hypothetical protein U929_00150 [Staphylococcus aureus 12S01399]
Protein Classification
DEAD/DEAH box helicase( domain architecture ID 11467865)
DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| ComFA super family | cl34713 | Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
20-355 | 1.42e-137 | ||||||
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair]; The actual alignment was detected with superfamily member COG4098: Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 398.86 E-value: 1.42e-137
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| Name | Accession | Description | Interval | E-value | ||||||
| ComFA | COG4098 | Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
20-355 | 1.42e-137 | ||||||
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair]; Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 398.86 E-value: 1.42e-137
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| DEXDc_ComFA | cd17925 | DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
30-171 | 3.10e-62 | ||||||
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs 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: 350683 [Multi-domain] Cd Length: 143 Bit Score: 195.60 E-value: 3.10e-62
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
214-318 | 2.35e-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: 59.92 E-value: 2.35e-11
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
20-205 | 1.65e-09 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 57.12 E-value: 1.65e-09
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
48-321 | 6.57e-09 | ||||||
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 56.69 E-value: 6.57e-09
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| PRK05580 | PRK05580 | primosome assembly protein PriA; Validated |
26-106 | 1.44e-06 | ||||||
primosome assembly protein PriA; Validated Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 50.16 E-value: 1.44e-06
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| Name | Accession | Description | Interval | E-value | ||||||
| ComFA | COG4098 | Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
20-355 | 1.42e-137 | ||||||
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair]; Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 398.86 E-value: 1.42e-137
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| DEXDc_ComFA | cd17925 | DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
30-171 | 3.10e-62 | ||||||
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs 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: 350683 [Multi-domain] Cd Length: 143 Bit Score: 195.60 E-value: 3.10e-62
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
49-319 | 1.99e-16 | ||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 80.45 E-value: 1.99e-16
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
214-318 | 2.35e-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: 59.92 E-value: 2.35e-11
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
49-171 | 4.41e-11 | ||||||
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: 60.11 E-value: 4.41e-11
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| Cas3 | COG1203 | CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
31-330 | 2.76e-10 | ||||||
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 61.64 E-value: 2.76e-10
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
20-205 | 1.65e-09 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 57.12 E-value: 1.65e-09
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
264-319 | 4.22e-09 | ||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 52.98 E-value: 4.22e-09
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
48-321 | 6.57e-09 | ||||||
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 56.69 E-value: 6.57e-09
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| DEXHc_priA | cd17929 | DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
31-110 | 2.24e-08 | ||||||
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain] Cd Length: 178 Bit Score: 53.37 E-value: 2.24e-08
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
25-173 | 7.25e-08 | ||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 51.52 E-value: 7.25e-08
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| Cas3_I | cd09639 | CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
48-319 | 3.24e-07 | ||||||
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 51.66 E-value: 3.24e-07
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| PriA | COG1198 | Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
25-106 | 9.58e-07 | ||||||
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 50.50 E-value: 9.58e-07
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
49-172 | 1.10e-06 | ||||||
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: 47.69 E-value: 1.10e-06
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| PRK05580 | PRK05580 | primosome assembly protein PriA; Validated |
26-106 | 1.44e-06 | ||||||
primosome assembly protein PriA; Validated Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 50.16 E-value: 1.44e-06
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| priA | TIGR00595 | primosomal protein N'; All proteins in this family for which functions are known are ... |
49-111 | 1.14e-05 | ||||||
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.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: 273162 [Multi-domain] Cd Length: 505 Bit Score: 46.99 E-value: 1.14e-05
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| SF2_C_Hrq | cd18797 | C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
266-318 | 1.75e-05 | ||||||
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain] Cd Length: 146 Bit Score: 44.17 E-value: 1.75e-05
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
262-330 | 3.00e-05 | ||||||
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: 41.92 E-value: 3.00e-05
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| SF2_C_UvrB | cd18790 | C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
253-347 | 3.68e-05 | ||||||
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: 43.77 E-value: 3.68e-05
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
203-318 | 5.12e-05 | ||||||
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: 42.49 E-value: 5.12e-05
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| YprA | COG1205 | ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
269-319 | 1.09e-04 | ||||||
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair]; Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 44.06 E-value: 1.09e-04
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| PRK09694 | PRK09694 | CRISPR-associated helicase/endonuclease Cas3; |
105-190 | 1.76e-03 | ||||||
CRISPR-associated helicase/endonuclease Cas3; Pssm-ID: 182031 [Multi-domain] Cd Length: 878 Bit Score: 40.18 E-value: 1.76e-03
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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 ... |
45-140 | 1.93e-03 | ||||||
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: 38.70 E-value: 1.93e-03
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| SF2_C_RecG | cd18811 | C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
272-318 | 2.11e-03 | ||||||
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 38.48 E-value: 2.11e-03
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| RAD55 | COG0467 | RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms]; |
42-171 | 2.76e-03 | ||||||
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms]; Pssm-ID: 440235 [Multi-domain] Cd Length: 221 Bit Score: 38.74 E-value: 2.76e-03
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| SF2_C_TRCF | cd18810 | C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
273-318 | 4.23e-03 | ||||||
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF 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: 350197 [Multi-domain] Cd Length: 151 Bit Score: 37.32 E-value: 4.23e-03
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
48-176 | 7.02e-03 | ||||||
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: 36.84 E-value: 7.02e-03
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| Blast search parameters | ||||
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