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Conserved domains on  [gi|1487549951|gb|AYG18161|]
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LysM peptidoglycan-binding domain-containing protein [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

M23 peptidase family protein( domain architecture ID 1000974)

M23 peptidase family protein similar to murein hydrolase activator NlpD and to Haemophilus somni LppB lipoprotein outer membrane antigen, a putative virulence determinant; NlpD/LppB contains LysM and M23 peptidase domains

Gene Ontology:  GO:0004222|GO:0009279
MEROPS:  M23
PubMed:  19759820|8478068

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
amid_act_ActS NF040883
amidase activator ActS;
7-251 2.97e-176

amidase activator ActS;


:

Pssm-ID: 468819 [Multi-domain]  Cd Length: 242  Bit Score: 484.27  E-value: 2.97e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951   7 NKKSLGIVMLLSVGLLLAGCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKLGG 86
Cdd:NF040883    1 LALWFRIAVCLTLGLLLAGCSGKKSDYDGSYSGSTYTVKRGDTLYRISRITGTSVSELARLNGISPPYTIEVGQKLRLNG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  87 AKSSsitRKSTAKSTTKTASVTPSSAVPKSSWPPVGQRCWLWPTTGKVIMPYSTADGGNKGIDISAPRGTPIYAAGAGKV 166
Cdd:NF040883   81 SSKS---KKSAAKSSTKTAKVTPSSAVPKSSWPPVGQRCWRWPTSGKVVLPYSTADGGNKGIDIAGKRGQPVYASGAGKV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 167 VYVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLPPQG 246
Cdd:NF040883  158 VYVGNQLRGYGNLIMIKHGEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTGADSVRLHFQIRYRATAIDPLRYLPPQG 237


                  ....*
gi 1487549951 247 SKPKC 251
Cdd:NF040883  238 SKPSC 242
 
Name Accession Description Interval E-value
amid_act_ActS NF040883
amidase activator ActS;
7-251 2.97e-176

amidase activator ActS;


Pssm-ID: 468819 [Multi-domain]  Cd Length: 242  Bit Score: 484.27  E-value: 2.97e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951   7 NKKSLGIVMLLSVGLLLAGCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKLGG 86
Cdd:NF040883    1 LALWFRIAVCLTLGLLLAGCSGKKSDYDGSYSGSTYTVKRGDTLYRISRITGTSVSELARLNGISPPYTIEVGQKLRLNG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  87 AKSSsitRKSTAKSTTKTASVTPSSAVPKSSWPPVGQRCWLWPTTGKVIMPYSTADGGNKGIDISAPRGTPIYAAGAGKV 166
Cdd:NF040883   81 SSKS---KKSAAKSSTKTAKVTPSSAVPKSSWPPVGQRCWRWPTSGKVVLPYSTADGGNKGIDIAGKRGQPVYASGAGKV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 167 VYVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLPPQG 246
Cdd:NF040883  158 VYVGNQLRGYGNLIMIKHGEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTGADSVRLHFQIRYRATAIDPLRYLPPQG 237


                  ....*
gi 1487549951 247 SKPKC 251
Cdd:NF040883  238 SKPSC 242
nlpD PRK10871
murein hydrolase activator NlpD;
1-243 2.69e-79

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 241.28  E-value: 2.69e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951   1 MSAGRLNKKSLGIVMLLSVGLLLAGCSGSKSSDT---------------------GTYSGSVYTVKRGDTLYRISRTTGT 59
Cdd:PRK10871    1 MSAGSPKFTVRRIAALSLVSLWLAGCSNTSNPPApvssvgngrivynrqygnipkGSYSGSTYTVKKGDTLFYIAWITGN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  60 SVKELARLNGISPPYTIEVGQKLKLGGAKSSSITRK-------------------------------------------- 95
Cdd:PRK10871   81 DFRDLAQRNNIQAPYSLNVGQTLQVGNASGTPITGGnaitqadaaeqgvvikpaqnstvavasqptitysessgeqsank 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  96 -----------STAKSTTKTASVTPSSAVPKSSWPPVGQrcWLWPTTGKVIMPYSTADGGNKGIDISAPRGTPIYAAGAG 164
Cdd:PRK10871  161 mlpnnkpaattVTAPVTAPTASTTEPTASSTSTSTPIST--WRWPTDGKVIENFSASEGGNKGIDIAGSKGQAIIATADG 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1487549951 165 KVVYVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLP 243
Cdd:PRK10871  239 RVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLHFEIRYKGKSVNPLRYLP 317
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 62-245 1.24e-49

