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Conserved domains on  [gi|586335985|gb|EWR38717|]
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DNA replication and repair protein recF [Staphylococcus aureus M1107]

Protein Classification

DNA replication/repair protein RecF( domain architecture ID 11489442)

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:0003697|GO:0005524|GO:0006260|GO:0009432
PubMed:  26874520|30657965

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-365 3.47e-179

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: 501.50  E-value: 3.47e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985    1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSY--RH 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKgdRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   79 GTMPLTMFITKKGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILK 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  159 QKNNYLKQLQlGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLkfdyaqneA 238
Cdd:TIGR00611 161 QRNAALKQAQ-RQYGDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL--------W 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  239 ARLEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 318
Cdd:TIGR00611 232 DKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDV 311

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 586335985  319 LSELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDH-EIMNNAKLYRINQ 365
Cdd:TIGR00611 312 ASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEmWDPNRVTIALVSV 360
 
Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-365 3.47e-179

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: 501.50  E-value: 3.47e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985    1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSY--RH 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKgdRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   79 GTMPLTMFITKKGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILK 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  159 QKNNYLKQLQlGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLkfdyaqneA 238
Cdd:TIGR00611 161 QRNAALKQAQ-RQYGDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL--------W 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  239 ARLEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 318
Cdd:TIGR00611 232 DKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDV 311

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 586335985  319 LSELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDH-EIMNNAKLYRINQ 365
Cdd:TIGR00611 312 ASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEmWDPNRVTIALVSV 360
recF PRK00064
recombination protein F; Reviewed
 1-368 4.85e-171

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 480.81  E-value: 4.85e-171
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGT 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  81 MPLTMFITKKG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQ 159
Cdd:PRK00064  81 LPLGLEIDKKGgRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 160 KNNYLKQlqlgqkKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLKFDYAQNEaa 239
Cdd:PRK00064 161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVEDDAEKIE-- 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 240 rlEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVL 319
Cdd:PRK00064 233 --EDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVA 310

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 586335985 320 SELDDSRQTHLLSTIQH-KVQTFVTTTSVDGIDHEImNNAKLYRINQGEI 368
Cdd:PRK00064 311 SELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-354 1.88e-154

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 438.43  E-value: 1.88e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   2 KLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTM 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  82 PLTMFITKKG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQK 160
Cdd:COG1195   81 RLGLGLSRGGkKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 161 NNYLKQlqlGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLKFDYAQNEaar 240
Cdd:COG1195  161 NALLKQ---GREADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYESAELE--- 234

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 241 lEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLS 320
Cdd:COG1195  235 -EALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFA 313

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 586335985 321 ELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDHEI 354
Cdd:COG1195  314 ELDEERREALLELLADLgGQVFITTTDPEDFPALL 348
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-368 1.66e-118

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: 343.90  E-value: 1.66e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   3 LNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTMP 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  83 LTMFITK-KGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQKN 161
Cdd:cd03242   81 LELTIRSgGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 162 NYLKqlqlgqkkdltmlevlnqqfaeyamkvtdkrahfiqeleslakpihagitndkealslnylpslkfdyaqneaarl 241
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 242 eeimsilsdnmqrekergislfGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLSE 321
Cdd:cd03242  165 ----------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAE 222

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 586335985 322 LDDSRQTHLLSTIQHKVQTFVTTTSVDGIDHEIMNNAKLYRINQGEI 368
Cdd:cd03242  223 LDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDAGTL 269
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-74 1.36e-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: 49.90  E-value: 1.36e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 586335985    1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLaLAKSHRTSNDKELIRFNADYAKIEGEL 74
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIF-LNNKEKFFEDDFLVLYLKDVIKIDKED 73
 
Name Accession Description Interval E-value
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-365 3.47e-179

