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Conserved domains on  [gi|1579913447|ref|WP_130538108|]
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type II toxin-antitoxin system HipA family toxin [Thiomicrorhabdus indica]

Protein Classification

type II toxin-antitoxin system HipA family toxin( domain architecture ID 11466423)

type II toxin-antitoxin (TA) system HipA family toxin similar to Escherichia coli HipA, a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu), and is also the toxin component of the HipA-HipB TA module

EC:  2.7.11.1
Gene Ontology:  GO:0110001|GO:0004674|GO:0016310
PubMed:  1715862|24095282|19179767|25056321|19150849|24343429

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipA COG3550
Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module ...
 4-416 8.54e-42

Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module [Signal transduction mechanisms];


:

Pssm-ID: 442771 [Multi-domain]  Cd Length: 398  Bit Score: 152.41  E-value: 8.54e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447   4 TLQVFHNQKwhDAAELkADTPSQNVSLDYLKpykiDFLFERlETACSVNYPV-EIFQTYQKQGWFGFIEDILPAGSSRRY 82
Cdd:COG3550     4 TLDVYLNGR--LVGTL-TRDDDGRISFEYDP----DWLAPD-GFPLSPSLPLrEGPYPFPGGGLPGFFADLLPDGWGRRL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447  83 WIRRLGLEGVarwkQDIILLQQATIAPIGNLRVKEAvPEKFADDLQERRFSVSDVVEHNIDFLE-YAQEMGAMSGGATGA 161
Cdd:COG3550    76 LARRLGISSL----DPFDLLAAVGRDCVGALRFLPE-GEGPEPPPEPEPLSLEELAEALRDLLEgEAPALGELLGGRSSL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 162 AGEAPKLLVRRNGESVWIDTyqdnlTNLDQHYLVKFPRGkgllRDQQILEAEYAYIKELNRLGfsaIDASKTHLQKQGDQ 241
Cdd:COG3550   151 GGAQPKAALLREDGRWALPA-----GGTPTTHILKFPSG----RLPDLVENEYLCLRLARAAG---LPVAETRLLRFGGR 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 242 ISLWLPRFDVSYDKGyvEHYGLESMYSILEKPAG------SLLNHFDVIQSICEklqelngfNANEFTKEWVKRDFLNVM 315
Cdd:COG3550   219 PALLVERFDRTADAG--RRLHQEDFCQLLGLPPGqkyespSYEDLARLLRRLSA--------LPAADLEELFRRMVFNVL 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 316 FANSDNHGRNHAFL-KKHGKIELAPIYDFAPMKADLEQIVRSIKWGRpyESGGDF---DWKGITQQLKehIQPTELWQEL 391
Cdd:COG3550   289 IGNTDDHAKNFSFLyDPGGRWRLAPAYDLVPTYPYPRDDKLAMAIGG--KKFDDItlrHLLAFAEAFG--LSERAALEII 364

                         410       420
                  ....*....|....*....|....*.
gi 1579913447 392 QALAAELV-GLKERLLDYGVNAEFLE 416
Cdd:COG3550   365 EEVAEAVPaAWPEVAAELGVPEELLD 390
 
Name Accession Description Interval E-value
HipA COG3550
Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module ...
 4-416 8.54e-42

Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module [Signal transduction mechanisms];


Pssm-ID: 442771 [Multi-domain]  Cd Length: 398  Bit Score: 152.41  E-value: 8.54e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447   4 TLQVFHNQKwhDAAELkADTPSQNVSLDYLKpykiDFLFERlETACSVNYPV-EIFQTYQKQGWFGFIEDILPAGSSRRY 82
Cdd:COG3550     4 TLDVYLNGR--LVGTL-TRDDDGRISFEYDP----DWLAPD-GFPLSPSLPLrEGPYPFPGGGLPGFFADLLPDGWGRRL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447  83 WIRRLGLEGVarwkQDIILLQQATIAPIGNLRVKEAvPEKFADDLQERRFSVSDVVEHNIDFLE-YAQEMGAMSGGATGA 161
Cdd:COG3550    76 LARRLGISSL----DPFDLLAAVGRDCVGALRFLPE-GEGPEPPPEPEPLSLEELAEALRDLLEgEAPALGELLGGRSSL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 162 AGEAPKLLVRRNGESVWIDTyqdnlTNLDQHYLVKFPRGkgllRDQQILEAEYAYIKELNRLGfsaIDASKTHLQKQGDQ 241
Cdd:COG3550   151 GGAQPKAALLREDGRWALPA-----GGTPTTHILKFPSG----RLPDLVENEYLCLRLARAAG---LPVAETRLLRFGGR 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 242 ISLWLPRFDVSYDKGyvEHYGLESMYSILEKPAG------SLLNHFDVIQSICEklqelngfNANEFTKEWVKRDFLNVM 315
Cdd:COG3550   219 PALLVERFDRTADAG--RRLHQEDFCQLLGLPPGqkyespSYEDLARLLRRLSA--------LPAADLEELFRRMVFNVL 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 316 FANSDNHGRNHAFL-KKHGKIELAPIYDFAPMKADLEQIVRSIKWGRpyESGGDF---DWKGITQQLKehIQPTELWQEL 391
Cdd:COG3550   289 IGNTDDHAKNFSFLyDPGGRWRLAPAYDLVPTYPYPRDDKLAMAIGG--KKFDDItlrHLLAFAEAFG--LSERAALEII 364

