MULTISPECIES: excinuclease ABC subunit UvrB [Citrobacter]
Protein Classification
excinuclease ABC subunit UvrB( domain architecture ID 11480575)
excinuclease ABC subunit UvrB is part of the UvrABC repair system that catalyzes the recognition and processing of DNA lesions
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| PRK05298 | PRK05298 | excinuclease ABC subunit UvrB; |
1-673 | 0e+00 | ||||||||||
excinuclease ABC subunit UvrB; : Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 1361.65 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||||
| PRK05298 | PRK05298 | excinuclease ABC subunit UvrB; |
1-673 | 0e+00 | ||||||||||
excinuclease ABC subunit UvrB; Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 1361.65 E-value: 0e+00
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| UvrB | COG0556 | Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
4-668 | 0e+00 | ||||||||||
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 1352.37 E-value: 0e+00
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| uvrb | TIGR00631 | excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ... |
4-666 | 0e+00 | ||||||||||
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain] Cd Length: 655 Bit Score: 1205.97 E-value: 0e+00
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| DEXHc_UvrB | cd17916 | DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ... |
5-414 | 0e+00 | ||||||||||
DEXH-box helicase domain of excinuclease ABC subunit B; 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, but its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a member of the DEAD-like helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350674 [Multi-domain] Cd Length: 299 Bit Score: 529.47 E-value: 0e+00
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| UvrB_inter | pfam17757 | UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
159-249 | 1.66e-42 | ||||||||||
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein. Pssm-ID: 465486 [Multi-domain] Cd Length: 91 Bit Score: 148.31 E-value: 1.66e-42
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
460-544 | 7.78e-19 | ||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 81.49 E-value: 7.78e-19
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| Name | Accession | Description | Interval | E-value | ||||||||||
| PRK05298 | PRK05298 | excinuclease ABC subunit UvrB; |
1-673 | 0e+00 | ||||||||||
excinuclease ABC subunit UvrB; Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 1361.65 E-value: 0e+00
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| UvrB | COG0556 | Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
4-668 | 0e+00 | ||||||||||
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 1352.37 E-value: 0e+00
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| uvrb | TIGR00631 | excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ... |
4-666 | 0e+00 | ||||||||||
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain] Cd Length: 655 Bit Score: 1205.97 E-value: 0e+00
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| DEXHc_UvrB | cd17916 | DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ... |
5-414 | 0e+00 | ||||||||||
DEXH-box helicase domain of excinuclease ABC subunit B; 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, but its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a member of the DEAD-like helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350674 [Multi-domain] Cd Length: 299 Bit Score: 529.47 E-value: 0e+00
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| SF2_C_UvrB | cd18790 | C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
420-590 | 6.00e-115 | ||||||||||
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: 341.92 E-value: 6.00e-115
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| Mfd | COG1197 | Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
31-524 | 1.42e-42 | ||||||||||
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription]; Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 166.01 E-value: 1.42e-42
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| UvrB_inter | pfam17757 | UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
159-249 | 1.66e-42 | ||||||||||
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein. Pssm-ID: 465486 [Multi-domain] Cd Length: 91 Bit Score: 148.31 E-value: 1.66e-42
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| UvrB | pfam12344 | Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ... |
552-593 | 2.79e-21 | ||||||||||
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00271, pfam02151, pfam04851. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species. Pssm-ID: 463540 [Multi-domain] Cd Length: 43 Bit Score: 87.06 E-value: 2.79e-21
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
432-544 | 3.51e-20 | ||||||||||
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: 86.11 E-value: 3.51e-20
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
460-544 | 7.78e-19 | ||||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 81.49 E-value: 7.78e-19
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
429-553 | 5.52e-17 | ||||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 84.69 E-value: 5.52e-17
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| mfd | TIGR00580 | transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
176-340 | 2.71e-14 | ||||||||||
transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273152 [Multi-domain] Cd Length: 926 Bit Score: 76.63 E-value: 2.71e-14
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
433-552 | 7.35e-13 | ||||||||||
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: 65.99 E-value: 7.35e-13
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| ComFA | COG4098 | Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
389-565 | 1.74e-12 | ||||||||||
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: 69.90 E-value: 1.74e-12
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
5-92 | 2.27e-12 | ||||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 66.36 E-value: 2.27e-12
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| SF2_C_priA | cd18804 | C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
455-552 | 1.82e-11 | ||||||||||
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' 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 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: 350191 [Multi-domain] Cd Length: 238 Bit Score: 64.57 E-value: 1.82e-11
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
420-518 | 7.19e-10 | ||||||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 61.70 E-value: 7.19e-10
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
34-102 | 7.88e-10 | ||||||||||
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: 57.80 E-value: 7.88e-10
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
444-549 | 2.79e-09 | ||||||||||
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: 55.26 E-value: 2.79e-09
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
17-85 | 2.91e-09 | ||||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 56.53 E-value: 2.91e-09
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| SF2_C_FANCM_Hef | cd18801 | C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
422-552 | 8.00e-09 | ||||||||||
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: 54.67 E-value: 8.00e-09
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| DEAD-like_helicase_N | cd17912 | N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ... |
34-96 | 1.78e-07 | ||||||||||
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region. Pssm-ID: 350670 [Multi-domain] Cd Length: 81 Bit Score: 49.05 E-value: 1.78e-07
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
448-553 | 1.83e-07 | ||||||||||
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: 48.85 E-value: 1.83e-07