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: 501.50  E-value: 3.47e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985    1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSY--RH 78
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLIRFGAEAFVIEGRVSKgdRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   79 GTMPLTMFITKKGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILK 158
Cdd:TIGR00611  81 VTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLFAPEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  159 QKNNYLKQLQlGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLkfdyaqneA 238
Cdd:TIGR00611 161 QRNAALKQAQ-RQYGDRTTLEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQLLLPELESLSLFYRGEL--------W 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  239 ARLEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 318
Cdd:TIGR00611 232 DKETDYAEALARNFERDLERGYTLVGPHRDDLRFRLNGLPVEDFASQGQLRSLALALRLAEGELLREEGGEYPILLLDDV 311

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 586335985  319 LSELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDH-EIMNNAKLYRINQ 365
Cdd:TIGR00611 312 ASELDDQRRRLLAELLQSLgVQVFVTAISLDHLKEmWDPNRVTIALVSV 360
recF PRK00064
recombination protein F; Reviewed
 1-368 4.85e-171

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 480.81  E-value: 4.85e-171
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGT 80
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIRFGAEAAVIHGRVEKGGRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  81 MPLTMFITKKG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQ 159
Cdd:PRK00064  81 LPLGLEIDKKGgRKVRINGEPQRKLAELAGLLNVVLFTPEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 160 KNNYLKQlqlgqkKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLKFDYAQNEaa 239
Cdd:PRK00064 161 RNALLKQ------ADYAWLDVWDEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSVEDDAEKIE-- 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 240 rlEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVL 319
Cdd:PRK00064 233 --EDLLEALAKNRERDRARGRTLVGPHRDDLRFRINGLPAADFGSTGQQKLLLLALKLAEAELLKEETGEAPILLLDDVA 310

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 586335985 320 SELDDSRQTHLLSTIQH-KVQTFVTTTSVDGIDHEImNNAKLYRINQGEI 368
Cdd:PRK00064 311 SELDDGRRAALLERLKGlGAQVFITTTDLEDLADLL-ENAKIFHVEQGKI 359
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-354 1.88e-154

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 438.43  E-value: 1.88e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   2 KLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTM 81
Cdd:COG1195    1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAIYLLATGRSFRTARDAELIRFGADGFRVRAEVERDGREV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  82 PLTMFITKKG-KQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQK 160
Cdd:COG1195   81 RLGLGLSRGGkKRVRINGKPVRRLSDLAGLLPVVLFSPEDLRLVKGGPSERRRFLDRLLFQLDPRYLDALSRYERALKQR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 161 NNYLKQlqlGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLKFDYAQNEaar 240
Cdd:COG1195  161 NALLKQ---GREADLALLDVWDEQLAELGAAIIAARLAFLERLAPLFAEIYAALSGGKEELELRYRSGWLYESAELE--- 234

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 241 lEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLS 320
Cdd:COG1195  235 -EALLEALAENRERDLARGRTLVGPHRDDLEFTLNGKPAKKFASQGQQKSLVLALKLAQAELLKEETGEAPILLLDDVFA 313

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 586335985 321 ELDDSRQTHLLSTIQHK-VQTFVTTTSVDGIDHEI 354
Cdd:COG1195  314 ELDEERREALLELLADLgGQVFITTTDPEDFPALL 348
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-368 1.66e-118

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: 343.90  E-value: 1.66e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   3 LNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTMP 82
Cdd:cd03242    1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIRWGAEEAKISAVLERQGGELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  83 LTMFITK-KGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQKN 161
Cdd:cd03242   81 LELTIRSgGGRKARLNGIKVRRLSDLLGVLNAVWFAPEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 162 NYLKqlqlgqkkdltmlevlnqqfaeyamkvtdkrahfiqeleslakpihagitndkealslnylpslkfdyaqneaarl 241
Cdd:cd03242  161 ALLK---------------------------------------------------------------------------- 164

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 242 eeimsilsdnmqrekergislfGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLSE 321
Cdd:cd03242  165 ----------------------GPHRDDLLFFLNDKPAADFGSQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAE 222