                         410       420
                  ....*....|....*....|....*.
gi 1579913447 392 QALAAELV-GLKERLLDYGVNAEFLE 416
Cdd:COG3550   365 EEVAEAVPaAWPEVAAELGVPEELLD 390
HipA_C pfam07804
HipA-like C-terminal domain; The members of this family are similar to a region close to the ...
 166-346 1.60e-20

HipA-like C-terminal domain; The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example Swiss:P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells, but it is usually tightly associated with HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products.


Pssm-ID: 462271 [Multi-domain]  Cd Length: 224  Bit Score: 89.67  E-value: 1.60e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 166 PKLLVRRNGESVwidtyqdnlTNLDQHYLVKFPRGkglLRDQQILEAEYAYIKELNRLGfsaIDASKTHLQKQGDQISLW 245
Cdd:pfam07804   8 PKAALLRDFLPK---------GSGPSTHILKFPPS---ADLPDSVENEYLCMRLARAAG---IDVAETRLVRFGGGRALL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 246 LPRFDVSYDKGYVeHYglESMYSILEKPA-------GSLLNHFDVIQSICEKLQELNgfnanefTKEWVKRDFLNVMFAN 318
Cdd:pfam07804  73 VERFDRRGDGRRL-HQ--EDACQLLGLDPaekyesgGSYEDLAKLLRRLSAPAPAAD-------LEELFRRMVFNVLIGN 142

                         170       180
                  ....*....|....*....|....*...
gi 1579913447 319 SDNHGRNHAFLKKHGKIELAPIYDFAPM 346
Cdd:pfam07804 143 TDDHLKNFSFLLGGGRWRLAPAYDLVST 170
HipA_So_like cd17809
type II toxin-antitoxin sytem toxin HipA from Shewanella oneidensis and similar proteins; This ...
 313-342 1.20e-04

type II toxin-antitoxin sytem toxin HipA from Shewanella oneidensis and similar proteins; This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Shewanella oneidensis HipA, a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. In the Shewanella oneidensis HipAB:DNA promoter complex, HipB forms a dimer that binds the duplex operator DNA, with each HipB monomer interacting with separate HipA monomers. The HipAB component of the complex is composed of two HipA and two HipB subunits.


Pssm-ID: 341494 [Multi-domain]  Cd Length: 405  Bit Score: 44.25  E-value: 1.20e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1579913447 313 NVMFANSDNHGRNHAFLKKHGKIELAPIYD 342
Cdd:cd17809   280 NLLIGNSDAHGKNISFFVGPSGIELAPAYD 309
 
Name Accession Description Interval E-value
HipA COG3550
Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module ...
 4-416 8.54e-42

Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module [Signal transduction mechanisms];


Pssm-ID: 442771 [Multi-domain]  Cd Length: 398  Bit Score: 152.41  E-value: 8.54e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447   4 TLQVFHNQKwhDAAELkADTPSQNVSLDYLKpykiDFLFERlETACSVNYPV-EIFQTYQKQGWFGFIEDILPAGSSRRY 82
Cdd:COG3550     4 TLDVYLNGR--LVGTL-TRDDDGRISFEYDP----DWLAPD-GFPLSPSLPLrEGPYPFPGGGLPGFFADLLPDGWGRRL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447  83 WIRRLGLEGVarwkQDIILLQQATIAPIGNLRVKEAvPEKFADDLQERRFSVSDVVEHNIDFLE-YAQEMGAMSGGATGA 161
Cdd:COG3550    76 LARRLGISSL----DPFDLLAAVGRDCVGALRFLPE-GEGPEPPPEPEPLSLEELAEALRDLLEgEAPALGELLGGRSSL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 162 AGEAPKLLVRRNGESVWIDTyqdnlTNLDQHYLVKFPRGkgllRDQQILEAEYAYIKELNRLGfsaIDASKTHLQKQGDQ 241
Cdd:COG3550   151 GGAQPKAALLREDGRWALPA-----GGTPTTHILKFPSG----RLPDLVENEYLCLRLARAAG---LPVAETRLLRFGGR 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 242 ISLWLPRFDVSYDKGyvEHYGLESMYSILEKPAG------SLLNHFDVIQSICEklqelngfNANEFTKEWVKRDFLNVM 315
Cdd:COG3550   219 PALLVERFDRTADAG--RRLHQEDFCQLLGLPPGqkyespSYEDLARLLRRLSA--------LPAADLEELFRRMVFNVL 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 316 FANSDNHGRNHAFL-KKHGKIELAPIYDFAPMKADLEQIVRSIKWGRpyESGGDF---DWKGITQQLKehIQPTELWQEL 391
Cdd:COG3550   289 IGNTDDHAKNFSFLyDPGGRWRLAPAYDLVPTYPYPRDDKLAMAIGG--KKFDDItlrHLLAFAEAFG--LSERAALEII 364

                         410       420
                  ....*....|....*....|....*.
gi 1579913447 392 QALAAELV-GLKERLLDYGVNAEFLE 416
Cdd:COG3550   365 EEVAEAVPaAWPEVAAELGVPEELLD 390
HipA_C pfam07804
HipA-like C-terminal domain; The members of this family are similar to a region close to the ...
 166-346 1.60e-20

HipA-like C-terminal domain; The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example Swiss:P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells, but it is usually tightly associated with HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products.


