NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|30699276|ref|NP_177886|]
View 

Peptidoglycan-binding LysM domain-containing protein [Arabidopsis thaliana]

Protein Classification

LysM peptidoglycan-binding domain-containing protein( domain architecture ID 13299056)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 175-217 1.25e-07

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: 47.78  E-value: 1.25e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 30699276   175 YVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAVP 217
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPNLYVGQKLKIP 43
mltD super family cl32574
membrane-bound lytic murein transglycosylase D; Provisional
 106-214 4.98e-06

membrane-bound lytic murein transglycosylase D; Provisional


The actual alignment was detected with superfamily member PRK10783:

Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 48.58  E-value: 4.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30699276  106 STHYKTRTSDTLGSIAdSVYGglVSPEQIQVANSETDlSVLDVGTKLVIPLPCACFNGTDESLPalyLSYVVRGIDTMAG 185
Cdd:PRK10783 343 SRSYKVRSGDTLSGIA-SRLN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNSDS---ITYRVRKGDSLSS 415

                         90       100
                 ....*....|....*....|....*....
gi 30699276  186 IAKRFSTSVTDLTNVNAMGAPDINPGDIL 214
Cdd:PRK10783 416 IAKRHGVNIKDVMRWNSDTAKNLQPGDKL 444
 
Name Accession Description Interval E-value
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 175-217 1.25e-07

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: 47.78  E-value: 1.25e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 30699276   175 YVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAVP 217
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPNLYVGQKLKIP 43
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
169-217 1.56e-06

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 47.78  E-value: 1.56e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30699276 169 PALYLSYVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAVP 217
Cdd:COG1388 106 APSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSSDTIRPGQKLKIP 154
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 106-214 4.98e-06

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 48.58  E-value: 4.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30699276  106 STHYKTRTSDTLGSIAdSVYGglVSPEQIQVANSETDlSVLDVGTKLVIPLPCACFNGTDESLPalyLSYVVRGIDTMAG 185
Cdd:PRK10783 343 SRSYKVRSGDTLSGIA-SRLN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNSDS---ITYRVRKGDSLSS 415

                         90       100
                 ....*....|....*....|....*....
gi 30699276  186 IAKRFSTSVTDLTNVNAMGAPDINPGDIL 214
Cdd:PRK10783 416 IAKRHGVNIKDVMRWNSDTAKNLQPGDKL 444
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 174-216 9.81e-05

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: 39.39  E-value: 9.81e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 30699276 174 SYVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPD-INPGDILAV 216
Cdd:cd00118   2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDcIYPGQKLKI 45
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 174-216 1.40e-04

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 43.96  E-value: 1.40e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 30699276  174 SYVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAV 216
Cdd:PRK10783 345 SYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTI 387
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
106-155 7.67e-04

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 40.08  E-value: 7.67e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30699276 106 STHYKTRTSDTLGSIADSvYGglVSPEQIQVANSETDlSVLDVGTKLVIP 155
Cdd:COG1388 109 PVTYTVKKGDTLWSIARR-YG--VSVEELKRWNGLSS-DTIRPGQKLKIP 154
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 109-155 1.25e-03

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: 36.22  E-value: 1.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 30699276   109 YKTRTSDTLGSIADSvYGglVSPEQIQVANsETDLSVLDVGTKLVIP 155
Cdd:pfam01476   1 YTVKKGDTLSSIAKR-YG--ITVEQLAELN-GLSSPNLYVGQKLKIP 43
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 107-154 3.79e-03

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: 35.15  E-value: 3.79e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30699276 107 THYKTRTSDTLGSIADSvYGglVSPEQIQVANSETDLSVLDVGTKLVI 154
Cdd:cd00118   1 KTYTVKPGDTLWSIAKK-YG--VTVEELAAANPLINPDCIYPGQKLKI 45
 
Name Accession Description Interval E-value
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 175-217 1.25e-07

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: 47.78  E-value: 1.25e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 30699276   175 YVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAVP 217
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPNLYVGQKLKIP 43
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
169-217 1.56e-06

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 47.78  E-value: 1.56e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30699276 169 PALYLSYVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAVP 217
Cdd:COG1388 106 APSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSSDTIRPGQKLKIP 154
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 106-214 4.98e-06

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 48.58  E-value: 4.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30699276  106 STHYKTRTSDTLGSIAdSVYGglVSPEQIQVANSETDlSVLDVGTKLVIPLPCACFNGTDESLPalyLSYVVRGIDTMAG 185
Cdd:PRK10783 343 SRSYKVRSGDTLSGIA-SRLN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNSDS---ITYRVRKGDSLSS 415

                         90       100
                 ....*....|....*....|....*....
gi 30699276  186 IAKRFSTSVTDLTNVNAMGAPDINPGDIL 214
Cdd:PRK10783 416 IAKRHGVNIKDVMRWNSDTAKNLQPGDKL 444
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 174-216 9.81e-05

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: 39.39  E-value: 9.81e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 30699276 174 SYVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPD-INPGDILAV 216
Cdd:cd00118   2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDcIYPGQKLKI 45
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 174-216 1.40e-04

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 43.96  E-value: 1.40e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 30699276  174 SYVVRGIDTMAGIAKRFSTSVTDLTNVNAMGAPDINPGDILAV 216
Cdd:PRK10783 345 SYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTI 387
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
106-155 7.67e-04

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 40.08  E-value: 7.67e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30699276 106 STHYKTRTSDTLGSIADSvYGglVSPEQIQVANSETDlSVLDVGTKLVIP 155
Cdd:COG1388 109 PVTYTVKKGDTLWSIARR-YG--VSVEELKRWNGLSS-DTIRPGQKLKIP 154
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 109-155 1.25e-03

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: 36.22  E-value: 1.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 30699276   109 YKTRTSDTLGSIADSvYGglVSPEQIQVANsETDLSVLDVGTKLVIP 155
Cdd:pfam01476   1 YTVKKGDTLSSIAKR-YG--ITVEQLAELN-GLSSPNLYVGQKLKIP 43
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 107-154 3.79e-03

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: 35.15  E-value: 3.79e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30699276 107 THYKTRTSDTLGSIADSvYGglVSPEQIQVANSETDLSVLDVGTKLVI 154
Cdd:cd00118   1 KTYTVKPGDTLWSIAKK-YG--VTVEELAAANPLINPDCIYPGQKLKI 45
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH