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Conserved domains on  [gi|1955990658|ref|WP_200012586|]
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LysM domain-containing protein, partial [Citrobacter freundii]

Protein Classification

LysM peptidoglycan-binding domain-containing protein( domain architecture ID 10061503)

LysM peptidoglycan-binding domain-containing protein may bind N-acetylglucosamine in carbohydrates such as chitin, chitio-oligosaccharides and peptidoglycan

CATH:  3.10.350.10
Gene Ontology:  GO:0097367
PubMed:  18430080|24652063
SCOP:  4000905

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 54-97 4.42e-12

Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes.


:

Pssm-ID: 212030 [Multi-domain]  Cd Length: 45  Bit Score: 60.58  E-value: 4.42e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1955990658  54 SVVVLKGDTLGQIANEYNCSVEELAKYNNIKNPGLIYPGQVINL 97
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 54-97 4.42e-12

Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes.


Pssm-ID: 212030 [Multi-domain]  Cd Length: 45  Bit Score: 60.58  E-value: 4.42e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1955990658  54 SVVVLKGDTLGQIANEYNCSVEELAKYNNIKNPGLIYPGQVINL 97
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
56-98 2.77e-11

LysM repeat [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 61.65  E-value: 2.77e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1955990658  56 VVLKGDTLGQIANEYNCSVEELAKYNNIKNpGLIYPGQVINLP 98
Cdd:COG1388   113 TVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKIP 154
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 55-98 5.83e-11

LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known.


Pssm-ID: 396179 [Multi-domain]  Cd Length: 43  Bit Score: 57.41  E-value: 5.83e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1955990658  55 VVVLKGDTLGQIANEYNCSVEELAKYNNIKNPGlIYPGQVINLP 98
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPN-LYVGQKLKIP 43
LysM smart00257
Lysin motif;
56-97 8.19e-11

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 56.69  E-value: 8.19e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1955990658   56 VVLKGDTLGQIANEYNCSVEELAKYNNIKNPGLIYPGQVINL 97
Cdd:smart00257   3 TVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
47-109 1.46e-04

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 44.30  E-value: 1.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1955990658  47 SLSPDQHSVVVLKGDTLGQIANEYNCSVEELAKYNNIKNpGLIYPGQVINLPPRHYTLTDTAE 109
Cdd:PRK06347  400 GTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTSNTNTSK 461
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 54-97 4.42e-12

Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes.


Pssm-ID: 212030 [Multi-domain]  Cd Length: 45  Bit Score: 60.58  E-value: 4.42e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1955990658  54 SVVVLKGDTLGQIANEYNCSVEELAKYNNIKNPGLIYPGQVINL 97
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
56-98 2.77e-11

LysM repeat [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 61.65  E-value: 2.77e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1955990658  56 VVLKGDTLGQIANEYNCSVEELAKYNNIKNpGLIYPGQVINLP 98
Cdd:COG1388   113 TVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKIP 154
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 55-98 5.83e-11

LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known.


Pssm-ID: 396179 [Multi-domain]  Cd Length: 43  Bit Score: 57.41  E-value: 5.83e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1955990658  55 VVVLKGDTLGQIANEYNCSVEELAKYNNIKNPGlIYPGQVINLP 98
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPN-LYVGQKLKIP 43
LysM smart00257
Lysin motif;
56-97 8.19e-11

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 56.69  E-value: 8.19e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1955990658   56 VVLKGDTLGQIANEYNCSVEELAKYNNIKNPGLIYPGQVINL 97
Cdd:smart00257   3 TVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 47-99 1.20e-09

Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion transport and metabolism];


Pssm-ID: 441258 [Multi-domain]  Cd Length: 163  Bit Score: 57.32  E-value: 1.20e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1955990658  47 SLSPDQ-HSVVVLKGDTLGQIANEY--NCS-VEELAKYN--NIKNPGLIYPGQVINLPP 99
Cdd:COG1652   103 ELAPDApKTYTVKPGDTLWGIAKRFygDPArWPEIAEANrdQIKNPDLIYPGQVLRIPA 161
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
47-109 1.46e-04

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 44.30  E-value: 1.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1955990658  47 SLSPDQHSVVVLKGDTLGQIANEYNCSVEELAKYNNIKNpGLIYPGQVINLPPRHYTLTDTAE 109
Cdd:PRK06347  400 GTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTSNTNTSK 461
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
57-93 1.92e-04

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 43.92  E-value: 1.92e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1955990658  57 VLKGDTLGQIANEYNCSVEELAKYNNIKNpGLIYPGQ 93
Cdd:PRK06347  335 VVKGDSLWRIANNHKVTVANLKAWNNLKS-DFIYPGQ 370
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 55-99 5.19e-04

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 40.28  E-value: 5.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1955990658  55 VVVLKGDTLGQIA-------NEYNCSVEelAKYNNIKNPGLIYPGQVINLPP 99
Cdd:PRK11198   98 YTVKSGDTLSAIAkkvygnaNKYNKIFE--ANKPMLKSPDKIYPGQVLRIPE 147
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
57-93 1.67e-03

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 40.83  E-value: 1.67e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1955990658  57 VLKGDTLGQIANEYNCSVEELAKYNNIKNpGLIYPGQ 93
Cdd:PRK06347  484 VAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQ 519
 
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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