DEAD/DEAH box helicase [Francisella hispaniensis]
Protein Classification
DEAD/DEAH box helicase( domain architecture ID 11582197)
DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; contains N-terminal phospholipase D (PLD) and C-terminal DUF3427 domains
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
102-697 | 2.11e-107 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; : Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 343.55 E-value: 2.11e-107
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| PLDc_N_DEXD_b2 | cd09204 | N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ... |
16-152 | 1.68e-61 | |||||||||
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. : Pssm-ID: 197298 [Multi-domain] Cd Length: 139 Bit Score: 204.70 E-value: 1.68e-61
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| DUF3427 | pfam11907 | Domain of unknown function (DUF3427); This presumed domain is functionally uncharacterized. ... |
647-906 | 1.09e-44 | |||||||||
Domain of unknown function (DUF3427); This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with pfam04851, pfam00271. : Pssm-ID: 463392 Cd Length: 278 Bit Score: 162.78 E-value: 1.09e-44
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| Name | Accession | Description | Interval | E-value | |||||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
102-697 | 2.11e-107 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 343.55 E-value: 2.11e-107
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| PLDc_N_DEXD_b2 | cd09204 | N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ... |
16-152 | 1.68e-61 | |||||||||
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. Pssm-ID: 197298 [Multi-domain] Cd Length: 139 Bit Score: 204.70 E-value: 1.68e-61
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| DEXHc_RE_I_III_res | cd18032 | DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
189-345 | 4.52e-59 | |||||||||
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 198.94 E-value: 4.52e-59
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| DUF3427 | pfam11907 | Domain of unknown function (DUF3427); This presumed domain is functionally uncharacterized. ... |
647-906 | 1.09e-44 | |||||||||
Domain of unknown function (DUF3427); This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with pfam04851, pfam00271. Pssm-ID: 463392 Cd Length: 278 Bit Score: 162.78 E-value: 1.09e-44
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
186-335 | 8.16e-37 | |||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 135.88 E-value: 8.16e-37
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
184-360 | 9.89e-16 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 76.76 E-value: 9.89e-16
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
193-505 | 2.34e-10 | |||||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 64.59 E-value: 2.34e-10
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| PLDc_2 | pfam13091 | PLD-like domain; |
21-151 | 2.36e-07 | |||||||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 50.75 E-value: 2.36e-07
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| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
157-363 | 5.66e-03 | |||||||||
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.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: 273168 [Multi-domain] Cd Length: 732 Bit Score: 40.55 E-value: 5.66e-03
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| Name | Accession | Description | Interval | E-value | |||||||||||||
| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
102-697 | 2.11e-107 | |||||||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 343.55 E-value: 2.11e-107
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| COG3886 | COG3886 | HKD family nuclease [Replication, recombination and repair]; |
1-913 | 1.18e-94 | |||||||||||||
HKD family nuclease [Replication, recombination and repair]; Pssm-ID: 443094 [Multi-domain] Cd Length: 941 Bit Score: 319.62 E-value: 1.18e-94
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| PLDc_N_DEXD_b2 | cd09204 | N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ... |
16-152 | 1.68e-61 | |||||||||||||
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. Pssm-ID: 197298 [Multi-domain] Cd Length: 139 Bit Score: 204.70 E-value: 1.68e-61
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| DEXHc_RE_I_III_res | cd18032 | DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
189-345 | 4.52e-59 | |||||||||||||
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 198.94 E-value: 4.52e-59
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| DUF3427 | pfam11907 | Domain of unknown function (DUF3427); This presumed domain is functionally uncharacterized. ... |
647-906 | 1.09e-44 | |||||||||||||
Domain of unknown function (DUF3427); This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with pfam04851, pfam00271. Pssm-ID: 463392 Cd Length: 278 Bit Score: 162.78 E-value: 1.09e-44
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
186-335 | 8.16e-37 | |||||||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 135.88 E-value: 8.16e-37
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
415-519 | 3.32e-35 | |||||||||||||
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 129.60 E-value: 3.32e-35
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| PLDc_N_DEXD_b | cd09180 | N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ... |
16-152 | 9.21e-33 | |||||||||||||
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. A few family members contain additional domains, like a C-terminal peptidase S24-like domain. Pssm-ID: 197277 [Multi-domain] Cd Length: 142 Bit Score: 123.60 E-value: 9.21e-33
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| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
128-669 | 3.60e-27 | |||||||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 118.79 E-value: 3.60e-27
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
193-333 | 3.91e-26 | |||||||||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part 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: 350684 [Multi-domain] Cd Length: 146 Bit Score: 104.70 E-value: 3.91e-26
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| PLDc_N_DEXD_b3 | cd09205 | N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ... |
18-152 | 3.39e-25 | |||||||||||||
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. A few family members contain additional domains, like a C-terminal peptidase S24-like domain. Pssm-ID: 197299 [Multi-domain] Cd Length: 143 Bit Score: 101.93 E-value: 3.39e-25
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| PLDc_N_DEXD_b1 | cd09203 | N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family ... |
20-149 | 6.05e-18 | |||||||||||||
N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. Pssm-ID: 197297 [Multi-domain] Cd Length: 143 Bit Score: 81.13 E-value: 6.05e-18
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
184-360 | 9.89e-16 | |||||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 76.76 E-value: 9.89e-16
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| PLDc_Bfil_DEXD_like | cd09117 | Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ... |
15-132 | 1.47e-14 | |||||||||||||
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, uncharacterized type III restriction endonuclease Res subunit, and uncharacterized DNA/RNA helicase superfamily II members. Proteins in this family are found mainly in prokaryotes. They contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain, and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events. Pssm-ID: 197216 [Multi-domain] Cd Length: 117 Bit Score: 70.89 E-value: 1.47e-14
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
426-506 | 1.17e-13 | |||||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 66.85 E-value: 1.17e-13
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
415-505 | 3.20e-11 | |||||||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 61.07 E-value: 3.20e-11
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| hsdR | PRK11448 | type I restriction enzyme EcoKI subunit R; Provisional |
193-505 | 2.34e-10 | |||||||||||||
type I restriction enzyme EcoKI subunit R; Provisional Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 64.59 E-value: 2.34e-10
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| PLDc_N_Snf2_like | cd09178 | N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative ... |
8-149 | 3.00e-10 | |||||||||||||
N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family; N-terminal putative catalytic domain of uncharacterized archaeal and prokaryotic HKD family nucleases fused to putative helicases from the Snf2-like family, which belong to the DNA/RNA helicase superfamily II (SF2). Although Snf2-like family enzymes do not possess helicase activity, they contain a helicase-like region, where seven helicase-related sequence motifs are found, similar to those in DEAD/DEAH box helicases, which represent the biggest family within the SF2 superfamily. In addition to the helicase-like region, members of this family also contain an N-terminal putative catalytic domain with one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. Pssm-ID: 197275 [Multi-domain] Cd Length: 134 Bit Score: 59.10 E-value: 3.00e-10
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
415-502 | 4.90e-10 | |||||||||||||
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 58.29 E-value: 4.90e-10
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
190-336 | 9.07e-09 | |||||||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 55.71 E-value: 9.07e-09
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
462-516 | 1.86e-08 | |||||||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 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: 350172 [Multi-domain] Cd Length: 77 Bit Score: 51.94 E-value: 1.86e-08
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
207-332 | 2.17e-07 | |||||||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 51.25 E-value: 2.17e-07
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| PLDc_2 | pfam13091 | PLD-like domain; |
21-151 | 2.36e-07 | |||||||||||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 50.75 E-value: 2.36e-07
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
187-333 | 2.39e-07 | |||||||||||||
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain] Cd Length: 200 Bit Score: 52.27 E-value: 2.39e-07
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| SF2_C_FANCM_Hef | cd18801 | C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
415-515 | 5.52e-07 | |||||||||||||
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350188 [Multi-domain] Cd Length: 143 Bit Score: 49.66 E-value: 5.52e-07
