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Conserved domains on  [gi|16766430|ref|NP_462045|]
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putative cytoplasmic protein [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

Protein Classification

anti-adapter protein IraD( domain architecture ID 10014587)

anti-adapter protein IraD inhibits RpoS proteolysis by regulating RssB activity, thereby increasing the stability of the sigma stress factor RpoS during oxidative stress

Gene Ontology:  GO:0034599|GO:0006974|GO:0043856

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
iraD PRK14128
anti-adapter protein IraD;
59-126 8.13e-41

anti-adapter protein IraD;


:

Pssm-ID: 184525  Cd Length: 69  Bit Score: 129.99  E-value: 8.13e-41
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16766430   59 NVGDKRVLNWFCRELRAAILRYEPSINMLKVSVKDAHHQTLALSLEAMLQDESEPLRLEIAYSNGRWR 126
Cdd:PRK14128   2 NVSDKRLQSWYCRQLRSALLFHEPRIAALQVNLKEAYCHTLAISLEAMLYHDDEPLTFDLVWDNGGWR 69
 
Name Accession Description Interval E-value
iraD PRK14128
anti-adapter protein IraD;
59-126 8.13e-41

anti-adapter protein IraD;


Pssm-ID: 184525  Cd Length: 69  Bit Score: 129.99  E-value: 8.13e-41
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16766430   59 NVGDKRVLNWFCRELRAAILRYEPSINMLKVSVKDAHHQTLALSLEAMLQDESEPLRLEIAYSNGRWR 126
Cdd:PRK14128   2 NVSDKRLQSWYCRQLRSALLFHEPRIAALQVNLKEAYCHTLAISLEAMLYHDDEPLTFDLVWDNGGWR 69
GPW_gp25 pfam04965
Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like ...
 22-110 6.44e-11

Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerization, playing a critical role in sheath assembly and contraction. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologs from the RpoS-mediated general stress response system (called IraD). This motif interacts with the 'core bundle' composed of orthologs of T4 gp6 and gp7 proteins in contractile injection systems.


Pssm-ID: 428225  Cd Length: 93  Bit Score: 54.51  E-value: 6.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16766430    22 HELVRRKLMCLFNSCAvpggETLPPLLTRGMPEWHEVNV-GDKRVLNWFCRELRAAILRYEPSINMLKVSVK--DAHHQT 98
Cdd:pfam04965   4 RESVRRDLEILLNTRP----GERVSRPNYGCPDLALLFApNDDATRALIERAIREAILRFEPRIRVVSVEVDpdPDSPGT 79

                          90
                  ....*....|..
gi 16766430    99 LALSLEAMLQDE 110
Cdd:pfam04965  80 LRFTIEYTLRAT 91
COG3518 COG3518
Predicted component of the type VI protein secretion system [Intracellular trafficking, ...
 9-126 4.57e-08

Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442740  Cd Length: 162  Bit Score: 48.82  E-value: 4.57e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16766430   9 ALFDRLL------------VEGISPHEL---VRRKLMCLFNS--CAVPGGETLPP----LLTRGMPEWHEVNVGDKRVLN 67
Cdd:COG3518  13 SLLDRLTddepdrsresplSRVVSLEQLresVRRDLEWLLNTrrGEASLLAAYPEvrrsVLNYGLPDLSGASLGSPDDRE 92

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16766430  68 WFCRELRAAILRYEPSInmLKVSVK-----DAHHQTLALSLEAML--QDESEPLRLEIA--YSNGRWR 126
Cdd:COG3518  93 AIERAIRQAILRFEPRL--RRVSVTvlpddDDSPNTLRFRIEAVLwaDPAPEPVRFDTVldLETGRVS 158
VI_zyme TIGR03357
type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 ...
 10-126 3.31e-05

type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.


