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Conserved domains on  [gi|489812084|ref|WP_003715932|]
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LysM peptidoglycan-binding domain-containing protein [Limosilactobacillus oris]

Protein Classification

LysM peptidoglycan-binding domain-containing protein( domain architecture ID 10061613)

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
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 1-79 5.45e-12

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: 61.18  E-value: 5.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084   1 MNTKKNLVKVFTTLGVVALGVSTTAVVANADMVYTVQSGDTLSSISYKFAKDNSLINEIAKDN--NLSDINQLHVGQKLL 78
Cdd:COG1652   79 MRAGAAAKLSPAVTVAEEAAAPSAELAPDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANrdQIKNPDLIYPGQVLR 158


                 .
gi 489812084  79 I 79
Cdd:COG1652  159 I 159
PRK13914 super family cl36314
invasion associated endopeptidase;
23-139 3.01e-04

invasion associated endopeptidase;


The actual alignment was detected with superfamily member PRK13914:

Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 40.56  E-value: 3.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084  23 TTAVVANADMVYTVQSGDTLSSISYKFAKDnslINEIAKDNNLSDiNQLHVGQKLLIKGNGEIAPlndNDQNAASQNSNE 102
Cdd:PRK13914 191 ETPVVDQNATTHAVKSGDTIWALSVKYGVS---VQDIMSWNNLSS-SSIYVGQKLAIKQTANTAT---PKAEVKTEAPAA 263

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489812084 103 DKDAAQKTSQSANLSSSEQAAKEWIAQRESGGSYTAQ 139
Cdd:PRK13914 264 EKQAAPVVKENTNTNTATTEKKETTTQQQTAPKAPTE 300
Lyz-like super family cl00222
lysozyme-like domains; This family contains several members, including soluble lytic ...
 125-180 1.51e-03

lysozyme-like domains; This family contains several members, including soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, chitosanases, and pesticin. Typical members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


The actual alignment was detected with superfamily member cd13925:

Pssm-ID: 469668 [Multi-domain]  Cd Length: 71  Bit Score: 35.82  E-value: 1.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489812084 125 EWIAQRESGGSYTAQN--GVHYGRYQLDL--------AYLGGDLSPQHQEEVAQQYMQNR-YGSWQA 180
Cdd:cd13925    4 DAIAQCESGGNWNAVNtgNGYYGGLQFLQgtwksvggLGYPDDATRAEQITRAERLYARQgAGAWPC 70
 
Name Accession Description Interval E-value
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 1-79 5.45e-12

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: 61.18  E-value: 5.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084   1 MNTKKNLVKVFTTLGVVALGVSTTAVVANADMVYTVQSGDTLSSISYKFAKDNSLINEIAKDN--NLSDINQLHVGQKLL 78
Cdd:COG1652   79 MRAGAAAKLSPAVTVAEEAAAPSAELAPDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANrdQIKNPDLIYPGQVLR 158


                 .
gi 489812084  79 I 79
Cdd:COG1652  159 I 159
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 33-79 2.37e-10

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: 53.64  E-value: 2.37e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 489812084  33 VYTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDINQLHVGQKLLI 79
Cdd:cd00118    2 TYTVKPGDTLWSIAKKY---GVTVEELAAANPLINPDCIYPGQKLKI 45
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 34-80 7.27e-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: 52.01  E-value: 7.27e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 489812084   34 YTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDINqLHVGQKLLIK 80
Cdd:pfam01476   1 YTVKKGDTLSSIAKRY---GITVEQLAELNGLSSPN-LYVGQKLKIP 43
LysM smart00257
Lysin motif;
34-79 4.68e-09

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 50.14  E-value: 4.68e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 489812084    34 YTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDINQLHVGQKLLI 79
Cdd:smart00257   2 YTVKKGDTLSSIARRY---GISVSDLLELNNILDPDNLQVGQKLKI 44
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 23-79 7.92e-05

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 41.05  E-value: 7.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489812084  23 TTAVVANADMVYTVQSGDTLSSISYKFAKDNSLINEIAKDNN--LSDINQLHVGQKLLI 79
Cdd:PRK11198  87 KVATPAPESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKpmLKSPDKIYPGQVLRI 145
PRK13914 PRK13914
invasion associated endopeptidase;
23-139 3.01e-04

