MULTISPECIES: exodeoxyribonuclease V subunit alpha [Enterobacteriaceae]
Protein Classification
exodeoxyribonuclease V subunit alpha( domain architecture ID 11485051)
exodeoxyribonuclease V subunit alpha is the RecD subunit of the RecBCD complex, which is involved in homologous double-strand break repair
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
3-608 | 0e+00 | |||||||||
exodeoxyribonuclease V subunit alpha; : Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 1126.96 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||||
| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
3-608 | 0e+00 | |||||||||
exodeoxyribonuclease V subunit alpha; Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 1126.96 E-value: 0e+00
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| recD | TIGR01447 | exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
7-598 | 0e+00 | |||||||||
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 554.37 E-value: 0e+00
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
23-603 | 9.21e-138 | |||||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 411.29 E-value: 9.21e-138
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| DEXSc_RecD-like | cd17933 | DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
153-315 | 7.46e-45 | |||||||||
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350691 [Multi-domain] Cd Length: 155 Bit Score: 156.56 E-value: 7.46e-45
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| AAA_19 | pfam13245 | AAA domain; |
154-304 | 4.68e-27 | |||||||||
AAA domain; Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 106.53 E-value: 4.68e-27
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| Name | Accession | Description | Interval | E-value | |||||||||
| recD | PRK10875 | exodeoxyribonuclease V subunit alpha; |
3-608 | 0e+00 | |||||||||
exodeoxyribonuclease V subunit alpha; Pssm-ID: 236783 [Multi-domain] Cd Length: 615 Bit Score: 1126.96 E-value: 0e+00
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| recD | TIGR01447 | exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
7-598 | 0e+00 | |||||||||
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 554.37 E-value: 0e+00
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
23-603 | 9.21e-138 | |||||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 411.29 E-value: 9.21e-138
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| recD_rel | TIGR01448 | helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ... |
199-604 | 6.98e-51 | |||||||||
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273632 [Multi-domain] Cd Length: 720 Bit Score: 187.30 E-value: 6.98e-51
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| DEXSc_RecD-like | cd17933 | DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
153-315 | 7.46e-45 | |||||||||
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350691 [Multi-domain] Cd Length: 155 Bit Score: 156.56 E-value: 7.46e-45
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| AAA_19 | pfam13245 | AAA domain; |
154-304 | 4.68e-27 | |||||||||
AAA domain; Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 106.53 E-value: 4.68e-27
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| DExxQc_SF1-N | cd17914 | DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
181-359 | 3.84e-25 | |||||||||
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438706 [Multi-domain] Cd Length: 121 Bit Score: 100.64 E-value: 3.84e-25
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
184-382 | 4.03e-23 | |||||||||
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 97.25 E-value: 4.03e-23
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| Helicase_RecD | pfam05127 | Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase ... |
181-354 | 3.67e-21 | |||||||||
Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases. Pssm-ID: 461555 [Multi-domain] Cd Length: 171 Bit Score: 90.67 E-value: 3.67e-21
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| SF1_C_RecD | cd18809 | C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
534-581 | 2.38e-18 | |||||||||
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350196 [Multi-domain] Cd Length: 80 Bit Score: 79.91 E-value: 2.38e-18
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| TraA_Ti | TIGR02768 | Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ... |
116-598 | 9.46e-14 | |||||||||
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer. Pssm-ID: 274289 [Multi-domain] Cd Length: 744 Bit Score: 74.46 E-value: 9.46e-14
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| SH3_13 | pfam18335 | ATP-dependent RecD-like DNA helicase SH3 domain; This is an SH3 (SRC homology domain 3) domain ... |
454-512 | 1.85e-11 | |||||||||
ATP-dependent RecD-like DNA helicase SH3 domain; This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. Structural analysis indicate that the extension of the 5'-tail of the unwound DNA duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves this SH3 domain that binds to a region of the RecB subunit. Studies of RecD in E. coli also revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail. Pssm-ID: 465715 [Multi-domain] Cd Length: 65 Bit Score: 59.80 E-value: 1.85e-11
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| UvrD_C_2 | pfam13538 | UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
534-580 | 4.37e-11 | |||||||||
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. Pssm-ID: 463913 [Multi-domain] Cd Length: 52 Bit Score: 58.35 E-value: 4.37e-11
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
534-581 | 3.37e-09 | |||||||||
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350173 [Multi-domain] Cd Length: 89 Bit Score: 53.98 E-value: 3.37e-09
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| DEXSc_Pif1_like | cd18037 | DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ... |
184-304 | 4.76e-06 | |||||||||
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350795 [Multi-domain] Cd Length: 183 Bit Score: 47.24 E-value: 4.76e-06
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| DEXXQc_Upf1-like | cd17934 | DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
205-301 | 1.20e-04 | |||||||||
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438708 [Multi-domain] Cd Length: 121 Bit Score: 41.84 E-value: 1.20e-04
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
535-581 | 1.49e-04 | |||||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 43.52 E-value: 1.49e-04
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| PRK13889 | PRK13889 | conjugal transfer relaxase TraA; Provisional |
264-308 | 3.48e-04 | |||||||||
conjugal transfer relaxase TraA; Provisional Pssm-ID: 237546 [Multi-domain] Cd Length: 988 Bit Score: 43.91 E-value: 3.48e-04
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| UvrD | COG0210 | Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
536-584 | 4.48e-04 | |||||||||
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 43.39 E-value: 4.48e-04
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| UvrD_C | pfam13361 | UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
536-577 | 2.16e-03 | |||||||||
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 40.85 E-value: 2.16e-03
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| COG3972 | COG3972 | Superfamily I DNA and RNA helicases [Replication, recombination and repair]; |
536-584 | 2.92e-03 | |||||||||
Superfamily I DNA and RNA helicases [Replication, recombination and repair]; Pssm-ID: 443172 [Multi-domain] Cd Length: 565 Bit Score: 40.59 E-value: 2.92e-03
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| SF1_C_UvrD | cd18807 | C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ... |
536-579 | 3.11e-03 | |||||||||
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350194 [Multi-domain] Cd Length: 150 Bit Score: 38.37 E-value: 3.11e-03
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| Blast search parameters | ||||
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