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Conserved domains on  [gi|737547326|ref|WP_035520354|]
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N-acetylmuramoyl-L-alanine amidase [Glaesserella parasuis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PGRP super family cl02712
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 8-171 2.39e-45

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity.


The actual alignment was detected with superfamily member PHA00447:

Pssm-ID: 470657 [Multi-domain]  Cd Length: 142  Bit Score: 146.08  E-value: 2.39e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   8 IVIHCSATRNGKSLkqsgksSAEVIDSWHKQRGFKrlagavktfnshleHLGYHFVIDVDGTVETGRQVGEMGAHVKGHN 87
Cdd:PHA00447  13 IFVHCSATKPSMDV------GVREIRQWHKEQGWL--------------DVGYHFIIRRDGTVEEGRPEDVVGSHVKGYN 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326  88 LHSVGICVVGGITASGKNHAEFTEAQWHALHRLLRELEAKYPNAKIYGHRDLSPdrngdgtiapnewvKDCPCFDVWAWL 167
Cdd:PHA00447  73 SNSVGVCLVGGIDDKGKFDANFTPAQMQSLKSLLVTLKAKYPGAEIKAHHDVAP--------------KACPSFDLQRWL 138


                 ....
gi 737547326 168 DSEE 171
Cdd:PHA00447 139 KKNE 142
 
Name Accession Description Interval E-value
PHA00447 PHA00447
lysozyme
 8-171 2.39e-45

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 146.08  E-value: 2.39e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   8 IVIHCSATRNGKSLkqsgksSAEVIDSWHKQRGFKrlagavktfnshleHLGYHFVIDVDGTVETGRQVGEMGAHVKGHN 87
Cdd:PHA00447  13 IFVHCSATKPSMDV------GVREIRQWHKEQGWL--------------DVGYHFIIRRDGTVEEGRPEDVVGSHVKGYN 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326  88 LHSVGICVVGGITASGKNHAEFTEAQWHALHRLLRELEAKYPNAKIYGHRDLSPdrngdgtiapnewvKDCPCFDVWAWL 167
Cdd:PHA00447  73 SNSVGVCLVGGIDDKGKFDANFTPAQMQSLKSLLVTLKAKYPGAEIKAHHDVAP--------------KACPSFDLQRWL 138


                 ....
gi 737547326 168 DSEE 171
Cdd:PHA00447 139 KKNE 142
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 4-144 6.41e-18

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity.


Pssm-ID: 133475 [Multi-domain]  Cd Length: 126  Bit Score: 75.40  E-value: 6.41e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   4 PIRKIVIHCSATRNGKSLKQSgkssaevIDSWHkqrgfkrlagavktfNSHLEH---LGYHFVIDVDGTVETGRQVGEMG 80
Cdd:cd06583    1 PVKYVVIHHTANPNCYTAAAA-------VRYLQ---------------NYHMRGwsdISYHFLVGGDGRIYQGRGWNYVG 58

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 737547326  81 AHVKG-HNLHSVGICVVGgitasGKNHAEFTEAQWHALHRLLRELEAKY---PNAKIYGHRDLSPDRN 144
Cdd:cd06583   59 WHAGGnYNSYSIGIELIG-----NFDGGPPTAAQLEALAELLAYLVKRYgipPDYRIVGHRDVSPGTE 121
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 4-140 4.52e-15

N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.


Pssm-ID: 460236 [Multi-domain]  Cd Length: 122  Bit Score: 67.77  E-value: 4.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326    4 PIRKIVIHCSATRNGkslkqsgkSSAEVIDSWHKQRGFKRLagavktfnshlehlGYHFVIDVDGTVETGRQVGEMGAH- 82
Cdd:pfam01510   1 PIRYIVIHHTAGPSF--------AGALLPYAACIARGWSDV--------------SYHYLIDRDGTIYQLVPENGRAWHa 58

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 737547326   83 -VKGHNLHSVGICVVGGitasgKNHAEFTEAQWHALHRLLRELEAKY---PNAKIYGHRDLS 140
Cdd:pfam01510  59 gNGGGNDRSIGIELEGN-----FGGDPPTDAQYEALARLLADLCKRYgipPDRRIVGHRDVG 115
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 1-139 1.69e-13

Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine.


