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Conserved domains on  [gi|18395044|ref|NP_564153|]
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lysm domain GPI-anchored protein 1 precursor [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

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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 ...
 178-220 1.17e-08

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: 50.47  E-value: 1.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 18395044   178 YVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSSGDILAVP 220
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPNLYVGQKLKIP 43
mltD super family cl32574
membrane-bound lytic murein transglycosylase D; Provisional
 109-217 8.83e-08

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: 53.97  E-value: 8.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18395044  109 STHYKTRPSDNLGSIAdSVYGglVSAEQIQEANSVNDpSLLDVGTSLVIPLPCACFNGTDNSLPavyLSYVVKEIDTLVG 188
Cdd:PRK10783 343 SRSYKVRSGDTLSGIA-SRLN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNSDS---ITYRVRKGDSLSS 415

                         90       100
                 ....*....|....*....|....*....
gi 18395044  189 IARRYSTTITDLMNVNAMGAPDVSSGDIL 217
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 ...
 178-220 1.17e-08

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: 50.47  E-value: 1.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 18395044   178 YVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSSGDILAVP 220
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPNLYVGQKLKIP 43
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 109-217 8.83e-08

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 53.97  E-value: 8.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18395044  109 STHYKTRPSDNLGSIAdSVYGglVSAEQIQEANSVNDpSLLDVGTSLVIPLPCACFNGTDNSLPavyLSYVVKEIDTLVG 188
Cdd:PRK10783 343 SRSYKVRSGDTLSGIA-SRLN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNSDS---ITYRVRKGDSLSS 415

                         90       100
                 ....*....|....*....|....*....
gi 18395044  189 IARRYSTTITDLMNVNAMGAPDVSSGDIL 217
Cdd:PRK10783 416 IAKRHGVNIKDVMRWNSDTAKNLQPGDKL 444
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
172-220 2.38e-07

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 50.09  E-value: 2.38e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18395044 172 PAVYLSYVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSSGDILAVP 220
Cdd:COG1388 106 APSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSSDTIRPGQKLKIP 154
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 112-158 4.60e-05

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: 40.46  E-value: 4.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 18395044   112 YKTRPSDNLGSIADSvYGglVSAEQIQEANSVNDPSlLDVGTSLVIP 158
Cdd:pfam01476   1 YTVKKGDTLSSIAKR-YG--ITVEQLAELNGLSSPN-LYVGQKLKIP 43
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 177-219 7.62e-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: 39.78  E-value: 7.62e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 18395044 177 SYVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSS-GDILAV 219
Cdd:cd00118   2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYpGQKLKI 45
LysM smart00257
Lysin motif;
178-211 4.73e-04

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 37.43  E-value: 4.73e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 18395044    178 YVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDV 211
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDN 35
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 106-158 1.25e-03

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: 39.22  E-value: 1.25e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18395044 106 KSVSTHYKTRPSDNLGSIADSVYGGLVSAEQIQEANS--VNDPSLLDVGTSLVIP 158
Cdd:COG1652 106 PDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANRdqIKNPDLIYPGQVLRIP 160
LysM smart00257
Lysin motif;
112-157 1.77e-03

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 35.88  E-value: 1.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 18395044    112 YKTRPSDNLGSIADSvYGglVSAEQIQEANSVNDPSLLDVGTSLVI 157
Cdd:smart00257   2 YTVKKGDTLSSIARR-YG--ISVSDLLELNNILDPDNLQVGQKLKI 44
 
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 ...
 178-220 1.17e-08

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: 50.47  E-value: 1.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 18395044   178 YVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSSGDILAVP 220
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPNLYVGQKLKIP 43
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 109-217 8.83e-08

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 53.97  E-value: 8.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18395044  109 STHYKTRPSDNLGSIAdSVYGglVSAEQIQEANSVNDpSLLDVGTSLVIPLPCACFNGTDNSLPavyLSYVVKEIDTLVG 188
Cdd:PRK10783 343 SRSYKVRSGDTLSGIA-SRLN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNSDS---ITYRVRKGDSLSS 415

                         90       100
                 ....*....|....*....|....*....
gi 18395044  189 IARRYSTTITDLMNVNAMGAPDVSSGDIL 217
Cdd:PRK10783 416 IAKRHGVNIKDVMRWNSDTAKNLQPGDKL 444
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
172-220 2.38e-07

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 50.09  E-value: 2.38e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18395044 172 PAVYLSYVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSSGDILAVP 220
Cdd:COG1388 106 APSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSSDTIRPGQKLKIP 154
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 112-158 4.60e-05

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: 40.46  E-value: 4.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 18395044   112 YKTRPSDNLGSIADSvYGglVSAEQIQEANSVNDPSlLDVGTSLVIP 158
Cdd:pfam01476   1 YTVKKGDTLSSIAKR-YG--ITVEQLAELNGLSSPN-LYVGQKLKIP 43
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 177-219 7.62e-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: 39.78  E-value: 7.62e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 18395044 177 SYVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDVSS-GDILAV 219
Cdd:cd00118   2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYpGQKLKI 45
LysM smart00257
Lysin motif;
178-211 4.73e-04

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 37.43  E-value: 4.73e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 18395044    178 YVVKEIDTLVGIARRYSTTITDLMNVNAMGAPDV 211
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDN 35
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 106-158 1.25e-03

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: 39.22  E-value: 1.25e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18395044 106 KSVSTHYKTRPSDNLGSIADSVYGGLVSAEQIQEANS--VNDPSLLDVGTSLVIP 158
Cdd:COG1652 106 PDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANRdqIKNPDLIYPGQVLRIP 160
LysM smart00257
Lysin motif;
112-157 1.77e-03

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 35.88  E-value: 1.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 18395044    112 YKTRPSDNLGSIADSvYGglVSAEQIQEANSVNDPSLLDVGTSLVI 157
Cdd:smart00257   2 YTVKKGDTLSSIARR-YG--ISVSDLLELNNILDPDNLQVGQKLKI 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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