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| SF2_C_XPB | cd18789 | C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
378-512 | 8.85e-07 | |||||||||||||
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 49.56 E-value: 8.85e-07
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| DEXHc_XPB | cd18029 | DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
188-337 | 1.05e-06 | |||||||||||||
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350787 [Multi-domain] Cd Length: 169 Bit Score: 49.61 E-value: 1.05e-06
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
396-485 | 1.33e-06 | |||||||||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 51.69 E-value: 1.33e-06
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| uvsW | PHA02558 | UvsW helicase; Provisional |
187-519 | 1.50e-06 | |||||||||||||
UvsW helicase; Provisional Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 51.93 E-value: 1.50e-06
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
390-516 | 2.06e-06 | |||||||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 51.65 E-value: 2.06e-06
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| COG0610 | COG0610 | Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
193-691 | 1.97e-05 | |||||||||||||
Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms]; Pssm-ID: 440375 [Multi-domain] Cd Length: 936 Bit Score: 48.71 E-value: 1.97e-05
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| DEXHc_RIG-I | cd17927 | DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
187-347 | 2.51e-05 | |||||||||||||
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part 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: 350685 [Multi-domain] Cd Length: 201 Bit Score: 46.27 E-value: 2.51e-05
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
190-307 | 1.06e-04 | |||||||||||||
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 43.79 E-value: 1.06e-04
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| DEXDc_RapA | cd18011 | DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
293-344 | 1.26e-04 | |||||||||||||
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part 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: 350769 [Multi-domain] Cd Length: 207 Bit Score: 44.20 E-value: 1.26e-04
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| PLDc_unchar2_2 | cd09130 | Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; ... |
83-153 | 2.28e-04 | |||||||||||||
Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. Pssm-ID: 197228 [Multi-domain] Cd Length: 157 Bit Score: 42.62 E-value: 2.28e-04
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
193-346 | 2.47e-04 | |||||||||||||
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins 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: 350677 [Multi-domain] Cd Length: 182 Bit Score: 42.94 E-value: 2.47e-04
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| PLDc_unchar6 | cd09176 | Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ... |
68-126 | 2.54e-04 | |||||||||||||
Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Pssm-ID: 197273 [Multi-domain] Cd Length: 114 Bit Score: 41.56 E-value: 2.54e-04
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
423-515 | 3.93e-04 | |||||||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 44.09 E-value: 3.93e-04
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
293-346 | 4.62e-04 | |||||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 44.06 E-value: 4.62e-04
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| SF2_C_UvrB | cd18790 | C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
425-519 | 6.29e-04 | |||||||||||||
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350177 [Multi-domain] Cd Length: 171 Bit Score: 41.46 E-value: 6.29e-04
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
389-516 | 9.40e-04 | |||||||||||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 40.27 E-value: 9.40e-04
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| PLDc_SF | cd00138 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
19-132 | 1.86e-03 | |||||||||||||
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. Pssm-ID: 197200 [Multi-domain] Cd Length: 119 Bit Score: 39.04 E-value: 1.86e-03
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| PLDc_PGS1_euk_2 | cd09137 | Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic ... |
54-156 | 2.00e-03 | |||||||||||||
Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer. Pssm-ID: 197235 Cd Length: 186 Bit Score: 40.25 E-value: 2.00e-03
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
208-333 | 3.36e-03 | |||||||||||||
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain] Cd Length: 181 Bit Score: 39.42 E-value: 3.36e-03
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
193-307 | 3.81e-03 | |||||||||||||
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 39.24 E-value: 3.81e-03
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| rad25 | TIGR00603 | DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
157-363 | 5.66e-03 | |||||||||||||
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.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: 273168 [Multi-domain] Cd Length: 732 Bit Score: 40.55 E-value: 5.66e-03
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