Pssm-ID: 128941  Cd Length: 142  Bit Score: 64.24  E-value: 1.69e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326     1 MTFPIRKIVIHCSATRNGKSLKQSgKSSAEVIDSWH-KQRGFKrlagavktfnshleHLGYHFVIDVDGTVETGRQVGEM 79
Cdd:smart00701  20 LTRPVRYVIIHHTATPNCYTDAQC-AQILRNIQAYHmEELGWC--------------DIGYNFLVGGDGKVYEGRGWNVV 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 737547326    80 GAHVKGHNLHSVGICVVGGITASGKNHAEFTEAQWHALHRLLR-ELEAKYpnaKIYGHRDL 139
Cdd:smart00701  85 GAHTGGYNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRgHLSPDY---KLVGHRQV 142
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
4-167 4.52e-11

N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442259  Cd Length: 167  Bit Score: 58.34  E-value: 4.52e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   4 PIRKIVIHCSATRNGkslkqsgkssaevidswhkqrgfkrlAGAVKTFNSHLEHLGYHFVIDVDGTV-----ETGR--QV 76
Cdd:COG3023   26 EIDLIVIHYTAGPPG--------------------------GGALDWLTDPALRVSAHYLIDRDGEIyqlvpEDDRawHA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326  77 GE-MGAHVKGHNLHSVGICVVGgitaSGKNHAEFTEAQWHALHRLLRELEAKYPNAK--IYGHRDLSPDRngdgtiapne 153
Cdd:COG3023   80 GVsSWRGRTNLNDFSIGIELEN----PGHGWAPFTEAQYEALAALLRDLCARYGIPPdhIVGHSDIAPGR---------- 145

                        170
                 ....*....|....*.
gi 737547326 154 wvKDCP--CFDvWAWL 167
Cdd:COG3023  146 --KTDPgpAFP-WARL 158
 
Name Accession Description Interval E-value
PHA00447 PHA00447
lysozyme
 8-171 2.39e-45

lysozyme


Pssm-ID: 177282 [Multi-domain]  Cd Length: 142  Bit Score: 146.08  E-value: 2.39e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   8 IVIHCSATRNGKSLkqsgksSAEVIDSWHKQRGFKrlagavktfnshleHLGYHFVIDVDGTVETGRQVGEMGAHVKGHN 87
Cdd:PHA00447  13 IFVHCSATKPSMDV------GVREIRQWHKEQGWL--------------DVGYHFIIRRDGTVEEGRPEDVVGSHVKGYN 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326  88 LHSVGICVVGGITASGKNHAEFTEAQWHALHRLLRELEAKYPNAKIYGHRDLSPdrngdgtiapnewvKDCPCFDVWAWL 167
Cdd:PHA00447  73 SNSVGVCLVGGIDDKGKFDANFTPAQMQSLKSLLVTLKAKYPGAEIKAHHDVAP--------------KACPSFDLQRWL 138


                 ....
gi 737547326 168 DSEE 171
Cdd:PHA00447 139 KKNE 142
PGRP cd06583
Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in ...
 4-144 6.41e-18

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity.


Pssm-ID: 133475 [Multi-domain]  Cd Length: 126  Bit Score: 75.40  E-value: 6.41e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   4 PIRKIVIHCSATRNGKSLKQSgkssaevIDSWHkqrgfkrlagavktfNSHLEH---LGYHFVIDVDGTVETGRQVGEMG 80
Cdd:cd06583    1 PVKYVVIHHTANPNCYTAAAA-------VRYLQ---------------NYHMRGwsdISYHFLVGGDGRIYQGRGWNYVG 58

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 737547326  81 AHVKG-HNLHSVGICVVGgitasGKNHAEFTEAQWHALHRLLRELEAKY---PNAKIYGHRDLSPDRN 144
Cdd:cd06583   59 WHAGGnYNSYSIGIELIG-----NFDGGPPTAAQLEALAELLAYLVKRYgipPDYRIVGHRDVSPGTE 121
Amidase_2 pfam01510
N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have ...
 4-140 4.52e-15

N-acetylmuramoyl-L-alanine amidase; This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.


