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Conserved domains on  [gi|1325404588|gb|PMB96035|]
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DNA replication/repair protein RecF [Staphylococcus sp. UMB0328]

Protein Classification

DNA replication/repair protein RecF( domain architecture ID 11477886)

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

Gene Ontology:  GO:0005524|GO:0003697|GO:0006281|GO:0006260

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
recF PRK00064
recombination protein F; Reviewed
 1-369 3.53e-172

recombination protein F; Reviewed


:

Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 483.89  E-value: 3.53e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGT 80
Cdd:PRK00064    1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  81 MPLTMFITKRG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQ 159
Cdd:PRK00064   81 LPLGLEIDKKGgRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 160 KNNYLKQlqignkTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqDQTES 239
Cdd:PRK00064  161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSV-----EDDAE 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 240 EMLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 319
Cdd:PRK00064  230 KIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1325404588 320 LSELDDSRQTHLLSTIQH-KVQTFVTTTSVDGIDHEImNNAKLYRINQGEI 369
Cdd:PRK00064  310 ASELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
 
Name Accession Description Interval E-value
recF PRK00064
recombination protein F; Reviewed
 1-369 3.53e-172

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 483.89  E-value: 3.53e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGT 80
Cdd:PRK00064    1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  81 MPLTMFITKRG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQ 159
Cdd:PRK00064   81 LPLGLEIDKKGgRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 160 KNNYLKQlqignkTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqDQTES 239
Cdd:PRK00064  161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSV-----EDDAE 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 240 EMLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 319
Cdd:PRK00064  230 KIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1325404588 320 LSELDDSRQTHLLSTIQH-KVQTFVTTTSVDGIDHEImNNAKLYRINQGEI 369
Cdd:PRK00064  310 ASELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-366 7.24e-168

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: 473.00  E-value: 7.24e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGEL--NYRH 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVskGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  79 GTMPLTMFITKRGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILK 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 159 QKNNYLKQLQiGNKTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqdqte 238
Cdd:TIGR00611 161 QRNAALKQAQ-RQYGDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL--------- 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 239 SEMLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDD 318
Cdd:TIGR00611 231 WDKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDD 310

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 1325404588 319 VLSELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDH-EIMNNAKLYRINQ 366
Cdd:TIGR00611 311 VASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEmWDPNRVTIALVSV 360
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-355 7.36e-153

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 434.58  E-value: 7.36e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   2 KLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGTM 81
Cdd:COG1195     1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  82 PLTMFITKRG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQK 160
Cdd:COG1195    81 RLGLGLSRGGkKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 161 NNYLKQlqiGNKTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqDQTESE 240
Cdd:COG1195   161 NALLKQ---GREADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGW-----LYESAE 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 241 MLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVL 320
Cdd:COG1195   233 LEEALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1325404588 321 SELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDHEI 355
Cdd:COG1195   313 AELDEERREALLELLADLgGQVFITTTDPEDFPALL 348
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-369 1.74e-115

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: 336.58  E-value: 1.74e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   3 LNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGTMP 82
Cdd:cd03242     1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  83 LTMFITK-RGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQKN 161
Cdd:cd03242    81 LELTIRSgGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 162 NYLKqlqignktdttmlevlnqqfaeyalkvtlrrehfikeleqlaqpihagitnereqlalkylpslklshqdqtesem 241
Cdd:cd03242   161 ALLK---------------------------------------------------------------------------- 164

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 242 leeiltllndnlqrekdrgvclfGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLS 321
Cdd:cd03242   165 -----------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLA 221

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 1325404588 322 ELDDSRQTHLLSTIQHKVQTFVTTTSVDGIDHEIMNNAKLYRINQGEI 369
Cdd:cd03242   222 ELDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDAGTL 269
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-74 9.97e-08

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: 53.37  E-value: 9.97e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLaLAKSHRTSNDKELIRFDSEYAKIEGEL 74
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIF-LNNKEKFFEDDFLVLYLKDVIKIDKED 73
 
Name Accession Description Interval E-value
recF PRK00064
recombination protein F; Reviewed
 1-369 3.53e-172

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 483.89  E-value: 3.53e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGT 80
Cdd:PRK00064    1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  81 MPLTMFITKRG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQ 159
Cdd:PRK00064   81 LPLGLEIDKKGgRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 160 KNNYLKQlqignkTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqDQTES 239
Cdd:PRK00064  161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSV-----EDDAE 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 240 EMLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 319
Cdd:PRK00064  230 KIEEDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDV 309

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1325404588 320 LSELDDSRQTHLLSTIQH-KVQTFVTTTSVDGIDHEImNNAKLYRINQGEI 369
Cdd:PRK00064  310 ASELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-366 7.24e-168

