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYALSTGKSIKAKYDRDMINYSAQFSAASADIEN 76
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIFLNNKEKFFEDDFLVLYLKDVIKIDKEDLNI 76
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-145 8.42e-06

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 47.59  E-value: 8.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAI-YALSTGKsiKAKYDRDMINYSAQFSAASADIENSSG 79
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIrFALFTDK--RTEKIEDMIKKGKNNLEVELEFRIGGH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  80 KYLLEMQVIK-----------EPDASNISSKKTKVNK-VSKSLASFS-GIFNSVMFSP--EDLNVVTGSPSERRKYMDAI 144
Cdd:PRK01156  79 VYQIRRSIERrgkgsrreayiKKDGSIIAEGFDDTTKyIEKNILGISkDVFLNSIFVGqgEMDSLISGDPAQRKKILDEI 158


                 .
gi 818624219 145 L 145
Cdd:PRK01156 159 L 159
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 3-178 1.19e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 47.37  E-value: 1.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219     3 ILELRLTNFRNH-KKLKLGLDYGIVLLTGKNGAGKTNILEAI---YALSTGKSIKAKYDRDMIN-----YSAQFSAASAD 73
Cdd:TIGR02169    2 IERIELENFKSFgKKKVIPFSKGFTVISGPNGSGKSNIGDAIlfaLGLSSSKAMRAERLSDLISngkngQSGNEAYVTVT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    74 IENSSGKYLLEMQV---IKEPDASNISSkkTKVNKVSKSLASFSGIFNSVMFSPEDLNVV-----TG----SPSERRKYM 141
Cdd:TIGR02169   82 FKNDDGKFPDELEVvrrLKVTDDGKYSY--YYLNGQRVRLSEIHDFLAAAGIYPEGYNVVlqgdvTDfismSPVERRKII 159

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 818624219   142 DAIL-VQTNKNYKRNTAAYLKAVRQRNKILEKIAEENR 178
Cdd:TIGR02169  160 DEIAgVAEFDRKKEKALEELEEVEENIERLDLIIDEKR 197
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-47 8.34e-05

ATPase/GTPase, AAA15 family [General function prediction only];


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 43.88  E-value: 8.34e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 818624219   3 ILELRLTNFRN-HKKLKLGLDYG------IVLLTGKNGAGKTNILEAIYALS 47
Cdd:COG1106    2 LISFSIENFRSfKDELTLSMVASglrllrVNLIYGANASGKSNLLEALYFLR 53
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-42 1.16e-04

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 43.88  E-value: 1.16e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEA 42
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEA 42
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-46 1.81e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 43.22  E-value: 1.81e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 818624219   1 MKILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAIYAL 46
Cdd:COG4717    1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFIRAM 46
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 276-343 4.93e-04

ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 40.31  E-value: 4.93e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818624219 276 SRGEQRSAMLALKLCEinfieqendERPVLLLDDIFSELDENHRSSVFNIL----EQQQTIITSTEPPDFLA 343
Cdd:cd00267   82 SGGQRQRVALARALLL---------NPDLLLLDEPTSGLDPASRERLLELLrelaEEGRTVIIVTHDPELAE 144
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-335 6.33e-04

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 41.22  E-value: 6.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   25 IVLLTGKNGAGKTNILEAIYALSTgksikAKYDRDMINYSAQFSAASADIENSSGKYLLEMQVIKEPDASNISSKK---- 100
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLAD-----FDALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRyryg 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  101 --TKVNKVSKSLASFSGIFNSVMFSPEDLNVVTGSPSERRKYMDAILVQTNKNYKRNTAAYLKAVRQRNKILEKIAEENR 178
Cdd:pfam13304  76 ldLEREDVEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEELRLGLDVEERIELSLSELSDLISGLLLLSIISPLSFLL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  179 GWDEIGYwtkkclEHGTYIQEQRKKLFdYFNNKLPGAVEKLNGKDTEVEIKYLMNEISEERLKKHEEHEVHAKTTLVGPH 258
Cdd:pfam13304 156 LLDEGLL------LEDWAVLDLAADLA-LFPDLKELLQRLVRGLKLADLNLSDLGEGIEKSLLVDDRLRERGLILLENGG 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219  259 RDDFCIFQKnhnlaefgSRGEQR-SAMLALklceinfIEQENDERPVLLLDDIFSELDENHRSSVFNILEQQ-----QTI 332
Cdd:pfam13304 229 GGELPAFEL--------SDGTKRlLALLAA-------LLSALPKGGLLLIDEPESGLHPKLLRRLLELLKELsrngaQLI 293


