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Conserved domains on  [gi|2249081054|gb|URR26218|]
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pesticin C-terminus-like muramidase [Vibrio alginolyticus]

Protein Classification

lysozyme family protein; lytic transglycosylase domain-containing protein( domain architecture ID 13014144)

lysozyme family protein; lytic transglycosylase domain-containing protein similar to lytic transglycosylase which catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pesticin_lyz cd16902
lysozyme-like C-terminal domain of pesticin; Pesticin (Pst) is an anti-bacterial toxin ...
 490-662 3.74e-82

lysozyme-like C-terminal domain of pesticin; Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


:

Pssm-ID: 381621 [Multi-domain]  Cd Length: 178  Bit Score: 257.19  E-value: 3.74e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 490 IDHEFIGELEGSRKKGYVPDPKN-SKSGVTIATGFDLGARNIVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNPLTI 568
Cdd:cd16902     2 VDKDFISKLEGGRRKGYVPDPNGgGNSGVTIGTGVDLGQRDEADLRELGVPESLIDKLRPYLGLKGQEAVDKLAKNPLTL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 569 NEDELLLINHVVKKHETEKIIALYNKNS--QIEFACLPSQAQTVIASVAYQYG-YLPRETRKFWFQAVNQKWEEMYDNLM 645
Cdd:cd16902    82 SEEEADLLDDAVKDKFTERIARLYNRASagLKRFEDLPPEQQTVIASVAYQYGsNSSRRTPKFWGQVTEQDWQGAINELR 161

                         170
                  ....*....|....*..
gi 2249081054 646 DFRDLYPTRRKKEALLL 662
Cdd:cd16902   162 NFGDKYPTRRNKEADLL 178
NlpD super family cl34026
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 35-120 5.58e-03

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


The actual alignment was detected with superfamily member COG0739:

Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 38.80  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054  35 IGQGYGWHSGIHLtskMLPWGkglRPIQAMLDGKIVAFRINPDYltstyqeqefkysNNFVLIEHEavnpednedvFKFY 114
Cdd:COG0739    90 VTGRRRFHKGIDI---AAPTG---TPVYAAADGTVVFAGWNGGY-------------GNLVIIDHG----------NGYT 140


                  ....*.
gi 2249081054 115 TLYMHL 120
Cdd:COG0739   141 TLYAHL 146
 
Name Accession Description Interval E-value
pesticin_lyz cd16902
lysozyme-like C-terminal domain of pesticin; Pesticin (Pst) is an anti-bacterial toxin ...
 490-662 3.74e-82

lysozyme-like C-terminal domain of pesticin; Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


Pssm-ID: 381621 [Multi-domain]  Cd Length: 178  Bit Score: 257.19  E-value: 3.74e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 490 IDHEFIGELEGSRKKGYVPDPKN-SKSGVTIATGFDLGARNIVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNPLTI 568
Cdd:cd16902     2 VDKDFISKLEGGRRKGYVPDPNGgGNSGVTIGTGVDLGQRDEADLRELGVPESLIDKLRPYLGLKGQEAVDKLAKNPLTL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 569 NEDELLLINHVVKKHETEKIIALYNKNS--QIEFACLPSQAQTVIASVAYQYG-YLPRETRKFWFQAVNQKWEEMYDNLM 645
Cdd:cd16902    82 SEEEADLLDDAVKDKFTERIARLYNRASagLKRFEDLPPEQQTVIASVAYQYGsNSSRRTPKFWGQVTEQDWQGAINELR 161

                         170
                  ....*....|....*..
gi 2249081054 646 DFRDLYPTRRKKEALLL 662
Cdd:cd16902   162 NFGDKYPTRRNKEADLL 178
Pesticin pfam16754
Bacterial toxin homolog of phage lysozyme, C-term; This the C-terminal activator domain of ...
 490-638 9.78e-45

Bacterial toxin homolog of phage lysozyme, C-term; This the C-terminal activator domain of pesticin, a hydrolase enzyme secreted by Yersinia pestis and other Gammaproteobacteria to kill related bacteria occupying the same ecological niche. It is referred to as a bacteriocin and it leads to the hydrolysis of peptidoglycan. Its immunity protein is Pim. Pesticin carries an elongated N-terminal translocation domain, an intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologs. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane. The receptor domain is necessary for the close contact with the outer membrane; the N-terminal is a type of translocational, TonB box; the C-terminal domain is the death-delivering domain.


Pssm-ID: 435562  Cd Length: 155  Bit Score: 156.94  E-value: 9.78e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 490 IDHEFIGELEGSRKKGYVPDPKNS----KSGVTIATGFDLGARNIVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNP 565
Cdd:pfam16754   2 IDKDFISNNEGFSPTGYVPDSPSStvfgKSGVTVGTGFDLGQQSKDELKSLGLPPSLADKLSPYTGLKGQEAKDFLSKNP 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2249081054 566 LTINEDELLLINHVVKKHETEKIIALYNK-NSQIEFACLPSQAQTVIASVAYQYGYLPRETRKFWFQAVNQKWE 638
Cdd:pfam16754  82 LSLSEQEAHLIDKAVKDKFSAKLAKLYNAaNAVKPFKDLPLPVQTVIASVAHQYGNLSKRTPNFWNKVTANDWN 155
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 35-120 5.58e-03

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 38.80  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054  35 IGQGYGWHSGIHLtskMLPWGkglRPIQAMLDGKIVAFRINPDYltstyqeqefkysNNFVLIEHEavnpednedvFKFY 114
Cdd:COG0739    90 VTGRRRFHKGIDI---AAPTG---TPVYAAADGTVVFAGWNGGY-------------GNLVIIDHG----------NGYT 140