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 586335985 322 LDDSRQTHLLSTIQHKVQTFVTTTSVDGIDHEIMNNAKLYRINQGEI 368
Cdd:cd03242  223 LDLGRQAALLDAIEGRVQTFVTTTDLADFDALWLRRAQIFRVDAGTL 269
recF PRK14079
recombination protein F; Provisional
 1-345 1.61e-61

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 201.17  E-value: 1.61e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYtLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGT 80
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIY-LALTGELPNGRLADLVRFGEGEAWVHAEVETGGGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  81 MPLTMFITKKGKQVKVNhlEQSRLTQYIGHL-NVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQ 159
Cdd:PRK14079  80 SRLEVGLGPGRRELKLD--GVRVSLRELARLpGAVLIRPEDLELVLGPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQ 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 160 KNNYLKQLQlgqkkDLTMlEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKE-ALSLNylpslkfdyaqnEA 238
Cdd:PRK14079 158 RNAALKSGG-----GWGL-HVWDDELVKLGDEIMALRRRALTRLSELAREAYAELGSRKPlRLELS------------ES 219

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 239 ARLEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDV 318
Cdd:PRK14079 220 TAPEGYLAALEARRAEELARGATVVGPHRDDLVLTLEGRPAHRYASRGEARTVALALRLAEHRLLWEHFGEAPVLLVDDF 299

                        330       340
                 ....*....|....*....|....*..
gi 586335985 319 LSELDDSRQTHLLSTIQHKVQTFVTTT 345
Cdd:PRK14079 300 TAELDPRRRGALLALAASLPQAIVAGT 326
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-75 6.45e-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: 6.45e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 586335985   1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIyTLALAKSHRTSNDKELIRFNADYAKIEGELS 75
Cdd:COG3593    1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEAL-RLLLGPSSSRKFDEEDFYLGDDPDLPEIEIE 74
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-46 9.77e-08

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 52.69  E-value: 9.77e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 586335985   1 MKLNTLQLENYRNYD--EVTLKCHPDVNILIGENAQGKTNLLESIYTL 46
Cdd:COG3950    1 MRIKSLTIENFRGFEdlEIDFDNPPRLTVLVGENGSGKTTLLEAIALA 48
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-80 6.88e-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: 6.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   2 KLNTLQLENYRNY-DEVTLKCHPDVNILIGENAQGKTNLLESIyTLALAKSHRTSND--KELIRFNADYAKIEGELSYRH 78
Cdd:COG0419    1 KLLRLRLENFRSYrDTETIDFDDGLNLIVGPNGAGKSTILEAI-RYALYGKARSRSKlrSDLINVGSEEASVELEFEHGG 79


                 ..
gi 586335985  79 GT 80
Cdd:COG0419   80 KR 81
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-47 1.11e-06

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 49.93  E-value: 1.11e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 586335985   2 KLNTLQLENYRNYDEVTLKCHPdVNILIGENAQGKTNLLESIYTLA 47
Cdd:COG4637    1 MITRIRIKNFKSLRDLELPLGP-LTVLIGANGSGKSNLLDALRFLS 45
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-74 1.36e-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: 49.90  E-value: 1.36e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 586335985    1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLaLAKSHRTSNDKELIRFNADYAKIEGEL 74
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEALDIF-LNNKEKFFEDDFLVLYLKDVIKIDKED 73
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-75 3.11e-05

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 45.42  E-value: 3.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   3 LNTLQLENYRNY-DEVTLKCHPD------VNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELS 75
Cdd:COG1106    2 LISFSIENFRSFkDELTLSMVASglrllrVNLIYGANASGKSNLLEALYFLRNLVLNSSQPGDKLVEPFLLDSESKNEPS 81
AAA_23 pfam13476
AAA domain;
6-179 4.19e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 44.02  E-value: 4.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985    6 LQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIyTLALAKSHRTSNDKELIRFNADYAKIEG--------ELSYR 77
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAI-KLALYGKTSRLKRKSGGGFVKGDIRIGLegkgkayvEITFE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   78 HGTMPLTMFIT-------KKGKQVKVNHLEQ---SRLTQYIGHLNVVLFapEDLNIVKGSPQIRR-RFIDMELGQISAVY 146
Cdd:pfam13476  80 NNDGRYTYAIErsrelskKKGKTKKKEILEIleiDELQQFISELLKSDK--IILPLLVFLGQEREeEFERKEKKERLEEL 157