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 166.86  E-value: 1.24e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  62 KELARLNGISPPYTIEVGQKLKLGGAKSSSITRKSTAKSTTKTASVTPSSAVPKSSWPpvgqrcwlWPTTGKVIMPYSTA 141
Cdd:COG4942   199 KLLARLEKELAELAAELAELQQEAEELEALIARLEAEAAAAAERTPAAGFAALKGKLP--------WPVSGRVVRRFGER 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 142 DGG---NKGIDISAPRGTPIYAAGAGKVVYVGNqLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGST 218
Cdd:COG4942   271 DGGggrNKGIDIAAPPGAPVRAVADGTVVYAGW-LRGYGNLVIIDHGGGYLTLYAHLSSLLVKVGQRVKAGQPIGTVGSS 349

                         170       180
                  ....*....|....*....|....*...
gi 1487549951 219 DAAS-VRLHFQIRYRATAIDPLRYLPPQ 245
Cdd:COG4942   350 GGQGgPTLYFELRKNGKPVDPLPWLAKR 377
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 143-238 5.19e-41

Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.


Pssm-ID: 460250 [Multi-domain]  Cd Length: 96  Bit Score: 136.14  E-value: 5.19e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 143 GGNKGIDISAPRGTPIYAAGAGKVVYVGNqLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAAS 222
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGW-LGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTGRST 79

                          90
                  ....*....|....*..
gi 1487549951 223 -VRLHFQIRYRATAIDP 238
Cdd:pfam01551  80 gPHLHFEIRKNGKPVDP 96
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 145-229 8.02e-32

M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; This model describes the metallopeptidase M23 family, which includes beta-lytic metallopeptidase and lysostaphin. Members of this family are zinc endopeptidases that lyse bacterial cell wall peptidoglycans; they cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase) or a bond within the cross-linking peptide (e.g. stapholysin, and lysostaphin). Beta-lytic metallopeptidase, formerly known as beta-lytic protease, has a preference for cleavage of Gly-X bonds and favors hydrophobic or apolar residues on either side. It inhibits growth of sensitive organisms and may potentially serve as an antimicrobial agent. Lysostaphin, produced by Staphylococcus genus, cleaves pentaglycine cross-bridges of cell wall peptidoglycan, acting as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Staphylolysin (also known as LasA) is implicated in a range of processes related to Pseudomonas virulence, including stimulating shedding of the ectodomain of cell surface heparan sulphate proteoglycan syndecan-1, and elastin degradation in connective tissue. Its active site is less constricted and contains a five-coordinate zinc ion with trigonal bipyramidal geometry and two metal-bound water molecules, possibly contributing to its activity against a wider range of substrates than those used by related lytic enzymes, consistent with its multiple roles in Pseudomonas virulence. The family includes members that do not appear to have the conserved zinc-binding site and might be lipoproteins lacking proteolytic activity.


Pssm-ID: 410984 [Multi-domain]  Cd Length: 85  Bit Score: 111.91  E-value: 8.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 145 NKGIDISAPRGTPIYAAGAGKVVYVGNQlRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAAS-V 223
Cdd:cd12797     1 HNGIDIAAPEGTPVYAAADGTVVFAGWD-GGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNTGRSTgP 79


                  ....*.
gi 1487549951 224 RLHFQI 229
Cdd:cd12797    80 HLHFEI 85
LysM smart00257
Lysin motif;
42-84 6.85e-14

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 64.00  E-value: 6.85e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1487549951   42 YTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKL 84
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
 