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 40.56  E-value: 3.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084  23 TTAVVANADMVYTVQSGDTLSSISYKFAKDnslINEIAKDNNLSDiNQLHVGQKLLIKGNGEIAPlndNDQNAASQNSNE 102
Cdd:PRK13914 191 ETPVVDQNATTHAVKSGDTIWALSVKYGVS---VQDIMSWNNLSS-SSIYVGQKLAIKQTANTAT---PKAEVKTEAPAA 263

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489812084 103 DKDAAQKTSQSANLSSSEQAAKEWIAQRESGGSYTAQ 139
Cdd:PRK13914 264 EKQAAPVVKENTNTNTATTEKKETTTQQQTAPKAPTE 300
RPF cd13925
core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting ...
 125-180 1.51e-03

core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting factor (RPF) proteins, found in various (G+C)-rich Gram-positive bacteria, act to reactivate cultures from stationary phase. This protein shares elements of the structural core of lysozyme and related proteins. Furthermore, it shares a conserved active site glutamate which is required for activity, and has a polysaccharide binding cleft that corresponds to the peptidoglycan binding cleft of lysozyme. Muralytic activity of Rpf in Micrococcus luteus correlates with resuscitation, supporting a mechanism dependent on cleavage of peptidoglycan by RPF.


Pssm-ID: 381607 [Multi-domain]  Cd Length: 71  Bit Score: 35.82  E-value: 1.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489812084 125 EWIAQRESGGSYTAQN--GVHYGRYQLDL--------AYLGGDLSPQHQEEVAQQYMQNR-YGSWQA 180
Cdd:cd13925    4 DAIAQCESGGNWNAVNtgNGYYGGLQFLQgtwksvggLGYPDDATRAEQITRAERLYARQgAGAWPC 70
 
Name Accession Description Interval E-value
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 1-79 5.45e-12

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: 61.18  E-value: 5.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084   1 MNTKKNLVKVFTTLGVVALGVSTTAVVANADMVYTVQSGDTLSSISYKFAKDNSLINEIAKDN--NLSDINQLHVGQKLL 78
Cdd:COG1652   79 MRAGAAAKLSPAVTVAEEAAAPSAELAPDAPKTYTVKPGDTLWGIAKRFYGDPARWPEIAEANrdQIKNPDLIYPGQVLR 158


                 .
gi 489812084  79 I 79
Cdd:COG1652  159 I 159
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 33-79 2.37e-10

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: 53.64  E-value: 2.37e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 489812084  33 VYTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDINQLHVGQKLLI 79
Cdd:cd00118    2 TYTVKPGDTLWSIAKKY---GVTVEELAAANPLINPDCIYPGQKLKI 45
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
8-82 2.47e-10

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 56.64  E-value: 2.47e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489812084   8 VKVFTTLGVVALGVSTTAVVANAdmVYTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDiNQLHVGQKLLIKGN 82
Cdd:COG1388   88 VKSGDTLSGIARRYGAAAAPSPV--TYTVKKGDTLWSIARRY---GVSVEELKRWNGLSS-DTIRPGQKLKIPAS 156
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 34-80 7.27e-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: 52.01  E-value: 7.27e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 489812084   34 YTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDINqLHVGQKLLIK 80
Cdd:pfam01476   1 YTVKKGDTLSSIAKRY---GITVEQLAELNGLSSPN-LYVGQKLKIP 43
LysM smart00257
Lysin motif;
34-79 4.68e-09

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 50.14  E-value: 4.68e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 489812084    34 YTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDINQLHVGQKLLI 79
Cdd:smart00257   2 YTVKKGDTLSSIARRY---GISVSDLLELNNILDPDNLQVGQKLKI 44
PRK11198 PRK11198
LysM domain/BON superfamily protein; Provisional
 23-79 7.92e-05

LysM domain/BON superfamily protein; Provisional


Pssm-ID: 236880 [Multi-domain]  Cd Length: 147  Bit Score: 41.05  E-value: 7.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489812084  23 TTAVVANADMVYTVQSGDTLSSISYKFAKDNSLINEIAKDNN--LSDINQLHVGQKLLI 79
Cdd:PRK11198  87 KVATPAPESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKpmLKSPDKIYPGQVLRI 145
OapA COG3061
Cell division protein YtfB/OapA (opacity-associated protein A) [Cell cycle control, cell ...
 34-125 1.84e-04

