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Conserved domains on  [gi|1277810775|gb|PIU24636|]
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hypothetical protein COT12_00035, partial [Candidatus Berkelbacteria bacterium CG08_land_8_20_14_0_20_39_8]

Protein Classification

LysM peptidoglycan-binding domain-containing protein( domain architecture ID 11443400)

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 COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
42-175 8.69e-14

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


:

Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 65.50  E-value: 8.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277810775  42 NVLVARGANNLYDLIPADPSSQIAIATSISKYTPLISNGSVAVEQAVSKTADPNSGVFIATAKLTSTEvttPDPKPATQE 121
Cdd:COG1388    25 LLAAALAAVALLLLAALAPAGLSLAAALNGEALLLLLPAAAAAAKAALAAAPEAAAAAAARYTVKSGD---TLSGIARRY 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277810775 122 SAGPREKNIYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKIP 175
Cdd:COG1388   102 GAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKIP 154
 
Name Accession Description Interval E-value
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
42-175 8.69e-14

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 65.50  E-value: 8.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277810775  42 NVLVARGANNLYDLIPADPSSQIAIATSISKYTPLISNGSVAVEQAVSKTADPNSGVFIATAKLTSTEvttPDPKPATQE 121
Cdd:COG1388    25 LLAAALAAVALLLLAALAPAGLSLAAALNGEALLLLLPAAAAAAKAALAAAPEAAAAAAARYTVKSGD---TLSGIARRY 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277810775 122 SAGPREKNIYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKIP 175
Cdd:COG1388   102 GAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKIP 154
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 130-174 5.36e-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: 57.50  E-value: 5.36e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1277810775 130 IYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNIDMIRPGDNLKI 174
Cdd:cd00118     1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM smart00257
Lysin motif;
131-174 4.39e-09

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 50.14  E-value: 4.39e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1277810775  131 YYTVQGGDTLSGLSMRFNVKISSLQFANNLSNIDMIRPGDNLKI 174
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 132-175 9.05e-09

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: 48.93  E-value: 9.05e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1277810775 132 YTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKIP 175
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSS-PNLYVGQKLKIP 43
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 132-174 6.76e-07

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 48.19  E-value: 6.76e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1277810775 132 YTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKI 174
Cdd:PRK10783  346 YKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTI 387
 
Name Accession Description Interval E-value
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
42-175 8.69e-14

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 65.50  E-value: 8.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277810775  42 NVLVARGANNLYDLIPADPSSQIAIATSISKYTPLISNGSVAVEQAVSKTADPNSGVFIATAKLTSTEvttPDPKPATQE 121
Cdd:COG1388    25 LLAAALAAVALLLLAALAPAGLSLAAALNGEALLLLLPAAAAAAKAALAAAPEAAAAAAARYTVKSGD---TLSGIARRY 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277810775 122 SAGPREKNIYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKIP 175
Cdd:COG1388   102 GAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLKIP 154
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 130-174 5.36e-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: 57.50  E-value: 5.36e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1277810775 130 IYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNIDMIRPGDNLKI 174
Cdd:cd00118     1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM smart00257
Lysin motif;
131-174 4.39e-09

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 50.14  E-value: 4.39e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1277810775  131 YYTVQGGDTLSGLSMRFNVKISSLQFANNLSNIDMIRPGDNLKI 174
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 132-175 9.05e-09

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: 48.93  E-value: 9.05e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1277810775 132 YTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKIP 175
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSS-PNLYVGQKLKIP 43
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 30-178 2.57e-08

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: 50.77  E-value: 2.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277810775  30 LIVAFGLLVALCNVLVARGANNLYDLIPADPSSQIAIATSISKYTPLISNGSVAVEQAVSKTADPNSGVFIATAKLTSTE 109
Cdd:COG1652     9 ALAALLPAVSAAAATVLALAAAAALAVVAGLGAAVGAGGALAAALPLAAGLAAAVAAAAAAAVLIAPVAVMRAGAAAKLS 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277810775 110 VTTPDPKPATQESAGPREKNI-YYTVQGGDTLSGLSMRF---NVKISSLQFAN--NLSNIDMIRPGDNLKIPPDG 178
Cdd:COG1652    89 PAVTVAEEAAAPSAELAPDAPkTYTVKPGDTLWGIAKRFygdPARWPEIAEANrdQIKNPDLIYPGQVLRIPALE 163
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 132-174 6.76e-07

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 48.19  E-value: 6.76e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1277810775 132 YTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKI 174
Cdd:PRK10783  346 YKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTI 387
PRK13914 PRK13914
invasion associated endopeptidase;
72-174 4.26e-05

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 42.87  E-value: 4.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277810775  72 KY-TPLISNGSVAVEQAVSKTADPNSgvfIATAKLTSTEV------TTPDPKPATQESAGPREKN-IYYTVQGGDTLSGL 143
Cdd:PRK13914  137 KYlTDKVTSTPVAPTQEVKKETTTQQ---AAPAAETKTEVkqttqaTTPAPKVAETKETPVVDQNaTTHAVKSGDTIWAL 213

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1277810775 144 SMRFNVKISSLQFANNLSNiDMIRPGDNLKI 174
Cdd:PRK13914  214 SVKYGVSVQDIMSWNNLSS-SSIYVGQKLAI 243
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
107-174 1.03e-03

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 38.91  E-value: 1.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277810775 107 STEVTTPDPKPATQESAGprekniYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKI 174
Cdd:PRK06347  389 STGTSTSKPSTGTSTNAK------VYTVVKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKV 449
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 123-176 1.12e-03

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 37.59  E-value: 1.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277810775 123 AGPREKNIYYTVQGGDTLSGLSMRF------NVKIsslqFANN---LSNIDMIRPGDNLKIPP 176
Cdd:PRK11198   89 ATPAPESQFYTVKSGDTLSAIAKKVygnankYNKI----FEANkpmLKSPDKIYPGQVLRIPE 147
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
106-174 5.07e-03

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 36.98  E-value: 5.07e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1277810775 106 TSTEVTTPDPKPAT---QESAGPREKNIYYTVQGGDTLSGLSMRFNVKISSLQFANNLSNiDMIRPGDNLKI 174
Cdd:PRK06347  453 STSNTNTSKPSTNTntsKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKV 523
 
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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