Lysin motif;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1046311721   16 YTIKAGDTLAAIARIYGTTVQDIINANPDIDPYYLRVGQQICI 58
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44

L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046311721 127 VNVAERTLTVYRDGRIYRTYRIALENPASPIPRGTFTVLNKQVDP------------GVEMGARWIGLS--EAGFGIHGT 192
Cdd:cd16913     4 VDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPtwtgppsippgpYNPLGPYALRLSgpGSGIGIHGT 83

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1046311721 193 NTPEFIDVVSTGNSIVMSNEDVSELFNLVPVGTIVTI 229
Cdd:cd16913    84 PWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVI 120

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1046311721  16 YTIKAGDTLAAIARIYGTTVQDIINANPDIDPYYLRVGQQICI 58
Cdd:cd00118     3 YTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1046311721   5 YQRQCPTGSVPYTIKAGDTLAAIARIYGTTVQDIINANPdIDPYYLRVGQQICIP 59
Cdd:COG1388   101 YGAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNG-LSSDTIRPGQKLKIP 154

L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046311721 122 PVTVNVNVAE-RTLTVYRDGRIYRTYRIALENPASPIPRGTFTVlnkqvdpgvemgarwiglseagFGIHGTNTPEfIDV 200
Cdd:pfam03734   1 DRYIVVDLSEqRLLYLYENGGLVLRYPVSVGRGDGPTPTGTFRI----------------------IYIHDTGTPD-LFG 57

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1046311721 201 VSTGNS---IVMSNEDVSELFNLVPVGTIVTI 229
Cdd:pfam03734  58 LGRRRShgcIRLSNEDAKELYDRVLVGTPVVI 89

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1046311721  73 YYVVRPEDTLESIAAYFNITPQQLLYSNYGIDPTDLYVDQILCI 116
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45

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]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1046311721  18 IKAGDTLAAIARIYGTTVQDIINANPDI-DPYYLRVGQQICIP 59
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVDFDELIQANPQLsNPNLIYPGMKIKIP 43

L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046311721 127 VNVAERTLTVYRDGRIYRTYRIALENPASPIPRGTFTVLNKQVDP------------GVEMGARWIGLS--EAGFGIHGT 192
Cdd:cd16913     4 VDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPtwtgppsippgpYNPLGPYALRLSgpGSGIGIHGT 83

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1046311721 193 NTPEFIDVVSTGNSIVMSNEDVSELFNLVPVGTIVTI 229
Cdd:cd16913    84 PWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVI 120

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1046311721  16 YTIKAGDTLAAIARIYGTTVQDIINANPDIDPYYLRVGQQICI 58
Cdd:cd00118     3 YTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1046311721   5 YQRQCPTGSVPYTIKAGDTLAAIARIYGTTVQDIINANPdIDPYYLRVGQQICIP 59
Cdd:COG1388   101 YGAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNG-LSSDTIRPGQKLKIP 154

L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046311721 122 PVTVNVNVAE-RTLTVYRDGRIYRTYRIALENPASPIPRGTFTVlnkqvdpgvemgarwiglseagFGIHGTNTPEfIDV 200
Cdd:pfam03734   1 DRYIVVDLSEqRLLYLYENGGLVLRYPVSVGRGDGPTPTGTFRI----------------------IYIHDTGTPD-LFG 57

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1046311721 201 VSTGNS---IVMSNEDVSELFNLVPVGTIVTI 229
Cdd:pfam03734  58 LGRRRShgcIRLSNEDAKELYDRVLVGTPVVI 89

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046311721  10 PTGSVPYTIKAGDTLAAIARIYGTtvqdiinanpdidpyylrvgqqicipltmqiyPSCPTTNYYVVRPEDTLESIAAYF 89
Cdd:COG1388    80 AAAAARYTVKSGDTLSGIARRYGA--------------------------------AAAPSPVTYTVKKGDTLWSIARRY 127

                          90       100       110
                  ....*....|....*....|....*....|
gi 1046311721  90 NITPQQLLYSNyGIDPTDLYVDQILCIPVA 119
Cdd:COG1388   128 GVSVEELKRWN-GLSSDTIRPGQKLKIPAS 156

Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion transport and metabolism];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1046311721  10 PTGSVPYTIKAGDTLAAIA-RIYGTTVQ--DIINANPDI--DPYYLRVGQQICIP 59
Cdd:COG1652   106 PDAPKTYTVKPGDTLWGIAkRFYGDPARwpEIAEANRDQikNPDLIYPGQVLRIP 160

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]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1046311721  18 IKAGDTLAAIARIYGTTVQDIINANPDI-DPYYLRVGQQICIP 59
Cdd:TIGR02899   1 VQKGDTLWKIAKKYGVDFDELIQANPQLsNPNLIYPGMKIKIP 43

hypothetical protein; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1046311721 117 PVAPP--PVTVNVNVAERTLTVYRDGRIYRTYRIALENPASPIPRGTFTVLNKQVD 170
Cdd:PRK06132   53 PEAKPqgPLVIVVSLDEQRLYVYDNGILIAVSTVSTGKRGHETPTGVFSILQKDKD 108