Pssm-ID: 462271 [Multi-domain]  Cd Length: 224  Bit Score: 89.67  E-value: 1.60e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 166 PKLLVRRNGESVwidtyqdnlTNLDQHYLVKFPRGkglLRDQQILEAEYAYIKELNRLGfsaIDASKTHLQKQGDQISLW 245
Cdd:pfam07804   8 PKAALLRDFLPK---------GSGPSTHILKFPPS---ADLPDSVENEYLCMRLARAAG---IDVAETRLVRFGGGRALL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 246 LPRFDVSYDKGYVeHYglESMYSILEKPA-------GSLLNHFDVIQSICEKLQELNgfnanefTKEWVKRDFLNVMFAN 318
Cdd:pfam07804  73 VERFDRRGDGRRL-HQ--EDACQLLGLDPaekyesgGSYEDLAKLLRRLSAPAPAAD-------LEELFRRMVFNVLIGN 142

                         170       180
                  ....*....|....*....|....*...
gi 1579913447 319 SDNHGRNHAFLKKHGKIELAPIYDFAPM 346
Cdd:pfam07804 143 TDDHLKNFSFLLGGGRWRLAPAYDLVST 170
HipA_So_like cd17809
type II toxin-antitoxin sytem toxin HipA from Shewanella oneidensis and similar proteins; This ...
 313-342 1.20e-04

type II toxin-antitoxin sytem toxin HipA from Shewanella oneidensis and similar proteins; This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Shewanella oneidensis HipA, a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. In the Shewanella oneidensis HipAB:DNA promoter complex, HipB forms a dimer that binds the duplex operator DNA, with each HipB monomer interacting with separate HipA monomers. The HipAB component of the complex is composed of two HipA and two HipB subunits.


Pssm-ID: 341494 [Multi-domain]  Cd Length: 405  Bit Score: 44.25  E-value: 1.20e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1579913447 313 NVMFANSDNHGRNHAFLKKHGKIELAPIYD 342
Cdd:cd17809   280 NLLIGNSDAHGKNISFFVGPSGIELAPAYD 309
CtkA cd17792
serine/threonine-protein kinase CtkA and similar proteins; The Helicobacter pylori serine ...
 263-358 1.56e-04

serine/threonine-protein kinase CtkA and similar proteins; The Helicobacter pylori serine/threonine-protein kinase CtkA (proinflammatory kinase), encoded by the jhp940 gene, has been shown to be secreted by the bacterium and to induce cytokines in gastric epithelial cells. It may play a role in chronic gastric inflammation. CtkA autophosphorylates itself at a threonine residue near the N-terminus and it translocates into cultured human cells. It also enhances phosphorylation of the NF-kappaB p65 subunit at Ser276 in human epithelial cancer cells; phosphorylation at this position is known to activate the transcriptional activity of NF-kappaB.


Pssm-ID: 341491  Cd Length: 281  Bit Score: 43.34  E-value: 1.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 263 LESMYSILEKPAGSLLNHFDVIQSICEklqelngfNANEFTKEWVKRDFLNvMF------ANSDNHGRNHAFL--KKHGK 334
Cdd:cd17792    93 LKNSILDESSSSGYGTELSDILEVIEE--------QPLLINIEGLKERFWD-MFvvdaliGNFDRHNGNWGFLvnEDTGE 163

                          90       100
                  ....*....|....*....|....*...
gi 1579913447 335 IELAPIYD----FAPMKADlEQIVRSIK 358
Cdd:cd17792   164 VELAPVYDngssLYPKLSD-EKIKKILK 190
HipA cd17793
type II toxin-antitoxin sytem toxin HipA and similar proteins; This family contains type II ...
 308-406 2.15e-04

type II toxin-antitoxin sytem toxin HipA and similar proteins; This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Escherichia coli and Shewanella oneidensis HipA, which is a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. Structures of HipAB:DNA complexes from both Escherichia coli and Shewanella oneidensis reveal distinct complex assembly.


Pssm-ID: 341492 [Multi-domain]  Cd Length: 358  Bit Score: 43.35  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1579913447 308 KRDFL-----NVMFANSDNHGRNHAFLKKHGKIELAPIYDFAPmkadleqivrsikwGRPYES---------GGDFDWKG 373
Cdd:cd17793   225 RQALLrwvifNLLIGNADAHAKNLSLLYRPGGPRLAPFYDLVS--------------TRVYPDlsrklamaiGGERRPDE 290

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1579913447 374 ITqqlKEHiqptelwqeLQALAAELvGLKERLL 406
Cdd:cd17793   291 IT---PRH---------WEAFAEEL-GLRPRLV 310
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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