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Conserved domains on  [gi|23503313|ref|NP_699205|]
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lysM and putative peptidoglycan-binding domain-containing protein 2 isoform 1 [Homo sapiens]

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];
45-117 1.75e-14

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


:

Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 68.20  E-value: 1.75e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 23503313  45 ARTKTRSYGSTASVRAPLGAGVIERHVEHRVRAGDTLQGIALKYGVTMEQIKRANKLfTNDCIFLKKTLNIPV 117
Cdd:COG1388  84 ARYTVKSGDTLSGIARRYGAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGL-SSDTIRPGQKLKIPA 155
Nup88 super family cl25737
Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal ...
 101-206 5.33e-04

Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.


The actual alignment was detected with superfamily member pfam10168:

Pssm-ID: 462975 [Multi-domain]  Cd Length: 713  Bit Score: 40.41  E-value: 5.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23503313   101 LFTNDCIFLKKTLNIPVISEKPLLFNGLNSIDSPENETADNSFSQE---------EEPVVAGEDLPPPSPQESDVQPVQP 171
Cdd:pfam10168 461 LSSGEVISLPLLIDAVPPSPPLLCSKEDVTVDEPLRGLQEDSFEDHiksilqrsvSNPILSADKLSSPSPQECLQLLSRA 540

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 23503313   172 EEVSARDFLQRLDL-------QIK-LSTQAAKKLKEESRDEES 206
Cdd:pfam10168 541 TQVFREEYLKKHDLareeiqkRVKlLKLQKEQQLQELQSLEEE 583
 
Name Accession Description Interval E-value
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
45-117 1.75e-14

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 68.20  E-value: 1.75e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 23503313  45 ARTKTRSYGSTASVRAPLGAGVIERHVEHRVRAGDTLQGIALKYGVTMEQIKRANKLfTNDCIFLKKTLNIPV 117
Cdd:COG1388  84 ARYTVKSGDTLSGIARRYGAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGL-SSDTIRPGQKLKIPA 155
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 71-115 1.11e-13

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: 62.89  E-value: 1.11e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 23503313  71 VEHRVRAGDTLQGIALKYGVTMEQIKRANKLFTNDCIFLKKTLNI 115
Cdd:cd00118   1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 73-116 1.14e-10

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: 54.71  E-value: 1.14e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 23503313    73 HRVRAGDTLQGIALKYGVTMEQIKRANKLfTNDCIFLKKTLNIP 116
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGL-SSPNLYVGQKLKIP 43
LysM smart00257
Lysin motif;
72-115 1.20e-09

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 52.06  E-value: 1.20e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 23503313     72 EHRVRAGDTLQGIALKYGVTMEQIKRANKLFTNDCIFLKKTLNI 115
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 35-131 5.15e-05

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 43.18  E-value: 5.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23503313   35 SEEAELS-LSLARTKTRSYGSTASVRAPLGAGVI---ERHVE-----------------------------HRVRAGDTL 81
Cdd:PRK10783 275 AQAAEMAgMSLTKLKTFNAGYKRSTTAPSGPHYImvpKKHADqlreslasgeiaavqstlvadntplnsrsYKVRSGDTL 354

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 23503313   82 QGIALKYGVTMEQIKRANKLFTNDcifLK--KTLNIPVISEKPLLFNGLNSI 131
Cdd:PRK10783 355 SGIASRLNVSTKDLQQWNNLRGSK---LKvgQTLTIGAGSSAQRLANNSDSI 403
spore_safA TIGR02899
spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found ...
 75-116 2.42e-04

spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found at the interface of the spore cortex and spore coat, and is dependent on SpoVID for its localization. This model is based on the N-terminal LysM (lysin motif) domain (see pfamAM model pfam01476) of SafA and, from several other spore-forming species, the protein with the most similar N-terminal region. However, this set of proteins differs greatly in C-terminal of the LysM domaim; blocks of 12-residue and 13-residue repeats are found in the Bacillus cereus group, tandem LysM domains in Thermoanaerobacter tengcongensis MB4, etc. in which one of which is found in most examples of endospore-forming bacteria. [Cellular processes, Sporulation and germination]


Pssm-ID: 131945 [Multi-domain]  Cd Length: 44  Bit Score: 37.47  E-value: 2.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 23503313    75 VRAGDTLQGIALKYGVTMEQIKRANKLFTN-DCIFLKKTLNIP 116
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNpNLIYPGMKIKIP 43
Nup88 pfam10168
Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal ...
 101-206 5.33e-04

Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.