Pssm-ID: 460236 [Multi-domain]  Cd Length: 122  Bit Score: 67.77  E-value: 4.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326    4 PIRKIVIHCSATRNGkslkqsgkSSAEVIDSWHKQRGFKRLagavktfnshlehlGYHFVIDVDGTVETGRQVGEMGAH- 82
Cdd:pfam01510   1 PIRYIVIHHTAGPSF--------AGALLPYAACIARGWSDV--------------SYHYLIDRDGTIYQLVPENGRAWHa 58

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 737547326   83 -VKGHNLHSVGICVVGGitasgKNHAEFTEAQWHALHRLLRELEAKY---PNAKIYGHRDLS 140
Cdd:pfam01510  59 gNGGGNDRSIGIELEGN-----FGGDPPTDAQYEALARLLADLCKRYgipPDRRIVGHRDVG 115
PGRP smart00701
Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The ...
 1-139 1.69e-13

Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme; The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine.


Pssm-ID: 128941  Cd Length: 142  Bit Score: 64.24  E-value: 1.69e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326     1 MTFPIRKIVIHCSATRNGKSLKQSgKSSAEVIDSWH-KQRGFKrlagavktfnshleHLGYHFVIDVDGTVETGRQVGEM 79
Cdd:smart00701  20 LTRPVRYVIIHHTATPNCYTDAQC-AQILRNIQAYHmEELGWC--------------DIGYNFLVGGDGKVYEGRGWNVV 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 737547326    80 GAHVKGHNLHSVGICVVGGITASGKNHAEFTEAQWHALHRLLR-ELEAKYpnaKIYGHRDL 139
Cdd:smart00701  85 GAHTGGYNDISLGIAFIGNFTDKLPTDAALDAAQDLLACAVQRgHLSPDY---KLVGHRQV 142
Ami_2 smart00644
Ami_2 domain;
4-143 3.12e-12

Ami_2 domain;


Pssm-ID: 214760 [Multi-domain]  Cd Length: 126  Bit Score: 60.45  E-value: 3.12e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326     4 PIRKIVIHCSATRNgkslkqsgkSSAEVIDSWHkqrgfkrlagavktFNSHLEHLGYHFVIDVDGTVETGRQVGE----- 78
Cdd:smart00644   2 PPRGIVIHHTANSN---------ASCANEARYM--------------QNNHMNDIGYHFLVGGDGRVYQGVGWNYvawha 58

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 737547326    79 MGAHVKGHNLHSVGICVVGGITasgKNHAEFTEAQWHALHRLLRELEAKYP----NAKIYGHRDLSPDR 143
Cdd:smart00644  59 GGAHTPGYNDISIGIEFIGSFD---SDDEPFAEALYAALDLLAKLLKGAGLppdgRYRIVGHRDVAPTE 124
AmpD COG3023
N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];
4-167 4.52e-11

N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442259  Cd Length: 167  Bit Score: 58.34  E-value: 4.52e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326   4 PIRKIVIHCSATRNGkslkqsgkssaevidswhkqrgfkrlAGAVKTFNSHLEHLGYHFVIDVDGTV-----ETGR--QV 76
Cdd:COG3023   26 EIDLIVIHYTAGPPG--------------------------GGALDWLTDPALRVSAHYLIDRDGEIyqlvpEDDRawHA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737547326  77 GE-MGAHVKGHNLHSVGICVVGgitaSGKNHAEFTEAQWHALHRLLRELEAKYPNAK--IYGHRDLSPDRngdgtiapne 153
Cdd:COG3023   80 GVsSWRGRTNLNDFSIGIELEN----PGHGWAPFTEAQYEALAALLRDLCARYGIPPdhIVGHSDIAPGR---------- 145

                        170
                 ....*....|....*.
gi 737547326 154 wvKDCP--CFDvWAWL 167
Cdd:COG3023  146 --KTDPgpAFP-WARL 158
PRK11789 PRK11789
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;
98-165 2.31e-05

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD;


Pssm-ID: 236984  Cd Length: 185  Bit Score: 42.87  E-value: 2.31e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 737547326  98 GITASGKNHAEFTEAQWHALHRLLRELEAKYP--NAKIYGHRDLSPDRNGD-GtiapnewvkdcPCFDvWA 165
Cdd:PRK11789 116 GIELEGTDTLPFTDAQYQALAALTRALRAAYPiiAERITGHSDIAPGRKTDpG-----------PAFD-WQ 174
 
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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