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Conserved domains on  [gi|492916667|ref|WP_006044876|]
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LysM peptidoglycan-binding domain-containing protein [Prevotella pallens]

Protein Classification

amino acid ABC transporter substrate-binding protein( domain architecture ID 10061504)

amino acid ABC transporter substrate-binding protein functions as the initial receptor in the ABC transport of amino acids

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 ...
 30-58 4.53e-06

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: 43.24  E-value: 4.53e-06
                         10        20
                 ....*....|....*....|....*....
gi 492916667  30 IHKVKKKETIFGIAKDYGVSIQELIDANP 58
Cdd:cd00118    2 TYTVKPGDTLWSIAKKYGVTVEELAAANP 30
LivK COG0683
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ...
 106-299 7.46e-06

ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism];


:

Pssm-ID: 440447 [Multi-domain]  Cd Length: 314  Bit Score: 47.62  E-value: 7.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 106 NAIRIGVMLPL---HREDGDglrmvEYYRGILLALEQMKQEG------INTDV--HAWNVPKDADIKTTLLDKNAPtlDI 174
Cdd:COG0683    2 DPIKIGVLLPLtgpYAALGQ-----PIKNGAELAVEEINAAGgvlgrkIELVVedDASDPDTAVAAARKLIDQDKV--DA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 175 IFGPLYSNQVKPLGDFCQRNNIKMVIPFSIESK--EVDTNPYIFQVYQDNNRLNRKAIACFFERFQKThHPIFINCNDID 252
Cdd:COG0683   75 IVGPLSSGVALAVAPVAEEAGVPLISPSATAPAltGPECSPYVFRTAPSDAQQAEALADYLAKKLGAK-KVALLYDDYAY 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 492916667 253 SQVGLftNGLRKQLELA--KIHYNITnLNTPQVDFAKQFST---SQPNVVII 299
Cdd:COG0683  154 GQGLA--AAFKAALKAAggEVVGEEY-YPPGTTDFSAQLTKikaAGPDAVFL 202
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 30-58 4.53e-06

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: 43.24  E-value: 4.53e-06
                         10        20
                 ....*....|....*....|....*....
gi 492916667  30 IHKVKKKETIFGIAKDYGVSIQELIDANP 58
Cdd:cd00118    2 TYTVKPGDTLWSIAKKYGVTVEELAAANP 30
LivK COG0683
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ...
 106-299 7.46e-06

ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 440447 [Multi-domain]  Cd Length: 314  Bit Score: 47.62  E-value: 7.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 106 NAIRIGVMLPL---HREDGDglrmvEYYRGILLALEQMKQEG------INTDV--HAWNVPKDADIKTTLLDKNAPtlDI 174
Cdd:COG0683    2 DPIKIGVLLPLtgpYAALGQ-----PIKNGAELAVEEINAAGgvlgrkIELVVedDASDPDTAVAAARKLIDQDKV--DA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 175 IFGPLYSNQVKPLGDFCQRNNIKMVIPFSIESK--EVDTNPYIFQVYQDNNRLNRKAIACFFERFQKThHPIFINCNDID 252
Cdd:COG0683   75 IVGPLSSGVALAVAPVAEEAGVPLISPSATAPAltGPECSPYVFRTAPSDAQQAEALADYLAKKLGAK-KVALLYDDYAY 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 492916667 253 SQVGLftNGLRKQLELA--KIHYNITnLNTPQVDFAKQFST---SQPNVVII 299
Cdd:COG0683  154 GQGLA--AAFKAALKAAggEVVGEEY-YPPGTTDFSAQLTKikaAGPDAVFL 202
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
30-58 1.47e-05

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 45.08  E-value: 1.47e-05
                         10        20
                 ....*....|....*....|....*....
gi 492916667  30 IHKVKKKETIFGIAKDYGVSIQELIDANP 58
Cdd:COG1388  111 TYTVKKGDTLWSIARRYGVSVEELKRWNG 139
LysM smart00257
Lysin motif;
30-61 2.59e-05

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 41.28  E-value: 2.59e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 492916667    30 IHKVKKKETIFGIAKDYGVSIQELIDANPEMK 61
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILD 32
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 31-57 5.64e-05

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: 40.07  E-value: 5.64e-05
                          10        20
                  ....*....|....*....|....*..
gi 492916667   31 HKVKKKETIFGIAKDYGVSIQELIDAN 57
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELN 27
PBP1_YraM_LppC_lipoprotein-like cd06339
periplasmic binding component of lipoprotein LppC, an immunodominant antigen; This subgroup ...
 109-217 2.58e-03

periplasmic binding component of lipoprotein LppC, an immunodominant antigen; This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).


