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Conserved domains on  [gi|1403298830|emb|SQF26103|]
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LysM domain-containing protein [Streptococcus thermophilus]

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 ...
 33-76 1.61e-16

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: 69.44  E-value: 1.61e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1403298830  33 TYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANKIYIGQKLTI 76
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
PRK13914 super family cl36314
invasion associated endopeptidase;
30-118 7.39e-06

invasion associated endopeptidase;


The actual alignment was detected with superfamily member PRK13914:

Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 45.18  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1403298830  30 NAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTINETT-------EEPAETPALVETSTDSTQSESN 102
Cdd:PRK13914  198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLS-SSSIYVGQKLAIKQTAntatpkaEVKTEAPAAEKQAAPVVKENTN 276

                          90
                  ....*....|....*.
gi 1403298830 103 QTTDTNLSSSEAAAKE 118
Cdd:PRK13914  277 TNTATTEKKETTTQQQ 292
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 33-76 1.61e-16

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: 69.44  E-value: 1.61e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1403298830  33 TYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANKIYIGQKLTI 76
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM smart00257
Lysin motif;
33-76 8.97e-16

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 67.47  E-value: 8.97e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1403298830   33 TYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANKIYIGQKLTI 76
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
24-76 2.27e-15

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 69.74  E-value: 2.27e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1403298830  24 GATALANAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDaNKIYIGQKLTI 76
Cdd:COG1388   102 GAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKI 153
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 34-76 8.84e-15

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: 64.72  E-value: 8.84e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1403298830  34 YTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANkIYIGQKLTI 76
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPN-LYVGQKLKI 42
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 25-76 5.31e-10

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 54.92  E-value: 5.31e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1403298830  25 ATALANAETYTVQKGDTLSAIAKK---NGTTVDEIVSKNG--IQDANKIYIGQKLTI 76
Cdd:PRK11198   89 ATPAPESQFYTVKSGDTLSAIAKKvygNANKYNKIFEANKpmLKSPDKIYPGQVLRI 145
PRK13914 PRK13914
invasion associated endopeptidase;
30-118 7.39e-06

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 45.18  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1403298830  30 NAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTINETT-------EEPAETPALVETSTDSTQSESN 102
Cdd:PRK13914  198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLS-SSSIYVGQKLAIKQTAntatpkaEVKTEAPAAEKQAAPVVKENTN 276

                          90
                  ....*....|....*.
gi 1403298830 103 QTTDTNLSSSEAAAKE 118
Cdd:PRK13914  277 TNTATTEKKETTTQQQ 292
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 33-76 1.61e-16

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: 69.44  E-value: 1.61e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1403298830  33 TYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANKIYIGQKLTI 76
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM smart00257
Lysin motif;
33-76 8.97e-16

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 67.47  E-value: 8.97e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1403298830   33 TYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANKIYIGQKLTI 76
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
24-76 2.27e-15

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 69.74  E-value: 2.27e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1403298830  24 GATALANAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDaNKIYIGQKLTI 76
Cdd:COG1388   102 GAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKI 153
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 34-76 8.84e-15

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: 64.72  E-value: 8.84e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1403298830  34 YTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANkIYIGQKLTI 76
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSPN-LYVGQKLKI 42
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 25-76 6.96e-11

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: 58.09  E-value: 6.96e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1403298830  25 ATALANAETYTVQKGDTLSAIAKK---NGTTVDEIVSKN--GIQDANKIYIGQKLTI 76
Cdd:COG1652   103 ELAPDAPKTYTVKPGDTLWGIAKRfygDPARWPEIAEANrdQIKNPDLIYPGQVLRI 159
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 25-76 5.31e-10

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 54.92  E-value: 5.31e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1403298830  25 ATALANAETYTVQKGDTLSAIAKK---NGTTVDEIVSKNG--IQDANKIYIGQKLTI 76
Cdd:PRK11198   89 ATPAPESQFYTVKSGDTLSAIAKKvygNANKYNKIFEANKpmLKSPDKIYPGQVLRI 145
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 22-76 5.11e-06

