MULTISPECIES: DNA replication/repair protein RecF [Listeria]
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
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| recF | PRK00064 | recombination protein F; Reviewed |
1-367 | 1.60e-172 | ||||||
recombination protein F; Reviewed : Pssm-ID: 234608 [Multi-domain] Cd Length: 361 Bit Score: 484.66 E-value: 1.60e-172
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| Name | Accession | Description | Interval | E-value | ||||||
| recF | PRK00064 | recombination protein F; Reviewed |
1-367 | 1.60e-172 | ||||||
recombination protein F; Reviewed Pssm-ID: 234608 [Multi-domain] Cd Length: 361 Bit Score: 484.66 E-value: 1.60e-172
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| RecF | COG1195 | Recombinational DNA repair ATPase RecF [Replication, recombination and repair]; |
2-352 | 5.17e-158 | ||||||
Recombinational DNA repair ATPase RecF [Replication, recombination and repair]; Pssm-ID: 440808 [Multi-domain] Cd Length: 352 Bit Score: 447.29 E-value: 5.17e-158
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| recf | TIGR00611 | recF protein; All proteins in this family for which functions are known are DNA binding ... |
1-367 | 5.87e-144 | ||||||
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: 412.52 E-value: 5.87e-144
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| ABC_RecF | cd03242 | ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ... |
3-368 | 2.48e-139 | ||||||
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: 397.05 E-value: 2.48e-139
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| AAA_23 | pfam13476 | AAA domain; |
6-69 | 2.83e-07 | ||||||
AAA domain; Pssm-ID: 463890 [Multi-domain] Cd Length: 190 Bit Score: 50.19 E-value: 2.83e-07
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| Name | Accession | Description | Interval | E-value | ||||||
| recF | PRK00064 | recombination protein F; Reviewed |
1-367 | 1.60e-172 | ||||||
recombination protein F; Reviewed Pssm-ID: 234608 [Multi-domain] Cd Length: 361 Bit Score: 484.66 E-value: 1.60e-172
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| RecF | COG1195 | Recombinational DNA repair ATPase RecF [Replication, recombination and repair]; |
2-352 | 5.17e-158 | ||||||
Recombinational DNA repair ATPase RecF [Replication, recombination and repair]; Pssm-ID: 440808 [Multi-domain] Cd Length: 352 Bit Score: 447.29 E-value: 5.17e-158
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| recf | TIGR00611 | recF protein; All proteins in this family for which functions are known are DNA binding ... |
1-367 | 5.87e-144 | ||||||
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: 412.52 E-value: 5.87e-144
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| ABC_RecF | cd03242 | ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ... |
3-368 | 2.48e-139 | ||||||
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: 397.05 E-value: 2.48e-139
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| recF | PRK14079 | recombination protein F; Provisional |
1-348 | 3.87e-54 | ||||||
recombination protein F; Provisional Pssm-ID: 184491 [Multi-domain] Cd Length: 349 Bit Score: 181.91 E-value: 3.87e-54
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| YbjD | COG3593 | Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ... |
1-60 | 2.38e-12 | ||||||
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: 67.33 E-value: 2.38e-12
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| COG3950 | COG3950 | Predicted ATP-binding protein involved in virulence [General function prediction only]; |
1-43 | 1.53e-09 | ||||||
Predicted ATP-binding protein involved in virulence [General function prediction only]; Pssm-ID: 443150 [Multi-domain] Cd Length: 276 Bit Score: 58.09 E-value: 1.53e-09
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| COG4637 | COG4637 | Predicted ATPase [General function prediction only]; |
3-47 | 1.65e-09 | ||||||
Predicted ATPase [General function prediction only]; Pssm-ID: 443675 [Multi-domain] Cd Length: 371 Bit Score: 58.79 E-value: 1.65e-09
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| ABC_SMC6_euk | cd03276 | ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ... |
3-80 | 1.15e-07 | ||||||
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: 51.44 E-value: 1.15e-07
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| AAA_23 | pfam13476 | AAA domain; |
6-69 | 2.83e-07 | ||||||
AAA domain; Pssm-ID: 463890 [Multi-domain] Cd Length: 190 Bit Score: 50.19 E-value: 2.83e-07
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| AAA_15 | pfam13175 | AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ... |
1-76 | 4.97e-07 | ||||||
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: 51.06 E-value: 4.97e-07
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
1-94 | 1.36e-06 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 50.42 E-value: 1.36e-06
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| SbcC | COG0419 | DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; |
2-71 | 2.91e-06 | ||||||
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; Pssm-ID: 440188 [Multi-domain] Cd Length: 204 Bit Score: 47.70 E-value: 2.91e-06
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
1-44 | 1.15e-05 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 47.37 E-value: 1.15e-05
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| PRK01156 | PRK01156 | chromosome segregation protein; Provisional |
1-97 | 1.60e-05 | ||||||
chromosome segregation protein; Provisional Pssm-ID: 100796 [Multi-domain] Cd Length: 895 Bit Score: 46.82 E-value: 1.60e-05
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| DUF2813 | pfam11398 | Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which ... |
1-49 | 4.80e-05 | ||||||
Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase. Pssm-ID: 431868 [Multi-domain] Cd Length: 372 Bit Score: 45.04 E-value: 4.80e-05
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
1-168 | 4.93e-05 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 45.14 E-value: 4.93e-05
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| COG4938 | COG4938 | Predicted ATPase [General function prediction only]; |
3-46 | 5.37e-05 | ||||||
Predicted ATPase [General function prediction only]; Pssm-ID: 443965 [Multi-domain] Cd Length: 277 Bit Score: 44.19 E-value: 5.37e-05
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| COG1106 | COG1106 | ATPase/GTPase, AAA15 family [General function prediction only]; |
2-58 | 8.83e-05 | ||||||
ATPase/GTPase, AAA15 family [General function prediction only]; Pssm-ID: 440723 [Multi-domain] Cd Length: 330 Bit Score: 43.88 E-value: 8.83e-05
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| ABC_RecN | cd03241 | ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ... |
3-73 | 1.09e-04 | ||||||
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC (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 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 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: 213208 [Multi-domain] Cd Length: 276 Bit Score: 43.34 E-value: 1.09e-04
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| ABC_SMC5_euk | cd03277 | ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ... |
5-78 | 1.39e-04 | ||||||
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: 42.58 E-value: 1.39e-04
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| ABC_Class2 | cd03227 | ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ... |
5-60 | 1.64e-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: 41.58 E-value: 1.64e-04
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| ABC_Rad50 | cd03240 | ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ... |
3-58 | 1.79e-04 | ||||||
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: 42.21 E-value: 1.79e-04
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| SMC_N | pfam02463 | RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ... |
2-44 | 6.42e-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: 41.88 E-value: 6.42e-04
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| ABC_SMC_barmotin | cd03278 | ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ... |
3-61 | 1.75e-03 | ||||||
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: 38.99 E-value: 1.75e-03
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| ABC_SMC2_euk | cd03273 | ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ... |
1-61 | 8.28e-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: 8.28e-03
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| Blast search parameters | ||||
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