Pssm-ID: 380562 [Multi-domain]  Cd Length: 331  Bit Score: 39.95  E-value: 2.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 109 RIGVMLPL---HREDGDGLRmveyyRGILLALEQMKQEGINTDVHAWNVPKDA-DIKTTLLDKNAptlDIIFGPLYSNQV 184
Cdd:cd06339    1 RIALLLPLsgpYAAAGQAIR-----DGIELALFDAGGSRPELRVYDTGGPEGAaAAYQQAVAEGA---DLIIGPLLKSSV 72

                         90       100       110
                 ....*....|....*....|....*....|...
gi 492916667 185 KPLGDFCQRNNIKmVIPFSiESKEVDTNPYIFQ 217
Cdd:cd06339   73 AALAAAAQALGVP-VLALN-NDESATAGPGLFQ 103
spore_safA TIGR02899
spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found ...
 33-61 5.57e-03

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: 34.77  E-value: 5.57e-03
                          10        20
                  ....*....|....*....|....*....
gi 492916667   33 VKKKETIFGIAKDYGVSIQELIDANPEMK 61
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVDFDELIQANPQLS 29
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 30-58 4.53e-06

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: 43.24  E-value: 4.53e-06
                         10        20
                 ....*....|....*....|....*....
gi 492916667  30 IHKVKKKETIFGIAKDYGVSIQELIDANP 58
Cdd:cd00118    2 TYTVKPGDTLWSIAKKYGVTVEELAAANP 30
LivK COG0683
ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid ...
 106-299 7.46e-06

ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism];


Pssm-ID: 440447 [Multi-domain]  Cd Length: 314  Bit Score: 47.62  E-value: 7.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 106 NAIRIGVMLPL---HREDGDglrmvEYYRGILLALEQMKQEG------INTDV--HAWNVPKDADIKTTLLDKNAPtlDI 174
Cdd:COG0683    2 DPIKIGVLLPLtgpYAALGQ-----PIKNGAELAVEEINAAGgvlgrkIELVVedDASDPDTAVAAARKLIDQDKV--DA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 175 IFGPLYSNQVKPLGDFCQRNNIKMVIPFSIESK--EVDTNPYIFQVYQDNNRLNRKAIACFFERFQKThHPIFINCNDID 252
Cdd:COG0683   75 IVGPLSSGVALAVAPVAEEAGVPLISPSATAPAltGPECSPYVFRTAPSDAQQAEALADYLAKKLGAK-KVALLYDDYAY 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 492916667 253 SQVGLftNGLRKQLELA--KIHYNITnLNTPQVDFAKQFST---SQPNVVII 299
Cdd:COG0683  154 GQGLA--AAFKAALKAAggEVVGEEY-YPPGTTDFSAQLTKikaAGPDAVFL 202
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
30-58 1.47e-05

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 45.08  E-value: 1.47e-05
                         10        20
                 ....*....|....*....|....*....
gi 492916667  30 IHKVKKKETIFGIAKDYGVSIQELIDANP 58
Cdd:COG1388  111 TYTVKKGDTLWSIARRYGVSVEELKRWNG 139
LysM smart00257
Lysin motif;
30-61 2.59e-05

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 41.28  E-value: 2.59e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 492916667    30 IHKVKKKETIFGIAKDYGVSIQELIDANPEMK 61
Cdd:smart00257   1 TYTVKKGDTLSSIARRYGISVSDLLELNNILD 32
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 31-57 5.64e-05

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: 40.07  E-value: 5.64e-05
                          10        20
                  ....*....|....*....|....*..
gi 492916667   31 HKVKKKETIFGIAKDYGVSIQELIDAN 57
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELN 27
PBP1_YraM_LppC_lipoprotein-like cd06339
periplasmic binding component of lipoprotein LppC, an immunodominant antigen; This subgroup ...
 109-217 2.58e-03

periplasmic binding component of lipoprotein LppC, an immunodominant antigen; This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).


Pssm-ID: 380562 [Multi-domain]  Cd Length: 331  Bit Score: 39.95  E-value: 2.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492916667 109 RIGVMLPL---HREDGDGLRmveyyRGILLALEQMKQEGINTDVHAWNVPKDA-DIKTTLLDKNAptlDIIFGPLYSNQV 184
Cdd:cd06339    1 RIALLLPLsgpYAAAGQAIR-----DGIELALFDAGGSRPELRVYDTGGPEGAaAAYQQAVAEGA---DLIIGPLLKSSV 72

                         90       100       110
                 ....*....|....*....|....*....|...
gi 492916667 185 KPLGDFCQRNNIKmVIPFSiESKEVDTNPYIFQ 217
Cdd:cd06339   73 AALAAAAQALGVP-VLALN-NDESATAGPGLFQ 103
spore_safA TIGR02899
spore coat assembly protein SafA; SafA (YrbB) (SafA) of Bacillus subtilis is a protein found ...
 33-61 5.57e-03

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: 34.77  E-value: 5.57e-03
                          10        20
                  ....*....|....*....|....*....
gi 492916667   33 VKKKETIFGIAKDYGVSIQELIDANPEMK 61
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVDFDELIQANPQLS 29
 
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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