Name Accession Description Interval E-value
amid_act_ActS NF040883
amidase activator ActS;
7-251 2.97e-176

amidase activator ActS;


Pssm-ID: 468819 [Multi-domain]  Cd Length: 242  Bit Score: 484.27  E-value: 2.97e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951   7 NKKSLGIVMLLSVGLLLAGCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKLGG 86
Cdd:NF040883    1 LALWFRIAVCLTLGLLLAGCSGKKSDYDGSYSGSTYTVKRGDTLYRISRITGTSVSELARLNGISPPYTIEVGQKLRLNG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  87 AKSSsitRKSTAKSTTKTASVTPSSAVPKSSWPPVGQRCWLWPTTGKVIMPYSTADGGNKGIDISAPRGTPIYAAGAGKV 166
Cdd:NF040883   81 SSKS---KKSAAKSSTKTAKVTPSSAVPKSSWPPVGQRCWRWPTSGKVVLPYSTADGGNKGIDIAGKRGQPVYASGAGKV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 167 VYVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLPPQG 246
Cdd:NF040883  158 VYVGNQLRGYGNLIMIKHGEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTGADSVRLHFQIRYRATAIDPLRYLPPQG 237


                  ....*
gi 1487549951 247 SKPKC 251
Cdd:NF040883  238 SKPSC 242
nlpD PRK10871
murein hydrolase activator NlpD;
1-243 2.69e-79

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 241.28  E-value: 2.69e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951   1 MSAGRLNKKSLGIVMLLSVGLLLAGCSGSKSSDT---------------------GTYSGSVYTVKRGDTLYRISRTTGT 59
Cdd:PRK10871    1 MSAGSPKFTVRRIAALSLVSLWLAGCSNTSNPPApvssvgngrivynrqygnipkGSYSGSTYTVKKGDTLFYIAWITGN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  60 SVKELARLNGISPPYTIEVGQKLKLGGAKSSSITRK-------------------------------------------- 95
Cdd:PRK10871   81 DFRDLAQRNNIQAPYSLNVGQTLQVGNASGTPITGGnaitqadaaeqgvvikpaqnstvavasqptitysessgeqsank 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  96 -----------STAKSTTKTASVTPSSAVPKSSWPPVGQrcWLWPTTGKVIMPYSTADGGNKGIDISAPRGTPIYAAGAG 164
Cdd:PRK10871  161 mlpnnkpaattVTAPVTAPTASTTEPTASSTSTSTPIST--WRWPTDGKVIENFSASEGGNKGIDIAGSKGQAIIATADG 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1487549951 165 KVVYVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLP 243
Cdd:PRK10871  239 RVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLHFEIRYKGKSVNPLRYLP 317
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 62-245 1.24e-49

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 166.86  E-value: 1.24e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  62 KELARLNGISPPYTIEVGQKLKLGGAKSSSITRKSTAKSTTKTASVTPSSAVPKSSWPpvgqrcwlWPTTGKVIMPYSTA 141
Cdd:COG4942   199 KLLARLEKELAELAAELAELQQEAEELEALIARLEAEAAAAAERTPAAGFAALKGKLP--------WPVSGRVVRRFGER 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 142 DGG---NKGIDISAPRGTPIYAAGAGKVVYVGNqLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGST 218
Cdd:COG4942   271 DGGggrNKGIDIAAPPGAPVRAVADGTVVYAGW-LRGYGNLVIIDHGGGYLTLYAHLSSLLVKVGQRVKAGQPIGTVGSS 349

                         170       180
                  ....*....|....*....|....*...
gi 1487549951 219 DAAS-VRLHFQIRYRATAIDPLRYLPPQ 245
Cdd:COG4942   350 GGQGgPTLYFELRKNGKPVDPLPWLAKR 377
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 128-244 2.17e-46

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 153.20  E-value: 2.17e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 128 WPTTGKVIMPY-------STADGGNKGIDISAPRGTPIYAAGAGKVVYVGNQlRGYGNLIMIKHSEDYITAYAHNDTMLV 200
Cdd:COG0739    73 WPVKGRITSGFgyrrhpvTGRRRFHKGIDIAAPTGTPVYAAADGTVVFAGWN-GGYGNLVIIDHGNGYTTLYAHLSSILV 151

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1487549951 201 NNGQSVKAGQKIATMGSTDAAS-VRLHFQIRYRATAIDPLRYLPP 244
Cdd:COG0739   152 KVGQRVKAGQVIGYVGNTGRSTgPHLHFEVRVNGKPVDPLPFLPA 196
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 143-238 5.19e-41

Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.