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: 473.00  E-value: 7.24e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGEL--NYRH 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVskGDRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  79 GTMPLTMFITKRGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILK 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 159 QKNNYLKQLQiGNKTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqdqte 238
Cdd:TIGR00611 161 QRNAALKQAQ-RQYGDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL--------- 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 239 SEMLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDD 318
Cdd:TIGR00611 231 WDKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDD 310

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 1325404588 319 VLSELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDH-EIMNNAKLYRINQ 366
Cdd:TIGR00611 311 VASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEmWDPNRVTIALVSV 360
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-355 7.36e-153

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 434.58  E-value: 7.36e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   2 KLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGTM 81
Cdd:COG1195     1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  82 PLTMFITKRG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQK 160
Cdd:COG1195    81 RLGLGLSRGGkKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 161 NNYLKQlqiGNKTDTTMLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREQLALKYLPSLklshqDQTESE 240
Cdd:COG1195   161 NALLKQ---GREADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGW-----LYESAE 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 241 MLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVL 320
Cdd:COG1195   233 LEEALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVF 312

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1325404588 321 SELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDHEI 355
Cdd:COG1195   313 AELDEERREALLELLADLgGQVFITTTDPEDFPALL 348
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-369 1.74e-115

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: 336.58  E-value: 1.74e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   3 LNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGTMP 82
Cdd:cd03242     1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  83 LTMFITK-RGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQKN 161
Cdd:cd03242    81 LELTIRSgGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 162 NYLKqlqignktdttmlevlnqqfaeyalkvtlrrehfikeleqlaqpihagitnereqlalkylpslklshqdqtesem 241
Cdd:cd03242   161 ALLK---------------------------------------------------------------------------- 164

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 242 leeiltllndnlqrekdrgvclfGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLS 321
Cdd:cd03242   165 -----------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLA 221

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 1325404588 322 ELDDSRQTHLLSTIQHKVQTFVTTTSVDGIDHEIMNNAKLYRINQGEI 369
Cdd:cd03242   222 ELDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDAGTL 269
recF PRK14079
recombination protein F; Provisional
 1-346 1.43e-62

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 203.86  E-value: 1.43e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYtLALAKSHRTSNDKELIRFDSEYAKIEGELNYRHGT 80
Cdd:PRK14079    1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIY-LALTGELPNGRLADLVRFGEGEAWVHAEVETGGGL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  81 MPLTMFITKRGKQVKVNhlEQSRLTQYIGHL-NVVLFAPEDLNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILKQ 159
Cdd:PRK14079   80 SRLEVGLGPGRRELKLD--GVRVSLRELARLpGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQ 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 160 KNNYLKQLqiGNKTdttmLEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAGITNEREqlalkylpsLKLSHqdqTES 239
Cdd:PRK14079  158 RNAALKSG--GGWG----LHVWDDELVKLGDEIMALRRRALTRLSELAREAYAELGSRKP---------LRLEL---SES 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 240 EMLEEILTLLNDNLQREKDRGVCLFGPHRDDLGFNVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 319
Cdd:PRK14079  220 TAPEGYLAALEARRAEELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDF 299

                         330       340
                  ....*....|....*....|....*..
gi 1325404588 320 LSELDDSRQTHLLSTIQHKVQTFVTTT 346
Cdd:PRK14079  300 TAELDPRRRGALLALAASLPQAIVAGT 326
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-74 6.98e-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: 6.98e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIyTLALAKSHRTSNDKELIRFDSEYAKIEGEL 74
Cdd:COG3593     1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEAL-RLLLGPSSSRKFDEEDFYLGDDPDLPEIEI 73
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-46 1.37e-08

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 55.39  E-value: 1.37e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1325404588   1 MKLNTLQLENYRNYEQVTID--CHPEVNILIGENAQGKTNLLESIYTL 46
Cdd:COG3950     1 MRIKSLTIENFRGFEDLEIDfdNPPRLTVLVGENGSGKTTLLEAIALA 48
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-74 9.97e-08

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: 53.37  E-value: 9.97e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLaLAKSHRTSNDKELIRFDSEYAKIEGEL 74
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIF-LNNKEKFFEDDFLVLYLKDVIKIDKED 73
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-74 7.52e-07

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 49.24  E-value: 7.52e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1325404588   2 KLNTLQLENYRNY-EQVTIDCHPEVNILIGENAQGKTNLLESIyTLALAKSHRTSND--KELIRFDSEYAKIEGEL 74
Cdd:COG0419     1 KLLRLRLENFRSYrDTETIDFDDGLNLIVGPNGAGKSTILEAI-RYALYGKARSRSKlrSDLINVGSEEASVELEF 75
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-47 9.99e-07

