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Conserved domains on  [gi|907034721|emb|CTM89053|]
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LysM domain-containing protein [Streptococcus pneumoniae]

Protein Classification

LysM peptidoglycan-binding domain-containing protein( domain architecture ID 10061503)

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
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 47-90 8.79e-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: 8.79e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 907034721  47 TSYTVQYGDTLSTIAEALGVDVTVLANLNKITNMDLIFPETVLT 90
Cdd:cd00118    1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLK 44
rne super family cl35953
ribonuclease E; Reviewed
 85-240 6.12e-09

ribonuclease E; Reviewed


The actual alignment was detected with superfamily member PRK10811:

Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 57.74  E-value: 6.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721   85 PETVLTTTVNEAEEVTEVEIQTPQADSSEEVTTATADLTTNQVIVDDQTVQVADLSQPIAEAPKEVASSSEVTKTVIASE 164
Cdd:PRK10811  880 EPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADI 959

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 907034721  165 EVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEKQETQASPQAASAVEVTttssEAKEVASSNGATAAVSTYQPE 240
Cdd:PRK10811  960 EEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT----VEHNHATAPMTRAPAPEYVPE 1031
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 47-90 8.79e-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: 8.79e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 907034721  47 TSYTVQYGDTLSTIAEALGVDVTVLANLNKITNMDLIFPETVLT 90
Cdd:cd00118    1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLK 44
rne PRK10811
ribonuclease E; Reviewed
 85-240 6.12e-09

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 57.74  E-value: 6.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721   85 PETVLTTTVNEAEEVTEVEIQTPQADSSEEVTTATADLTTNQVIVDDQTVQVADLSQPIAEAPKEVASSSEVTKTVIASE 164
Cdd:PRK10811  880 EPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADI 959

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 907034721  165 EVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEKQETQASPQAASAVEVTttssEAKEVASSNGATAAVSTYQPE 240
Cdd:PRK10811  960 EEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT----VEHNHATAPMTRAPAPEYVPE 1031
LysM smart00257
Lysin motif;
49-90 2.18e-08

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 49.75  E-value: 2.18e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 907034721    49 YTVQYGDTLSTIAEALGVDVTVLANLNKITNMDLIFPETVLT 90
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLK 43
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 49-90 4.13e-08

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: 48.93  E-value: 4.13e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 907034721   49 YTVQYGDTLSTIAEALGVDVTVLANLNKITNmDLIFPETVLT 90
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSS-PNLYVGQKLK 41
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
41-90 3.54e-07

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 49.32  E-value: 3.54e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 907034721  41 TKTDNKTSYTVQYGDTLSTIAEALGVDVTVLANLNKITNmDLIFPETVLT 90
Cdd:COG1388  104 AAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLK 152
COG5373 COG5373
Uncharacterized membrane protein [Function unknown];
135-213 2.10e-03

Uncharacterized membrane protein [Function unknown];


Pssm-ID: 444140 [Multi-domain]  Cd Length: 854  Bit Score: 40.37  E-value: 2.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721 135 QVADLSQPIAEAPKEVASSSE-VTKTVIASEEVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEKQETQASPQAASAVE 213
Cdd:COG5373   29 RVEELEAELAEAAEAASAPAEpEPEAAAAATAAAPEAAPAPVPEAPAAPPAAAEAPAPAAAAPPAEAEPAAAPAAASSFE 108
 
Name Accession Description Interval E-value
LysM cd00118
Lysin Motif is a small domain involved in binding peptidoglycan; LysM, a small globular domain ...
 47-90 8.79e-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: 8.79e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 907034721  47 TSYTVQYGDTLSTIAEALGVDVTVLANLNKITNMDLIFPETVLT 90
Cdd:cd00118    1 KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLK 44
rne PRK10811
ribonuclease E; Reviewed
 85-240 6.12e-09

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 57.74  E-value: 6.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721   85 PETVLTTTVNEAEEVTEVEIQTPQADSSEEVTTATADLTTNQVIVDDQTVQVADLSQPIAEAPKEVASSSEVTKTVIASE 164
Cdd:PRK10811  880 EPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADI 959

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 907034721  165 EVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEKQETQASPQAASAVEVTttssEAKEVASSNGATAAVSTYQPE 240
Cdd:PRK10811  960 EEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT----VEHNHATAPMTRAPAPEYVPE 1031
LysM smart00257
Lysin motif;
49-90 2.18e-08

Lysin motif;


Pssm-ID: 197609 [Multi-domain]  Cd Length: 44  Bit Score: 49.75  E-value: 2.18e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 907034721    49 YTVQYGDTLSTIAEALGVDVTVLANLNKITNMDLIFPETVLT 90
Cdd:smart00257   2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLK 43
LysM pfam01476
LysM domain; The LysM (lysin motif) domain is about 40 residues long. It is found in a variety ...
 49-90 4.13e-08

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: 48.93  E-value: 4.13e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 907034721   49 YTVQYGDTLSTIAEALGVDVTVLANLNKITNmDLIFPETVLT 90
Cdd:pfam01476   1 YTVKKGDTLSSIAKRYGITVEQLAELNGLSS-PNLYVGQKLK 41
rne PRK10811
ribonuclease E; Reviewed
 104-260 2.05e-07

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 53.12  E-value: 2.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721  104 IQTPQADSSEEVTTATADLTTNQVIVDDQTVQVADLS-QPIAEAPKEVASSSEVTKTVIASEEVAPSTGTSVP-----EE 177
Cdd:PRK10811  847 VVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVsAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEViaapvTE 926