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 45.88  E-value: 5.11e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1403298830  22 TLGATALANAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTI 76
Cdd:PRK10783  334 LVADNTPLNSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLR-GSKLKVGQTLTI 387
PRK13914 PRK13914
invasion associated endopeptidase;
18-82 7.05e-06

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 45.18  E-value: 7.05e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1403298830  18 VTVATLGATALANAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTINETTEE 82
Cdd:PRK13914   14 IAVTAFAAPTIASASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLT-TDKIVPGQKLQVNEVAAA 77
PRK13914 PRK13914
invasion associated endopeptidase;
30-118 7.39e-06

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 45.18  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1403298830  30 NAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTINETT-------EEPAETPALVETSTDSTQSESN 102
Cdd:PRK13914  198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLS-SSSIYVGQKLAIKQTAntatpkaEVKTEAPAAEKQAAPVVKENTN 276

                          90
                  ....*....|....*.
gi 1403298830 103 QTTDTNLSSSEAAAKE 118
Cdd:PRK13914  277 TNTATTEKKETTTQQQ 292
OapA COG3061
Cell division protein YtfB/OapA (opacity-associated protein A) [Cell cycle control, cell ...
 33-76 3.47e-05

Cell division protein YtfB/OapA (opacity-associated protein A) [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442295 [Multi-domain]  Cd Length: 425  Bit Score: 43.12  E-value: 3.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1403298830  33 TYTVQKGDTLSAIAKKNG---TTVDEIVSKNGIQDA-NKIYIGQKLTI 76
Cdd:COG3061    71 EYTVQSGDTLSQIFRRLGlsaSDLYALLAAEGDAKPlSRLKPGQELRF 118
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
32-76 4.26e-05

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 43.14  E-value: 4.26e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1403298830  32 ETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTI 76
Cdd:PRK06347  548 KTYTVKKGDSLWAISRQYKTTVDNIKAWNKLT-SNMIHVGQKLTI 591
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
30-107 4.77e-05

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 42.76  E-value: 4.77e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1403298830  30 NAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQdANKIYIGQKLTINETTeepaeTPALVETSTDSTQSESNQTTDT 107
Cdd:PRK06347  478 NAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLK-SDFIYPGQKLKVSAGS-----TTNNTNTAKPSTNKPSNSTVKT 549
nlpD PRK10871
murein hydrolase activator NlpD;
30-127 7.43e-05

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 42.13  E-value: 7.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1403298830  30 NAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANKIYIGQKLTINETTEEPAeTPALVETSTDSTQSeSNQTTDTNL 109
Cdd:PRK10871   59 SGSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNASGTPI-TGGNAITQADAAEQ-GVVIKPAQN 136

                          90
                  ....*....|....*...
gi 1403298830 110 SSSEAAAKEEIAQRESSG 127
Cdd:PRK10871  137 STVAVASQPTITYSESSG 154
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
30-108 1.65e-04

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 41.22  E-value: 1.65e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1403298830  30 NAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANkIYIGQKLTINETTEEPAETPalvETSTDSTQSESNQTTDTN 108
Cdd:PRK06347  404 NAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKSDF-IYPGQKLKVSAGSTSNTNTS---KPSTNTNTSKPSTNTNTN 478
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
29-106 3.63e-04

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 40.45  E-value: 3.63e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1403298830  29 ANAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANkIYIGQKLTINETTEEPAETPALVETSTDSTQSESNQTTD 106
Cdd:PRK06347  328 SNAKIYTVVKGDSLWRIANNHKVTVANLKAWNNLKSDF-IYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTSTN 404
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 29-76 1.18e-03

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 38.56  E-value: 1.18e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1403298830  29 ANAETYTVQKGDTLSAIAKKNGTTVDEIVSKNGIQDANkIYIGQKLTI 76
Cdd:PRK10783  400 SDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKN-LQPGDKLTL 446
 
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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