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Conserved domains on  [gi|2276380671|gb|UTV41920|]
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LysM peptidoglycan-binding domain-containing protein (plasmid) [Ensifer adhaerens]

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 ...
 1134-1194 2.45e-04

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: 39.78  E-value: 2.45e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276380671 1134 VYEVKRGDSIYKIAGNDHLIVSEIYRLNPwlddrleqwsqlgggprGRNPNELVEGDKLTI 1194
Cdd:cd00118      2 TYTVKPGDTLWSIAKKYGVTVEELAAANP-----------------LINPDCIYPGQKLKI 45
LysM super family cl43409
LysM repeat [Cell wall/membrane/envelope biogenesis];
1063-1197 3.15e-04

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


The actual alignment was detected with superfamily member COG1388:

Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 42.77  E-value: 3.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276380671 1063 KRAIYEYDPKTHVTEPRVTSMPIRPLSIEGLKNWLNAHGVPDPHYMDSVPVKPVEKANPPKQVPSPLDNINVYEVKRGDS 1142
Cdd:COG1388     40 ALAPAGLSLAAALNGEALLLLLPAAAAAAKAALAAAPEAAAAAAARYTVKSGDTLSGIARRYGAAAAPSPVTYTVKKGDT 119

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2276380671 1143 IYKIAGNDHLIVSEIYRLNPWLDDRLEqwsqlgggprgrnpnelvEGDKLTIPQG 1197
Cdd:COG1388    120 LWSIARRYGVSVEELKRWNGLSSDTIR------------------PGQKLKIPAS 156
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 1134-1194 2.45e-04

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: 39.78  E-value: 2.45e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276380671 1134 VYEVKRGDSIYKIAGNDHLIVSEIYRLNPwlddrleqwsqlgggprGRNPNELVEGDKLTI 1194
Cdd:cd00118      2 TYTVKPGDTLWSIAKKYGVTVEELAAANP-----------------LINPDCIYPGQKLKI 45
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
1063-1197 3.15e-04

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 42.77  E-value: 3.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276380671 1063 KRAIYEYDPKTHVTEPRVTSMPIRPLSIEGLKNWLNAHGVPDPHYMDSVPVKPVEKANPPKQVPSPLDNINVYEVKRGDS 1142
Cdd:COG1388     40 ALAPAGLSLAAALNGEALLLLLPAAAAAAKAALAAAPEAAAAAAARYTVKSGDTLSGIARRYGAAAAPSPVTYTVKKGDT 119

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2276380671 1143 IYKIAGNDHLIVSEIYRLNPWLDDRLEqwsqlgggprgrnpnelvEGDKLTIPQG 1197
Cdd:COG1388    120 LWSIARRYGVSVEELKRWNGLSSDTIR------------------PGQKLKIPAS 156
LysM smart00257
Lysin motif;
1135-1194 1.11e-03

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 37.81  E-value: 1.11e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276380671  1135 YEVKRGDSIYKIAGNDHLIVSEIYRLNPWLDdrleqwsqlgggprgrnPNELVEGDKLTI 1194
Cdd:smart00257    2 YTVKKGDTLSSIARRYGISVSDLLELNNILD-----------------PDNLQVGQKLKI 44
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 1134-1194 2.45e-04

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: 39.78  E-value: 2.45e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276380671 1134 VYEVKRGDSIYKIAGNDHLIVSEIYRLNPwlddrleqwsqlgggprGRNPNELVEGDKLTI 1194
Cdd:cd00118      2 TYTVKPGDTLWSIAKKYGVTVEELAAANP-----------------LINPDCIYPGQKLKI 45
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
1063-1197 3.15e-04

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 42.77  E-value: 3.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276380671 1063 KRAIYEYDPKTHVTEPRVTSMPIRPLSIEGLKNWLNAHGVPDPHYMDSVPVKPVEKANPPKQVPSPLDNINVYEVKRGDS 1142
Cdd:COG1388     40 ALAPAGLSLAAALNGEALLLLLPAAAAAAKAALAAAPEAAAAAAARYTVKSGDTLSGIARRYGAAAAPSPVTYTVKKGDT 119

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2276380671 1143 IYKIAGNDHLIVSEIYRLNPWLDDRLEqwsqlgggprgrnpnelvEGDKLTIPQG 1197
Cdd:COG1388    120 LWSIARRYGVSVEELKRWNGLSSDTIR------------------PGQKLKIPAS 156
LysM smart00257
Lysin motif;
1135-1194 1.11e-03

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 37.81  E-value: 1.11e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276380671  1135 YEVKRGDSIYKIAGNDHLIVSEIYRLNPWLDdrleqwsqlgggprgrnPNELVEGDKLTI 1194
Cdd:smart00257    2 YTVKKGDTLSSIARRYGISVSDLLELNNILD-----------------PDNLQVGQKLKI 44
 
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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