Pssm-ID: 462975 [Multi-domain]  Cd Length: 713  Bit Score: 40.41  E-value: 5.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23503313   101 LFTNDCIFLKKTLNIPVISEKPLLFNGLNSIDSPENETADNSFSQE---------EEPVVAGEDLPPPSPQESDVQPVQP 171
Cdd:pfam10168 461 LSSGEVISLPLLIDAVPPSPPLLCSKEDVTVDEPLRGLQEDSFEDHiksilqrsvSNPILSADKLSSPSPQECLQLLSRA 540

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 23503313   172 EEVSARDFLQRLDL-------QIK-LSTQAAKKLKEESRDEES 206
Cdd:pfam10168 541 TQVFREEYLKKHDLareeiqkRVKlLKLQKEQQLQELQSLEEE 583
 
Name Accession Description Interval E-value
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
45-117 1.75e-14

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 68.20  E-value: 1.75e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 23503313  45 ARTKTRSYGSTASVRAPLGAGVIERHVEHRVRAGDTLQGIALKYGVTMEQIKRANKLfTNDCIFLKKTLNIPV 117
Cdd:COG1388  84 ARYTVKSGDTLSGIARRYGAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGL-SSDTIRPGQKLKIPA 155
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 71-115 1.11e-13

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: 62.89  E-value: 1.11e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 23503313  71 VEHRVRAGDTLQGIALKYGVTMEQIKRANKLFTNDCIFLKKTLNI 115
Cdd:cd00118   1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 73-116 1.14e-10

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: 54.71  E-value: 1.14e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 23503313    73 HRVRAGDTLQGIALKYGVTMEQIKRANKLfTNDCIFLKKTLNIP 116
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGL-SSPNLYVGQKLKIP 43
LysM smart00257
Lysin motif;
72-115 1.20e-09

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 52.06  E-value: 1.20e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 23503313     72 EHRVRAGDTLQGIALKYGVTMEQIKRANKLFTNDCIFLKKTLNI 115
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 35-131 5.15e-05

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 43.18  E-value: 5.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23503313   35 SEEAELS-LSLARTKTRSYGSTASVRAPLGAGVI---ERHVE-----------------------------HRVRAGDTL 81
Cdd:PRK10783 275 AQAAEMAgMSLTKLKTFNAGYKRSTTAPSGPHYImvpKKHADqlreslasgeiaavqstlvadntplnsrsYKVRSGDTL 354

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 23503313   82 QGIALKYGVTMEQIKRANKLFTNDcifLK--KTLNIPVISEKPLLFNGLNSI 131
Cdd:PRK10783 355 SGIASRLNVSTKDLQQWNNLRGSK---LKvgQTLTIGAGSSAQRLANNSDSI 403
spore_safA TIGR02899
spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found ...
 75-116 2.42e-04

spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found at the interface of the spore cortex and spore coat, and is dependent on SpoVID for its localization. This model is based on the N-terminal LysM (lysin motif) domain (see pfamAM model pfam01476) of SafA and, from several other spore-forming species, the protein with the most similar N-terminal region. However, this set of proteins differs greatly in C-terminal of the LysM domaim; blocks of 12-residue and 13-residue repeats are found in the Bacillus cereus group, tandem LysM domains in Thermoanaerobacter tengcongensis MB4, etc. in which one of which is found in most examples of endospore-forming bacteria. [Cellular processes, Sporulation and germination]


Pssm-ID: 131945 [Multi-domain]  Cd Length: 44  Bit Score: 37.47  E-value: 2.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 23503313    75 VRAGDTLQGIALKYGVTMEQIKRANKLFTN-DCIFLKKTLNIP 116
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNpNLIYPGMKIKIP 43
Nup88 pfam10168
Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal ...
 101-206 5.33e-04

Nuclear pore component; Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.


Pssm-ID: 462975 [Multi-domain]  Cd Length: 713  Bit Score: 40.41  E-value: 5.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23503313   101 LFTNDCIFLKKTLNIPVISEKPLLFNGLNSIDSPENETADNSFSQE---------EEPVVAGEDLPPPSPQESDVQPVQP 171
Cdd:pfam10168 461 LSSGEVISLPLLIDAVPPSPPLLCSKEDVTVDEPLRGLQEDSFEDHiksilqrsvSNPILSADKLSSPSPQECLQLLSRA 540

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 23503313   172 EEVSARDFLQRLDL-------QIK-LSTQAAKKLKEESRDEES 206
Cdd:pfam10168 541 TQVFREEYLKKHDLareeiqkRVKlLKLQKEQQLQELQSLEEE 583
 
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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