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| DEAD-like_helicase_C | cd09300 | C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ... |
499-554 | 1.98e-07 | ||||||||||
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved 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: 350171 [Multi-domain] Cd Length: 59 Bit Score: 48.31 E-value: 1.98e-07
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| uvrC | PRK00558 | excinuclease ABC subunit UvrC; |
636-669 | 4.48e-07 | ||||||||||
excinuclease ABC subunit UvrC; Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 53.20 E-value: 4.48e-07
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| UvrC | COG0322 | Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
636-669 | 4.64e-07 | ||||||||||
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 53.20 E-value: 4.64e-07
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| DEXHc_RecG | cd17918 | DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
11-87 | 4.89e-07 | ||||||||||
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part 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: 350676 [Multi-domain] Cd Length: 180 Bit Score: 50.49 E-value: 4.89e-07
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
435-553 | 4.93e-07 | ||||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 53.20 E-value: 4.93e-07
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| PRK05580 | PRK05580 | primosome assembly protein PriA; Validated |
455-552 | 9.07e-07 | ||||||||||
primosome assembly protein PriA; Validated Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 52.08 E-value: 9.07e-07
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| PRK10689 | PRK10689 | transcription-repair coupling factor; Provisional |
170-336 | 3.63e-06 | ||||||||||
transcription-repair coupling factor; Provisional Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 50.51 E-value: 3.63e-06
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
25-89 | 5.48e-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: 46.53 E-value: 5.48e-06
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
446-551 | 1.32e-05 | ||||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 48.33 E-value: 1.32e-05
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| PTZ00424 | PTZ00424 | helicase 45; Provisional |
455-544 | 1.52e-05 | ||||||||||
helicase 45; Provisional Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 47.90 E-value: 1.52e-05
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| SF2_C_XPB | cd18789 | C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
446-553 | 2.21e-05 | ||||||||||
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: 44.93 E-value: 2.21e-05
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
446-542 | 2.43e-05 | ||||||||||
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: 44.50 E-value: 2.43e-05
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| PriA | COG1198 | Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
487-552 | 3.73e-05 | ||||||||||
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 47.04 E-value: 3.73e-05
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| SF2_C_RecQ | cd18794 | C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
424-544 | 3.75e-05 | ||||||||||
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 43.74 E-value: 3.75e-05
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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 ... |
17-85 | 6.43e-05 | ||||||||||
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: 43.70 E-value: 6.43e-05
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| Cas3 | COG1203 | CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
423-545 | 2.02e-04 | ||||||||||
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: 44.30 E-value: 2.02e-04
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
434-505 | 2.08e-04 | ||||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 44.45 E-value: 2.08e-04
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| YprA | COG1205 | ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
387-544 | 4.47e-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: 43.67 E-value: 4.47e-04
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| SF2_C_reverse_gyrase | cd18798 | C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological ... |
456-548 | 5.56e-04 | ||||||||||
C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase 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: 350185 [Multi-domain] Cd Length: 174 Bit Score: 41.14 E-value: 5.56e-04
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| McsA | COG3880 | Protein-arginine kinase activator protein McsA [Posttranslational modification, protein ... |
630-667 | 5.95e-04 | ||||||||||
Protein-arginine kinase activator protein McsA [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 443088 [Multi-domain] Cd Length: 173 Bit Score: 41.03 E-value: 5.95e-04
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
430-505 | 6.15e-04 | ||||||||||
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They 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: 350180 [Multi-domain] Cd Length: 135 Bit Score: 40.54 E-value: 6.15e-04
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| SF2_C_LHR | cd18796 | C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
449-549 | 6.79e-04 | ||||||||||
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 40.71 E-value: 6.79e-04
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| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
17-84 | 1.03e-03 | ||||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 42.52 E-value: 1.03e-03
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| UVR | pfam02151 | UvrB/uvrC motif; |
633-668 | 1.42e-03 | ||||||||||
UvrB/uvrC motif; Pssm-ID: 308001 [Multi-domain] Cd Length: 36 Bit Score: 36.61 E-value: 1.42e-03
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| SF2_C_RecG | cd18811 | C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
459-544 | 1.92e-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: 39.25 E-value: 1.92e-03
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| PLN00206 | PLN00206 | DEAD-box ATP-dependent RNA helicase; Provisional |
470-553 | 2.02e-03 | ||||||||||
DEAD-box ATP-dependent RNA helicase; Provisional Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 41.31 E-value: 2.02e-03
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| PRK11192 | PRK11192 | ATP-dependent RNA helicase SrmB; Provisional |
447-544 | 2.26e-03 | ||||||||||
ATP-dependent RNA helicase SrmB; Provisional Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 41.08 E-value: 2.26e-03
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
16-81 | 2.39e-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: 39.15 E-value: 2.39e-03
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| DEXHc_priA | cd17929 | DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
17-88 | 2.44e-03 | ||||||||||
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: 39.50 E-value: 2.44e-03
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| SF2_C_RecG_TRCF | cd18792 | C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
459-527 | 3.94e-03 | ||||||||||
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They 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: 350179 [Multi-domain] Cd Length: 160 Bit Score: 38.40 E-value: 3.94e-03
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| DDXDc_reverse_gyrase | cd17924 | DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
443-539 | 6.26e-03 | ||||||||||
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase 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: 350682 [Multi-domain] Cd Length: 189 Bit Score: 38.46 E-value: 6.26e-03
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
14-73 | 9.77e-03 | ||||||||||
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: 37.93 E-value: 9.77e-03
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