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: 41.19  E-value: 1.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084  34 YTVQSGDTLSSIsykFAK---DNSLINEIAK----DNNLSdinQLHVGQKLLIK--GNGEIAPL--NDNDQNAASQNSNE 102
Cdd:COG3061   72 YTVQSGDTLSQI---FRRlglSASDLYALLAaegdAKPLS---RLKPGQELRFQldADGQLQALryEVSRLETLLFTRQG 145

                         90       100
                 ....*....|....*....|...
gi 489812084 103 DKDAAQKTSQSANLSSSEQAAKE 125
Cdd:COG3061  146 DGFQRKRVTELSDGSFSADAALA 168
PRK13914 PRK13914
invasion associated endopeptidase;
23-139 3.01e-04

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 40.56  E-value: 3.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084  23 TTAVVANADMVYTVQSGDTLSSISYKFAKDnslINEIAKDNNLSDiNQLHVGQKLLIKGNGEIAPlndNDQNAASQNSNE 102
Cdd:PRK13914 191 ETPVVDQNATTHAVKSGDTIWALSVKYGVS---VQDIMSWNNLSS-SSIYVGQKLAIKQTANTAT---PKAEVKTEAPAA 263

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489812084 103 DKDAAQKTSQSANLSSSEQAAKEWIAQRESGGSYTAQ 139
Cdd:PRK13914 264 EKQAAPVVKENTNTNTATTEKKETTTQQQTAPKAPTE 300
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 19-92 4.17e-04

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 40.10  E-value: 4.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489812084  19 LGVSTTAVVANADM---VYTVQSGDTLSSISYKFakdNSLINEIAKDNNLSDiNQLHVGQKLLIKGNGEIAPLNDND 92
Cdd:PRK10783 328 AAVQSTLVADNTPLnsrSYKVRSGDTLSGIASRL---NVSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLANNS 400
RPF cd13925
core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting ...
 125-180 1.51e-03

core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting factor (RPF) proteins, found in various (G+C)-rich Gram-positive bacteria, act to reactivate cultures from stationary phase. This protein shares elements of the structural core of lysozyme and related proteins. Furthermore, it shares a conserved active site glutamate which is required for activity, and has a polysaccharide binding cleft that corresponds to the peptidoglycan binding cleft of lysozyme. Muralytic activity of Rpf in Micrococcus luteus correlates with resuscitation, supporting a mechanism dependent on cleavage of peptidoglycan by RPF.


Pssm-ID: 381607 [Multi-domain]  Cd Length: 71  Bit Score: 35.82  E-value: 1.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489812084 125 EWIAQRESGGSYTAQN--GVHYGRYQLDL--------AYLGGDLSPQHQEEVAQQYMQNR-YGSWQA 180
Cdd:cd13925    4 DAIAQCESGGNWNAVNtgNGYYGGLQFLQgtwksvggLGYPDDATRAEQITRAERLYARQgAGAWPC 70
PRK11649 PRK11649
putative peptidase; Provisional
 34-77 3.70e-03

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 37.34  E-value: 3.70e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 489812084  34 YTVQSGDTLSSISYKFAKDNSLINEIAKDNnlSDINQLHVGQKL 77
Cdd:PRK11649  98 YVVSTGDTLSSILNQYGIDMSDISQLAAQD--KELRNLKIGQQL 139
PRK14125 PRK14125
cell division suppressor protein YneA; Provisional
 1-79 8.93e-03

cell division suppressor protein YneA; Provisional


Pssm-ID: 184523 [Multi-domain]  Cd Length: 103  Bit Score: 34.62  E-value: 8.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489812084   1 MNTKKNLVKVFTTLGVVALGVSTTAVVANAD--MVYTVQSGDTLSSIS--YKFAKD---NSLINEIAKDNNLSDiNQLHV 73
Cdd:PRK14125   4 KESKIHVSIFFVLTALVLLIFVYATVPVDKNqyVEITVQEGDTLWALAdqYAGKHHmakNEFIEWVEDVNNLPS-GHIKA 82


                 ....*.
gi 489812084  74 GQKLLI 79
Cdd:PRK14125  83 GDKLVI 88
 
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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