                  ...
gi 818624219  333 ITS 335
Cdd:pfam13304 294 LTT 296
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 276-353 6.51e-04

ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 40.04  E-value: 6.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219 276 SRGEQRSAMLALKLceinfIEQENDERPVLLLDDIFSELDENHRSSVFNILEQQ-----QTIITSTEPPDFLASKSNAHE 350
Cdd:cd03227   79 SGGEKELSALALIL-----ALASLKPRPLYILDEIDRGLDPRDGQALAEAILEHlvkgaQVIVITHLPELAELADKLIHI 153


                 ...
gi 818624219 351 IKV 353
Cdd:cd03227  154 KKV 156
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 5-115 6.88e-04

ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213245 [Multi-domain]  Cd Length: 197  Bit Score: 40.14  E-value: 6.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219   5 ELRLTNFRNH-KKLKLGLDYGIVLLTGKNGAGKTNILEAI-YAL--STGKSIKAKYDRDMINYSAQFSAA------SADI 74
Cdd:cd03278    3 KLELKGFKSFaDKTTIPFPPGLTAIVGPNGSGKSNIIDAIrWVLgeQSAKSLRGEKMSDVIFAGSETRKPanfaevTLTF 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 818624219  75 ENSSGKYllemQVIKEPDASNISSKKTKvnKVsKSLASFSG 115
Cdd:cd03278   83 DNSDGRY----SIISQGDVSEIIEAPGK--KV-QRLSLLSG 116
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 2-178 7.58e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 41.50  E-value: 7.58e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219     2 KILELRLTNFRNHKKLKLG-LDYGIVLLTGKNGAGKTNILEAI---YALSTGKSIKAKYDRDMINYSAQFSAASADIE-- 75
Cdd:pfam02463    1 YLKRIEIEGFKSYAKTVILpFSPGFTAIVGPNGSGKSNILDAIlfvLGERSAKSLRSERLSDLIHSKSGAFVNSAEVEit 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624219    76 -NSSGKYLlemqVIKEPD------ASNISSKKTKVNKVSKSLASFSGIFNSVMFSPEDLNVVTG---------SPSERRK 139
Cdd:pfam02463   81 fDNEDHEL----PIDKEEvsirrrVYRGGDSEYYINGKNVTKKEVAELLESQGISPEAYNFLVQggkieiiamMKPERRL 156

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 818624219   140 YMDAILVQTnKNYKRNTAAYLKAVRQRNKILEKIAEENR 178
Cdd:pfam02463  157 EIEEEAAGS-RLKRKKKEALKKLIEETENLAELIIDLEE 194
PRK10246 PRK10246
exonuclease subunit SbcC; Provisional
 1-43 2.79e-03

exonuclease subunit SbcC; Provisional


Pssm-ID: 182330 [Multi-domain]  Cd Length: 1047  Bit Score: 39.78  E-value: 2.79e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 818624219    1 MKILELRLTNFrNHKKLKLGLDY--------GIVLLTGKNGAGKTNILEAI 43
Cdd:PRK10246    1 MKILSLRLKNL-NSLKGEWKIDFtaepfasnGLFAITGPTGAGKTTLLDAI 50
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 3-43 3.11e-03

ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213243 [Multi-domain]  Cd Length: 198  Bit Score: 38.35  E-value: 3.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 818624219   3 ILELRLTNFRNHKKLKLGLDYGIVLLTGKNGAGKTNILEAI 43
Cdd:cd03276    1 IESITLKNFMCHRHLQIEFGPRVNFIVGNNGSGKSAILTAL 41
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 1-66 7.62e-03

ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213240 [Multi-domain]  Cd Length: 251  Bit Score: 37.66  E-value: 7.62e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818624219   1 MKILELRLTNFRN--HKKLKLGLDYGIVLLTGKNGAGKTNILEAI---YALSTGKSIKAKYDRDMINYSAQ 66
Cdd:cd03273    1 MHIKEIILDGFKSyaTRTVISGFDPQFNAITGLNGSGKSNILDAIcfvLGITNLSTVRASNLQDLIYKRGQ 71
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 12-71 9.81e-03

ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 36.57  E-value: 9.81e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818624219  12 RNHKKLKLGLDYG-----IVLLTGKNGAGKTNILEAIYALSTGKSikAKYDRDMINYSAQFSAAS 71
Cdd:cd03227    5 GRFPSYFVPNDVTfgegsLTIITGPNGSGKSTILDAIGLALGGAQ--SATRRRSGVKAGCIVAAV 67
 
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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