Pssm-ID: 460250 [Multi-domain]  Cd Length: 96  Bit Score: 136.14  E-value: 5.19e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 143 GGNKGIDISAPRGTPIYAAGAGKVVYVGNqLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAAS 222
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGW-LGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTGRST 79

                          90
                  ....*....|....*..
gi 1487549951 223 -VRLHFQIRYRATAIDP 238
Cdd:pfam01551  80 gPHLHFEIRKNGKPVDP 96
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 90-244 1.32e-32

Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444523 [Multi-domain]  Cd Length: 200  Bit Score: 117.82  E-value: 1.32e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  90 SSITRKSTAKSTTKTASVTPSSAVPKSSWPPVgqrcWLWPTTGKVIMPYS-------TADG--GNKGIDISAPRGTPIYA 160
Cdd:COG5821    37 NNLNKLEEETVKNKSESNEKSKSKVTASTSNK----FLKPVSGKITREFGedlvyskTLNEwrTHTGIDIAAKEGTPVKA 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 161 AGAGKVVYVGNQLRgYGNLIMIKHSEDYITAYAH-NDTMLVNNGQSVKAGQKIATMGST----DAASVRLHFQIRYRATA 235
Cdd:COG5821   113 AADGVVVEVGKDPK-YGITVVIDHGNGIKTVYANlDSKIKVKVGQKVKKGQVIGKVGSTalfeSSEGPHLHFEVLKNGKP 191


                  ....*....
gi 1487549951 236 IDPLRYLPP 244
Cdd:COG5821   192 VDPMKYLKK 200
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 145-229 8.02e-32

M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; This model describes the metallopeptidase M23 family, which includes beta-lytic metallopeptidase and lysostaphin. Members of this family are zinc endopeptidases that lyse bacterial cell wall peptidoglycans; they cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase) or a bond within the cross-linking peptide (e.g. stapholysin, and lysostaphin). Beta-lytic metallopeptidase, formerly known as beta-lytic protease, has a preference for cleavage of Gly-X bonds and favors hydrophobic or apolar residues on either side. It inhibits growth of sensitive organisms and may potentially serve as an antimicrobial agent. Lysostaphin, produced by Staphylococcus genus, cleaves pentaglycine cross-bridges of cell wall peptidoglycan, acting as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Staphylolysin (also known as LasA) is implicated in a range of processes related to Pseudomonas virulence, including stimulating shedding of the ectodomain of cell surface heparan sulphate proteoglycan syndecan-1, and elastin degradation in connective tissue. Its active site is less constricted and contains a five-coordinate zinc ion with trigonal bipyramidal geometry and two metal-bound water molecules, possibly contributing to its activity against a wider range of substrates than those used by related lytic enzymes, consistent with its multiple roles in Pseudomonas virulence. The family includes members that do not appear to have the conserved zinc-binding site and might be lipoproteins lacking proteolytic activity.