                         170       180       190
                  ....*....|....*....|....*....|...
gi 586335985  147 LNDLAQYQRILKQKNNYLKQLQlgQKKDLTMLE 179
Cdd:pfam13476 158 EKALEEKEDEKKLLEKLLQLKE--KKKELEELK 188
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-257 9.52e-05

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 44.51  E-value: 9.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   1 MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIyTLALAKSHRTSNDKELIRFNADYakIEGELSYRHGT 80
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAI-RFALFTDKRTEKIEDMIKKGKNN--LEVELEFRIGG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  81 MPLTMF--ITKKGKQVKVNHL---EQSRLTQYIGHLNVVLfapeDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQR 155
Cdd:PRK01156  78 HVYQIRrsIERRGKGSRREAYikkDGSIIAEGFDDTTKYI----EKNILGISKDVFLNSIFVGQGEMDSLISGDPAQRKK 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985 156 ILKQKNNyLKQLQLGQKKDLTMLEVLNQQFAEYAmKVTDKRAHFIQELESLAKPI------HAGITNDKEALSLNYlpSL 229
Cdd:PRK01156 154 ILDEILE-INSLERNYDKLKDVIDMLRAEISNID-YLEEKLKSSNLELENIKKQIaddeksHSITLKEIERLSIEY--NN 229

                        250       260
                 ....*....|....*....|....*...
gi 586335985 230 KFDYAQNEAARLEEIMSILSDNMQREKE 257
Cdd:PRK01156 230 AMDDYNNLKSALNELSSLEDMKNRYESE 257
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-344 2.20e-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: 42.76  E-value: 2.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985   25 VNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNaDYAKIEGELSYRHGTMPLTMFITKkgkqvkvnHLEQSRL 104
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRNG-GIGGIPSLLNGIDPKEPIEFEISE--------FLEDGVR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  105 TQYighlnvvlfapedlNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQKNNYLKQLQLGQKKDLTMLevLNQQ 184
Cdd:pfam13304  72 YRY--------------GLDLEREDVEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEELRLGLDVEERIELS--LSEL 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  185 FAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLKFDYAQNEAARLEEIMSILSDNMQREKERGISLFG 264
Cdd:pfam13304 136 SDLISGLLLLSIISPLSFLLLLDEGLLLEDWAVLDLAADLALFPDLKELLQRLVRGLKLADLNLSDLGEGIEKSLLVDDR 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586335985  265 PHRDDISFDVNGMDAQTYG---SQGQQRTTALSIKLAEIelmnieVGEYPILLLDDVLSELDDSRQTHLLSTIQHK---- 337
Cdd:pfam13304 216 LRERGLILLENGGGGELPAfelSDGTKRLLALLAALLSA------LPKGGLLLIDEPESGLHPKLLRRLLELLKELsrng 289


                  ....*..
gi 586335985  338 VQTFVTT 344
Cdd:pfam13304 290 AQLILTT 296
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 8-74 3.90e-03

ATP-binding cassette domain of eukaryotic SMC5 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: 213244 [Multi-domain]  Cd Length: 213  Bit Score: 38.35  E-value: 3.90e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 586335985   8 LENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIyTLALAKS----HRTSNDKELIRFNADYAKIEGEL 74
Cdd:cd03277    8 LENFVTYDETEFRPGPSLNMIIGPNGSGKSSIVCAI-CLGLGGKpkllGRAKKVGEFVKRGCDEGTIEIEL 77
 
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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