Pssm-ID: 274540  Cd Length: 133  Bit Score: 40.67  E-value: 3.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16766430    10 LFDRLL--------VEGISPHEL---VRRKLMCLFNSCAVPggetLPPLLTRGMPEWHEVNVG---DKRvlnWFCRELRA 75
Cdd:TIGR03357   4 LFERLPdasgespsTRRSSAEQLresIRRHLERLLNTRRGS----CASLPDYGLPDLNDLSLSsadDRR---RIRRAIEQ 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 16766430    76 AILRYEPSINMLKVSV--KDAHHQTLALSLEAML--QDESEPLRLEIA-YSNGRWR 126
Cdd:TIGR03357  77 AIERYEPRLSRVRVTAlpDEEDPLALRFRIEAELdvDGGPEPVSFDALlDPSGRYR 132
 
Name Accession Description Interval E-value
iraD PRK14128
anti-adapter protein IraD;
59-126 8.13e-41

anti-adapter protein IraD;


Pssm-ID: 184525  Cd Length: 69  Bit Score: 129.99  E-value: 8.13e-41
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16766430   59 NVGDKRVLNWFCRELRAAILRYEPSINMLKVSVKDAHHQTLALSLEAMLQDESEPLRLEIAYSNGRWR 126
Cdd:PRK14128   2 NVSDKRLQSWYCRQLRSALLFHEPRIAALQVNLKEAYCHTLAISLEAMLYHDDEPLTFDLVWDNGGWR 69
GPW_gp25 pfam04965
Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like ...
 22-110 6.44e-11

Baseplate wedge protein gp25; This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerization, playing a critical role in sheath assembly and contraction. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologs from the RpoS-mediated general stress response system (called IraD). This motif interacts with the 'core bundle' composed of orthologs of T4 gp6 and gp7 proteins in contractile injection systems.


Pssm-ID: 428225  Cd Length: 93  Bit Score: 54.51  E-value: 6.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16766430    22 HELVRRKLMCLFNSCAvpggETLPPLLTRGMPEWHEVNV-GDKRVLNWFCRELRAAILRYEPSINMLKVSVK--DAHHQT 98
Cdd:pfam04965   4 RESVRRDLEILLNTRP----GERVSRPNYGCPDLALLFApNDDATRALIERAIREAILRFEPRIRVVSVEVDpdPDSPGT 79

                          90
                  ....*....|..
gi 16766430    99 LALSLEAMLQDE 110
Cdd:pfam04965  80 LRFTIEYTLRAT 91
COG3518 COG3518
Predicted component of the type VI protein secretion system [Intracellular trafficking, ...
 9-126 4.57e-08

Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442740  Cd Length: 162  Bit Score: 48.82  E-value: 4.57e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16766430   9 ALFDRLL------------VEGISPHEL---VRRKLMCLFNS--CAVPGGETLPP----LLTRGMPEWHEVNVGDKRVLN 67
Cdd:COG3518  13 SLLDRLTddepdrsresplSRVVSLEQLresVRRDLEWLLNTrrGEASLLAAYPEvrrsVLNYGLPDLSGASLGSPDDRE 92

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16766430  68 WFCRELRAAILRYEPSInmLKVSVK-----DAHHQTLALSLEAML--QDESEPLRLEIA--YSNGRWR 126
Cdd:COG3518  93 AIERAIRQAILRFEPRL--RRVSVTvlpddDDSPNTLRFRIEAVLwaDPAPEPVRFDTVldLETGRVS 158
VI_zyme TIGR03357
type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 ...
 10-126 3.31e-05

type VI secretion system lysozyme-like protein; The description for Pfam family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.


Pssm-ID: 274540  Cd Length: 133  Bit Score: 40.67  E-value: 3.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16766430    10 LFDRLL--------VEGISPHEL---VRRKLMCLFNSCAVPggetLPPLLTRGMPEWHEVNVG---DKRvlnWFCRELRA 75
Cdd:TIGR03357   4 LFERLPdasgespsTRRSSAEQLresIRRHLERLLNTRRGS----CASLPDYGLPDLNDLSLSsadDRR---RIRRAIEQ 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 16766430    76 AILRYEPSINMLKVSV--KDAHHQTLALSLEAML--QDESEPLRLEIA-YSNGRWR 126
Cdd:TIGR03357  77 AIERYEPRLSRVRVTAlpDEEDPLALRFRIEAELdvDGGPEPVSFDALlDPSGRYR 132
 
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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