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721  178 QTA---ETSSAVAEEAPQETTPAEKQETQASPqAASAVEVTTTSSEAKEVASSNGATAAVSTYQPEETKIISTTYEAPAA 254
Cdd:PRK10811  927 QPQvitESDVAVAQEVAEHAEPVVEPQDETAD-IEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQ 1005


                  ....*.
gi 907034721  255 PDYAGL 260
Cdd:PRK10811 1006 VPEATV 1011
LysM COG1388
LysM repeat [Cell wall/membrane/envelope biogenesis];
41-90 3.54e-07

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


Pssm-ID: 440998 [Multi-domain]  Cd Length: 156  Bit Score: 49.32  E-value: 3.54e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 907034721  41 TKTDNKTSYTVQYGDTLSTIAEALGVDVTVLANLNKITNmDLIFPETVLT 90
Cdd:COG1388  104 AAAPSPVTYTVKKGDTLWSIARRYGVSVEELKRWNGLSS-DTIRPGQKLK 152
XkdP COG1652
Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion ...
 41-90 4.06e-04

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: 40.76  E-value: 4.06e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 907034721  41 TKTDNKTSYTVQYGDTLSTIAEAL---GVDVTVLANLNK--ITNMDLIFPETVLT 90
Cdd:COG1652  104 LAPDAPKTYTVKPGDTLWGIAKRFygdPARWPEIAEANRdqIKNPDLIYPGQVLR 158
rne PRK10811
ribonuclease E; Reviewed
 128-293 7.01e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 41.95  E-value: 7.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721  128 IVDDQTVQVADLSQPIAEAPKEVASSSEVTKTVIASEEVAP-STGTSVPEEQTAETSSAVAEEAPQETTPAEKQET--QA 204
Cdd:PRK10811  847 VVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVvEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAApvTE 926

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721  205 SPQAASAVEVTT---TSSEAKEVASSNGATAAVStyQPEETKIISTTyEAPAAPDYAGLAVAKSENAGLQPQTAAFKEEI 281
Cdd:PRK10811  927 QPQVITESDVAVaqeVAEHAEPVVEPQDETADIE--EAAETAEVVVA-EPEVVAQPAAPVVAEVAAEVETVTAVEPEVAP 1003

                         170
                  ....*....|..
gi 907034721  282 ANLFGITSFSGY 293
Cdd:PRK10811 1004 AQVPEATVEHNH 1015
PRK11907 PRK11907
bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase;
162-248 1.01e-03

bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase;


Pssm-ID: 237019 [Multi-domain]  Cd Length: 814  Bit Score: 41.38  E-value: 1.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721 162 ASEEVAPSTGTSVPEEQTAETSSAVAEEAPQETTP---AEKQETQASPQAASAVEVTTTSSEAKEVASSNGATAAVSTYQ 238
Cdd:PRK11907  28 AEEIVTTTPATSTEAEQTTPVESDATEEADNTETPvaaTTAAEAPSSSETAETSDPTSEATDTTTSEARTVTPAATETSK 107

                         90
                 ....*....|....*
gi 907034721 239 PEE-----TKIISTT 248
Cdd:PRK11907 108 PVEgqtvdVRILSTT 122
COG5373 COG5373
Uncharacterized membrane protein [Function unknown];
135-213 2.10e-03

Uncharacterized membrane protein [Function unknown];


Pssm-ID: 444140 [Multi-domain]  Cd Length: 854  Bit Score: 40.37  E-value: 2.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721 135 QVADLSQPIAEAPKEVASSSE-VTKTVIASEEVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEKQETQASPQAASAVE 213
Cdd:COG5373   29 RVEELEAELAEAAEAASAPAEpEPEAAAAATAAAPEAAPAPVPEAPAAPPAAAEAPAPAAAAPPAEAEPAAAPAAASSFE 108
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 143-229 5.57e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 38.64  E-value: 5.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721 143 IAEAPKEVASSSEVTKTVIASEEVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEKQETQASPQAASAVEVTTTSSEAK 222
Cdd:PRK14950 360 LVPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVD 439


                 ....*..
gi 907034721 223 EVASSNG 229
Cdd:PRK14950 440 EKPKYTP 446
PRK11907 PRK11907
bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase;
152-253 7.07e-03

bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase;


Pssm-ID: 237019 [Multi-domain]  Cd Length: 814  Bit Score: 38.68  E-value: 7.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721 152 SSSEVTKTVIASEEVAPSTGTSVPEEQTAETSSAVAEEA-PQETTPAEKQETQASPQAASAvEVTTTSSEAKEVASSNGA 230
Cdd:PRK11907   7 SKSAVALTLALLTASNPKLAQAEEIVTTTPATSTEAEQTtPVESDATEEADNTETPVAATT-AAEAPSSSETAETSDPTS 85

                         90       100
                 ....*....|....*....|...
gi 907034721 231 TAAVSTYQPEETKIISTTYEAPA 253
Cdd:PRK11907  86 EATDTTTSEARTVTPAATETSKP 108
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
134-276 7.12e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 38.68  E-value: 7.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 907034721 134 VQVADLSQPIAEAPKEVASSSEVTKtVIASEEVAPSTGTSVPEEQTAETSSAVAEEAPQETTPAEkqetqASPQAASAVE 213
Cdd:PRK07003 393 ASAVPAVTAVTGAAGAALAPKAAAA-AAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANAR-----ASADSRCDER 466

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 907034721 214 VTTTSSEAKEVASSNGATAAVSTYQPEETKIISTTYEAPAAPDYAGLAVAKSENAGLQPQTAA 276
Cdd:PRK07003 467 DAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPA 529
 
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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