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 50.31  E-value: 9.99e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1325404588   2 KLNTLQLENYRNYEQVTIDCHPeVNILIGENAQGKTNLLESIYTLA 47
Cdd:COG4637     1 MITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFLS 45
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-74 4.71e-05

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 44.65  E-value: 4.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   3 LNTLQLENYRNY-EQVTIDCHPE------VNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELI---RFDSEYAKIEG 72
Cdd:COG1106     2 LISFSIENFRSFkDELTLSMVASglrllrVNLIYGANASGKSNLLEALYFLRNLVLNSSQPGDKLVepfLLDSESKNEPS 81


                  ..
gi 1325404588  73 EL 74
Cdd:COG1106    82 EF 83
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-97 7.00e-05

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 44.89  E-value: 7.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIyTLALAKSHRTSNDKELIRFDSEYakIEGELNYRHGT 80
Cdd:PRK01156    1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAI-RFALFTDKRTEKIEDMIKKGKNN--LEVELEFRIGG 77

                          90
                  ....*....|....*....
gi 1325404588  81 MPLTMF--ITKRGKQVKVN 97
Cdd:PRK01156   78 HVYQIRrsIERRGKGSRRE 96
AAA_23 pfam13476
AAA domain;
6-73 1.98e-04

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 41.71  E-value: 1.98e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325404588   6 LQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIyTLALAKSHRTSNDKELIRFDSEYAKIEGE 73
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAI-KLALYGKTSRLKRKSGGGFVKGDIRIGLE 67
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-345 9.48e-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: 40.84  E-value: 9.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  25 VNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFdSEYAKIEGELNYRHGTMPLTMFITKrgkqvkvnHLEQSRL 104
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRN-GGIGGIPSLLNGIDPKEPIEFEISE--------FLEDGVR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 105 TQYighlnvvlfapedlNIVKGSPLIRRRFIDMELGQISAVYLNDLSQYQRILK-QKNNYLKQLQIGNKTDTTMLEvlnq 183
Cdd:pfam13304  72 YRY--------------GLDLEREDVEEKLSSKPTLLEKRLLLREDSEEREPKFpPEAEELRLGLDVEERIELSLS---- 133

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 184 qfAEYALKVTLRREHFIKELEQLAQPIHAGITNE--REQLALKYLPSLKLSHQDQTESEMLEEILTLLNDNLQREKDRGV 261
Cdd:pfam13304 134 --ELSDLISGLLLLSIISPLSFLLLLDEGLLLEDwaVLDLAADLALFPDLKELLQRLVRGLKLADLNLSDLGEGIEKSLL 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 262 CLFGPHRDDLGFNVNGMDAQTYG---SQGQQRTTALSIKLAEIelmnieVGEYPILLLDDVLSELDDSRQTHLLSTIQHK 338
Cdd:pfam13304 212 VDDRLRERGLILLENGGGGELPAfelSDGTKRLLALLAALLSA------LPKGGLLLIDEPESGLHPKLLRRLLELLKEL 285

                         330
                  ....*....|.
gi 1325404588 339 ----VQTFVTT 345
Cdd:pfam13304 286 srngAQLILTT 296
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-249 1.91e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 40.14  E-value: 1.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588   1 MKLNTLQLENYRNYEQVTIDCHPEVNILIGENAQGKTNLLESIYTLALAKSHR------TSNDKELIRFDSEYAKIEGEL 74
Cdd:COG4717     1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFIRAMLLERLEKeadelfKPQGRKPELNLKELKELEEEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588  75 NYRHGTM----PLTMFITKRGKQVKVNHLEQSRLTQYIGHLNVVLFAPEdlnivkgsPLIRRRFIDMELGQISAVY---- 146
Cdd:COG4717    81 KEAEEKEeeyaELQEELEELEEELEELEAELEELREELEKLEKLLQLLP--------LYQELEALEAELAELPERLeele 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325404588 147 --LNDLSQYQRILKQKNNYLKQLQignktdttmlEVLNQQFAEYALKVTLRREHFIKELEQLAQPIHAgITNEREQL--- 221
Cdd:COG4717   153 erLEELRELEEELEELEAELAELQ----------EELEELLEQLSLATEEELQDLAEELEELQQRLAE-LEEELEEAqee 221

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1325404588 222 ---ALKYLPSLKLSHQDQTESEMLEEILTLL 249
Cdd:COG4717   222 leeLEEELEQLENELEAAALEERLKEARLLL 252
 
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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