Pssm-ID: 410984 [Multi-domain]  Cd Length: 85  Bit Score: 111.91  E-value: 8.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 145 NKGIDISAPRGTPIYAAGAGKVVYVGNQlRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKAGQKIATMGSTDAAS-V 223
Cdd:cd12797     1 HNGIDIAAPEGTPVYAAADGTVVFAGWD-GGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNTGRSTgP 79


                  ....*.
gi 1487549951 224 RLHFQI 229
Cdd:cd12797    80 HLHFEI 85
PRK11637 PRK11637
AmiB activator; Provisional
 120-242 8.25e-18

AmiB activator; Provisional


Pssm-ID: 236942 [Multi-domain]  Cd Length: 428  Bit Score: 81.66  E-value: 8.25e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 120 PVGQRcwLWPTTGKVIMPYSTADGGN---KGIDISAPRGTPIYAAGAGKVVyVGNQLRGYGNLIMIKHSEDYITAYAHND 196
Cdd:PRK11637  303 PRGQA--FWPVRGPTLHRFGEQLQGElrwKGMVIGASEGTEVKAIADGRVL-LADWLQGYGLVVVVEHGKGDMSLYGYNQ 379

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1487549951 197 TMLVNNGQSVKAGQKIATMGSTDAASV-RLHFQIRYRATAIDPLRYL 242
Cdd:PRK11637  380 SALVSVGAQVRAGQPIALVGSSGGQGRpSLYFEIRRQGQAVNPQPWL 426
SpoIVFA COG5833
Stage IV sporulation protein SpoIVFA, regulates SpoIVFB [Cell cycle control, cell division, ...
 126-243 6.80e-17

Stage IV sporulation protein SpoIVFA, regulates SpoIVFB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444535 [Multi-domain]  Cd Length: 219  Bit Score: 76.57  E-value: 6.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 126 WLWPTTGKVIMPYstADGGnKGIDISAPRGTPIYAAGAGKVVYVGNQlRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQS 205
Cdd:COG5833   104 FALPVSGKVVESF--QENG-KGVDIETPGGANVKAVKEGYVIFAGKD-EETGKTVIIQHADGSESWYGNLSSIDVKLYDF 179

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1487549951 206 VKAGQKIATMGSTDAASVRLHFQIRYRATAIDPLRYLP 243
Cdd:COG5833   180 VEAGQKIGTVPATEGEEGTFYFAIKKGGKFIDPIQVIS 217
PRK11649 PRK11649
putative peptidase; Provisional
 129-239 8.64e-16

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 75.86  E-value: 8.64e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951 129 PTTGKvIMPYstadggnKGIDISAPRGTPIYAAGAGKVVyVGNQLRGYGNLIMIKHSEDYITAYAHNDTMLVNNGQSVKA 208
Cdd:PRK11649  305 PVTGR-VAPH-------RGVDFAMPVGTPVLAVGDGEVV-VAKRSGAAGNYVAIRHGRQYTTRYMHLRKLLVKPGQKVKR 375

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1487549951 209 GQKIATMGSTDAAS-VRLHFQIRYRATAIDPL 239
Cdd:PRK11649  376 GDRIALSGNTGRSTgPHLHYEVWINQQAVNPL 407
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 41-84 1.77e-14

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: 65.58  E-value: 1.77e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1487549951  41 VYTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKL 84
Cdd:cd00118     2 TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 42-84 5.42e-14

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: 64.34  E-value: 5.42e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1487549951  42 YTVKRGDTLYRISRTTGTSVKELARLNGISPPyTIEVGQKLKL 84
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSSP-NLYVGQKLKI 42
LysM smart00257
Lysin motif;
42-84 6.85e-14

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 64.00  E-value: 6.85e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1487549951   42 YTVKRGDTLYRISRTTGTSVKELARLNGISPPYTIEVGQKLKL 84
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
29-84 5.11e-13

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 65.12  E-value: 5.11e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1487549951  29 SKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISpPYTIEVGQKLKL 84
Cdd:COG1388    99 RRYGAAAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLS-SDTIRPGQKLKI 153
PRK06148 PRK06148
hypothetical protein; Provisional
 147-229 9.07e-10

hypothetical protein; Provisional


Pssm-ID: 180426 [Multi-domain]  Cd Length: 1013  Bit Score: 58.50  E-value: 9.07e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  147 GIDISAPRGTPIYAAGAGKVVYVGNQLR--GYGNLIMIKHS----EDYITAYAHNDTMLVNN---GQSVKAGQKIATMGS 217
Cdd:PRK06148   443 GVDLFAPAGTPVYAPLAGTVRSVEIEAVplGYGGLVALEHEtpggDPFYTLYGHLAHEAVSRlkpGDRLAAGELFGAMGD 522

