putative addiction module antidote protein [Escherichia coli]
Protein Classification
type II toxin-antitoxin system ParD family antitoxin( domain architecture ID 10007598)
type II toxin-antitoxin system ParD family antitoxin neutralizes the effect of a ParE family toxin
List of domain hits
| Name | Accession | Description | Interval | E-value | ||
| ParD | COG3609 | Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain ... |
3-76 | 3.56e-19 | ||
Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain [Transcription]; : Pssm-ID: 442827 Cd Length: 77 Bit Score: 73.70 E-value: 3.56e-19
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| Name | Accession | Description | Interval | E-value | ||
| ParD | COG3609 | Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain ... |
3-76 | 3.56e-19 | ||
Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain [Transcription]; Pssm-ID: 442827 Cd Length: 77 Bit Score: 73.70 E-value: 3.56e-19
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| antidote_CC2985 | TIGR02606 | putative addiction module antidote protein, CC2985 family; This bacterial protein family has a ... |
4-67 | 1.29e-17 | ||
putative addiction module antidote protein, CC2985 family; This bacterial protein family has a very similar seed alignment to that of pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15. [Cellular processes, Other, Mobile and extrachromosomal element functions, Plasmid functions] Pssm-ID: 274227 Cd Length: 69 Bit Score: 69.64 E-value: 1.29e-17
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| ParD_antitoxin | pfam03693 | Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH; ParD is the antitoxin of a ... |
1-79 | 5.46e-16 | ||
Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH; ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, pfam05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins. Pssm-ID: 281658 Cd Length: 80 Bit Score: 65.63 E-value: 5.46e-16
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| RHH_NikR_HicB-like | cd22231 | ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ... |
3-46 | 2.28e-06 | ||
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ParD, and MazE, and similar proteins; This family includes the N-terminal domain of NikR, C-terminal domains of antitoxins HicB and ParD, as well as antitoxin MazE, and similar proteins, all of which belong to the ribbon-helix-helix (RHH) family of transcription factors. NikR is a nickel-responsive transcription factor that consists of an N-terminal DNA-binding RHH domain and a C-terminal metal-binding domain (MBD) with four nickel ions. In Helicobacter pylori, which colonizes the gastric epithelium of humans leading to gastric ulcers and gastric cancers, NikR (HpNikR) regulates multiple genes. It regulates urease, which protects H. pylori from acidic shock at low pH, by converting urea to ammonia and bicarbonate. It also plays a complex role in the intracellular physiology of nickel; occupation of nickel-binding sites results in NikR binding to its operator in the nickel permease nikABCDE promoter. Thus, there is weaker repression of NikABCDE transcription at low intracellular free nickel concentrations while strong repression prevails at higher concentrations, which would be potentially toxic. Antitoxin HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In the pathogen Burkholderia pseudomallei, the HicAB system plays a role in regulating the frequency of persister cells and may therefore play a role in disease. Structural studies of Yersinia pestis HicB show that it acts as an autoregulatory protein and HicA acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. Similarly, Caulobacter crescentus ParD antitoxin neutralizes the effect of cognate ParE toxin. In Bacillus subtilis, during stress conditions, antitoxin MazE binds to toxin MazF, an mRNA interferase, and inactivates it and cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. Pssm-ID: 409021 [Multi-domain] Cd Length: 44 Bit Score: 40.11 E-value: 2.28e-06
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| Name | Accession | Description | Interval | E-value | ||
| ParD | COG3609 | Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain ... |
3-76 | 3.56e-19 | ||
Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain [Transcription]; Pssm-ID: 442827 Cd Length: 77 Bit Score: 73.70 E-value: 3.56e-19
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| antidote_CC2985 | TIGR02606 | putative addiction module antidote protein, CC2985 family; This bacterial protein family has a ... |
4-67 | 1.29e-17 | ||
putative addiction module antidote protein, CC2985 family; This bacterial protein family has a very similar seed alignment to that of pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15. [Cellular processes, Other, Mobile and extrachromosomal element functions, Plasmid functions] Pssm-ID: 274227 Cd Length: 69 Bit Score: 69.64 E-value: 1.29e-17
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| ParD_antitoxin | pfam03693 | Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH; ParD is the antitoxin of a ... |
1-79 | 5.46e-16 | ||
Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH; ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, pfam05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins. Pssm-ID: 281658 Cd Length: 80 Bit Score: 65.63 E-value: 5.46e-16
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| RHH_NikR_HicB-like | cd22231 | ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ... |
3-46 | 2.28e-06 | ||
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ParD, and MazE, and similar proteins; This family includes the N-terminal domain of NikR, C-terminal domains of antitoxins HicB and ParD, as well as antitoxin MazE, and similar proteins, all of which belong to the ribbon-helix-helix (RHH) family of transcription factors. NikR is a nickel-responsive transcription factor that consists of an N-terminal DNA-binding RHH domain and a C-terminal metal-binding domain (MBD) with four nickel ions. In Helicobacter pylori, which colonizes the gastric epithelium of humans leading to gastric ulcers and gastric cancers, NikR (HpNikR) regulates multiple genes. It regulates urease, which protects H. pylori from acidic shock at low pH, by converting urea to ammonia and bicarbonate. It also plays a complex role in the intracellular physiology of nickel; occupation of nickel-binding sites results in NikR binding to its operator in the nickel permease nikABCDE promoter. Thus, there is weaker repression of NikABCDE transcription at low intracellular free nickel concentrations while strong repression prevails at higher concentrations, which would be potentially toxic. Antitoxin HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In the pathogen Burkholderia pseudomallei, the HicAB system plays a role in regulating the frequency of persister cells and may therefore play a role in disease. Structural studies of Yersinia pestis HicB show that it acts as an autoregulatory protein and HicA acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. Similarly, Caulobacter crescentus ParD antitoxin neutralizes the effect of cognate ParE toxin. In Bacillus subtilis, during stress conditions, antitoxin MazE binds to toxin MazF, an mRNA interferase, and inactivates it and cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. Pssm-ID: 409021 [Multi-domain] Cd Length: 44 Bit Score: 40.11 E-value: 2.28e-06
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| ASKHA_NBD_GDA1_CD39_NTPase | cd24003 | nucleotide-binding domain (NBD) of the GDA1/CD39 NTPase family; The GDA1/CD39 NTPase family ... |
8-58 | 6.02e-03 | ||
nucleotide-binding domain (NBD) of the GDA1/CD39 NTPase family; The GDA1/CD39 NTPase family contains a group of apyrases (also known as adenylpyrophophatase, or ATP-diphosphohydrolases; EC 3.6.1.5), which are enzymes that catalyze the hydrolysis of phosphoanhydride bonds of nucleoside tri- and diphosphates (NTPs and NDPs) in the presence of divalent cations. In vertebrate systems, especially in mammals, apyrases are more widely referred to as nucleoside triphosphate diphosphohydrolases (NTPDases). There are eight homologs of NTPDases (NTPDases 1-8) in mammals, two apyrase enzymes from yeast, GDA1 and YND1, and a total of seven homologs of apyrase, namely AtAPY1-7, found in Arabidopsis. The GDA1/CD39 NTPase family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. Pssm-ID: 466853 Cd Length: 332 Bit Score: 33.51 E-value: 6.02e-03
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