                  ....*.
gi 2249081054 115 TLYMHL 120
Cdd:COG0739   141 TLYAHL 146
 
Name Accession Description Interval E-value
pesticin_lyz cd16902
lysozyme-like C-terminal domain of pesticin; Pesticin (Pst) is an anti-bacterial toxin ...
 490-662 3.74e-82

lysozyme-like C-terminal domain of pesticin; Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


Pssm-ID: 381621 [Multi-domain]  Cd Length: 178  Bit Score: 257.19  E-value: 3.74e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 490 IDHEFIGELEGSRKKGYVPDPKN-SKSGVTIATGFDLGARNIVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNPLTI 568
Cdd:cd16902     2 VDKDFISKLEGGRRKGYVPDPNGgGNSGVTIGTGVDLGQRDEADLRELGVPESLIDKLRPYLGLKGQEAVDKLAKNPLTL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 569 NEDELLLINHVVKKHETEKIIALYNKNS--QIEFACLPSQAQTVIASVAYQYG-YLPRETRKFWFQAVNQKWEEMYDNLM 645
Cdd:cd16902    82 SEEEADLLDDAVKDKFTERIARLYNRASagLKRFEDLPPEQQTVIASVAYQYGsNSSRRTPKFWGQVTEQDWQGAINELR 161

                         170
                  ....*....|....*..
gi 2249081054 646 DFRDLYPTRRKKEALLL 662
Cdd:cd16902   162 NFGDKYPTRRNKEADLL 178
Pesticin pfam16754
Bacterial toxin homolog of phage lysozyme, C-term; This the C-terminal activator domain of ...
 490-638 9.78e-45

Bacterial toxin homolog of phage lysozyme, C-term; This the C-terminal activator domain of pesticin, a hydrolase enzyme secreted by Yersinia pestis and other Gammaproteobacteria to kill related bacteria occupying the same ecological niche. It is referred to as a bacteriocin and it leads to the hydrolysis of peptidoglycan. Its immunity protein is Pim. Pesticin carries an elongated N-terminal translocation domain, an intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologs. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane. The receptor domain is necessary for the close contact with the outer membrane; the N-terminal is a type of translocational, TonB box; the C-terminal domain is the death-delivering domain.


Pssm-ID: 435562  Cd Length: 155  Bit Score: 156.94  E-value: 9.78e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 490 IDHEFIGELEGSRKKGYVPDPKNS----KSGVTIATGFDLGARNIVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNP 565
Cdd:pfam16754   2 IDKDFISNNEGFSPTGYVPDSPSStvfgKSGVTVGTGFDLGQQSKDELKSLGLPPSLADKLSPYTGLKGQEAKDFLSKNP 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2249081054 566 LTINEDELLLINHVVKKHETEKIIALYNK-NSQIEFACLPSQAQTVIASVAYQYGYLPRETRKFWFQAVNQKWE 638
Cdd:pfam16754  82 LSLSEQEAHLIDKAVKDKFSAKLAKLYNAaNAVKPFKDLPLPVQTVIASVAHQYGNLSKRTPNFWNKVTANDWN 155
pesticin_lyz-like cd12799
lysozyme-like C-terminal domain of pesticin and related proteins; Pesticin (Pst) is an ...
 497-617 8.33e-11

lysozyme-like C-terminal domain of pesticin and related proteins; Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


Pssm-ID: 340366  Cd Length: 129  Bit Score: 59.98  E-value: 8.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 497 ELEGSRKKGYVPD-PKNSKSGVTIATGFDLGARNIVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNPLTINEDELLL 575
Cdd:cd12799     3 DIFSSNGFSGFSHwPGNPSSGVTIGSGYDLGQRSKQDLLNDGVPQYIADRLDGYYALRGKEAYDKVRTAPLTISDKEAHL 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2249081054 576 INHVVKKHETEKIIALYNKNSQIE-----FACLPSQAQTVIASVAYQ 617
Cdd:cd12799    83 LSNIYIDKFSHKAEGLFNDANRTEriglrFSDLPPRTRTALVSLGYQ 129
pesticin_lyz-like cd16903
pesticin C-terminal-like domain of uncharacterized proteins; This subfamily is composed of ...
 510-599 4.39e-08

pesticin C-terminal-like domain of uncharacterized proteins; This subfamily is composed of uncharacterized proteins containing a lysozyme-like domain similar to the C-terminal domain of pesticin. Some members also contain an EF hand domain. Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


Pssm-ID: 340389  Cd Length: 150  Bit Score: 52.60  E-value: 4.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054 510 PKNSKSGVTIATGFDLGARN----IVDLRKLELPSDLITKLTPYLGMKKFEAESFLKKNPLTI----NEDELLLINHVVK 581
Cdd:cd16903    30 PGNSGSGVTIGRGYDLGQRSkgeiYNDLTSAGVPEEQAKLISKGAGLKGCAAKDFVKDNRDSIgeitRKQQIKLFNIIYP 109

                          90
                  ....*....|....*....
gi 2249081054 582 KHETE-KIIalYNKNSQIE 599
Cdd:cd16903   110 EYEARaKRI--YNKWTTVE 126
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 35-120 5.58e-03

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 38.80  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2249081054  35 IGQGYGWHSGIHLtskMLPWGkglRPIQAMLDGKIVAFRINPDYltstyqeqefkysNNFVLIEHEavnpednedvFKFY 114
Cdd:COG0739    90 VTGRRRFHKGIDI---AAPTG---TPVYAAADGTVVFAGWNGGY-------------GNLVIIDHG----------NGYT 140


                  ....*.
gi 2249081054 115 TLYMHL 120
Cdd:COG0739   141 TLYAHL 146
 
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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