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Conserved domains on  [gi|390981309|gb|AFM31302|]
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hypothetical protein A458_00170 [Stutzerimonas stutzeri CCUG 29243]

Protein Classification

LysM peptidoglycan-binding domain-containing protein( domain architecture ID 11447265)

LysM peptidoglycan-binding domain-containing protein similar to Treponema pallidum treponemal membrane protein B (TmpB), which may serve as a porin or transport protein for large molecules

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 18-77 2.34e-24

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: 97.38  E-value: 2.34e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 390981309  18 QAAVQLKDNHPERYTVVKGDTLWDISGRFLREPWKWPELWHAN-PQIANPHLIYPGDTLSL 77
Cdd:COG1652   99 APSAELAPDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANrDQIKNPDLIYPGQVLRI 159
 
Name Accession Description Interval E-value
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 18-77 2.34e-24

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: 97.38  E-value: 2.34e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 390981309  18 QAAVQLKDNHPERYTVVKGDTLWDISGRFLREPWKWPELWHAN-PQIANPHLIYPGDTLSL 77
Cdd:COG1652   99 APSAELAPDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANrDQIKNPDLIYPGQVLRI 159
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 31-77 5.60e-09

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: 51.33  E-value: 5.60e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 390981309  31 YTVVKGDTLWDISGRFLrepWKWPELWHANPqIANPHLIYPGDTLSL 77
Cdd:cd00118    3 YTVKPGDTLWSIAKKYG---VTVEELAAANP-LINPDCIYPGQKLKI 45
spore_safA TIGR02899
spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found ...
 33-77 4.00e-08

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: 49.02  E-value: 4.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 390981309   33 VVKGDTLWDISGRFLREpwkWPELWHANPQIANPHLIYPGDTLSL 77
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVD---FDELIQANPQLSNPNLIYPGMKIKI 42
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 28-75 6.82e-07

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 47.99  E-value: 6.82e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 390981309  28 PERYTVVKGDTLWDISGRFLREPWKWPELWHAN-PQIANPHLIYPGDTL 75
Cdd:PRK11198  95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANkPMLKSPDKIYPGQVL 143
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 31-77 2.16e-06

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: 43.92  E-value: 2.16e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 390981309   31 YTVVKGDTLWDISGRFLrepWKWPELWHANpQIANPHlIYPGDTLSL 77
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYG---ITVEQLAELN-GLSSPN-LYVGQKLKI 42
LysM smart00257
Lysin motif;
31-77 3.26e-06

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 43.59  E-value: 3.26e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 390981309    31 YTVVKGDTLWDISGRFlrePWKWPELWHANPqIANPHLIYPGDTLSL 77
Cdd:smart00257   2 YTVKKGDTLSSIARRY---GISVSDLLELNN-ILDPDNLQVGQKLKI 44
 
Name Accession Description Interval E-value
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 18-77 2.34e-24

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: 97.38  E-value: 2.34e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 390981309  18 QAAVQLKDNHPERYTVVKGDTLWDISGRFLREPWKWPELWHAN-PQIANPHLIYPGDTLSL 77
Cdd:COG1652   99 APSAELAPDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANrDQIKNPDLIYPGQVLRI 159
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 31-77 5.60e-09

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: 51.33  E-value: 5.60e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 390981309  31 YTVVKGDTLWDISGRFLrepWKWPELWHANPqIANPHLIYPGDTLSL 77
Cdd:cd00118    3 YTVKPGDTLWSIAKKYG---VTVEELAAANP-LINPDCIYPGQKLKI 45
spore_safA TIGR02899
spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found ...
 33-77 4.00e-08

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: 49.02  E-value: 4.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 390981309   33 VVKGDTLWDISGRFLREpwkWPELWHANPQIANPHLIYPGDTLSL 77
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVD---FDELIQANPQLSNPNLIYPGMKIKI 42
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 28-75 6.82e-07

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 47.99  E-value: 6.82e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 390981309  28 PERYTVVKGDTLWDISGRFLREPWKWPELWHAN-PQIANPHLIYPGDTL 75
Cdd:PRK11198  95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANkPMLKSPDKIYPGQVL 143
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 31-77 2.16e-06

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: 43.92  E-value: 2.16e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 390981309   31 YTVVKGDTLWDISGRFLrepWKWPELWHANpQIANPHlIYPGDTLSL 77
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYG---ITVEQLAELN-GLSSPN-LYVGQKLKI 42
LysM smart00257
Lysin motif;
31-77 3.26e-06

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 43.59  E-value: 3.26e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 390981309    31 YTVVKGDTLWDISGRFlrePWKWPELWHANPqIANPHLIYPGDTLSL 77
Cdd:smart00257   2 YTVKKGDTLSSIARRY---GISVSDLLELNN-ILDPDNLQVGQKLKI 44
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
28-75 9.35e-04

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 39.31  E-value: 9.35e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 390981309  28 PERYTVVKGDTLWDISGRFlrePWKWPELWHANPqIANpHLIYPGDTL 75
Cdd:COG1388  109 PVTYTVKKGDTLWSIARRY---GVSVEELKRWNG-LSS-DTIRPGQKL 151
 
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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