                           90
                   ....*....|....*
gi 1487549951  218 TDAASVR---LHFQI 229
Cdd:PRK06148   523 AHENGGWaphLHFQL 537
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 12-84 5.80e-08

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: 51.16  E-value: 5.80e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487549951  12 GIVMLLSVGLLLAGCSGSKSSDTGTYSGSVYTVKRGDTLYRISRT---TGTSVKELARLN--GISPPYTIEVGQKLKL 84
Cdd:COG1652    82 GAAAKLSPAVTVAEEAAAPSAELAPDAPKTYTVKPGDTLWGIAKRfygDPARWPEIAEANrdQIKNPDLIYPGQVLRI 159
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
24-112 2.57e-07

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 51.23  E-value: 2.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  24 AGCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPYtIEVGQKLKLGGAKSSSITrkSTAKSTTK 103
Cdd:PRK06347  315 TGNSSNSSNTGNTSNAKIYTVVKGDSLWRIANNHKVTVANLKAWNNLKSDF-IYPGQKLKVSAGSTTSDT--NTSKPSTG 391


                  ....*....
gi 1487549951 104 TASVTPSSA 112
Cdd:PRK06347  392 TSTSKPSTG 400
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
25-112 4.65e-07

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 50.08  E-value: 4.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  25 GCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPYtIEVGQKLKL--GGAKSSSITRKSTAKSTT 102
Cdd:PRK06347  391 GTSTSKPSTGTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKSDF-IYPGQKLKVsaGSTSNTNTSKPSTNTNTS 469

                          90
                  ....*....|
gi 1487549951 103 KTASVTPSSA 112
Cdd:PRK06347  470 KPSTNTNTNA 479
mltD PRK10783
membrane-bound lytic murein transglycosylase D; Provisional
 38-95 6.36e-07

membrane-bound lytic murein transglycosylase D; Provisional


Pssm-ID: 182727 [Multi-domain]  Cd Length: 456  Bit Score: 49.73  E-value: 6.36e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1487549951  38 SGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPyTIEVGQKLKLGGA--------KSSSITRK 95
Cdd:PRK10783  342 NSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGS-KLKVGQTLTIGAGssaqrlanNSDSITYR 406
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
25-126 1.58e-06

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 48.54  E-value: 1.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  25 GCSGSKSSDTGTYSGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPyTIEVGQKLKLGGAKSSSITrkstakSTTKT 104
Cdd:PRK06347  465 NTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSD-FIYPGQKLKVSAGSTTNNT------NTAKP 537

                          90       100
                  ....*....|....*....|..
gi 1487549951 105 ASVTPSSAVPKSSWPPVGQRCW 126
Cdd:PRK06347  538 STNKPSNSTVKTYTVKKGDSLW 559
PRK13914 PRK13914
invasion associated endopeptidase;
38-121 1.63e-04

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 42.48  E-value: 1.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487549951  38 SGSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPyTIEVGQKLKLggaksssitrKSTAKSTTKTASV-TPSSAVPKS 116
Cdd:PRK13914  198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSS-SIYVGQKLAI----------KQTANTATPKAEVkTEAPAAEKQ 266


                  ....*
gi 1487549951 117 SWPPV 121
Cdd:PRK13914  267 AAPVV 271
PRK06347 PRK06347
1,4-beta-N-acetylmuramoylhydrolase;
27-84 3.55e-03

1,4-beta-N-acetylmuramoylhydrolase;


Pssm-ID: 180536 [Multi-domain]  Cd Length: 592  Bit Score: 38.52  E-value: 3.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487549951  27 SGSKSSDTGTysgSVYTVKRGDTLYRISRTTGTSVKELARLNGISPPyTIEVGQKLKL 84
Cdd:PRK06347  538 STNKPSNSTV---KTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSN-MIHVGQKLTI 591
 
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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