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Conserved domains on  [gi|328809840|gb|AEB44012|]
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putative muramoyl-pentapeptide carboxypeptidase [Micromonospora maris AB-18-032]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_M15_3 super family cl42048
Peptidase M15;
123-234 3.37e-33

Peptidase M15;


The actual alignment was detected with superfamily member pfam08291:

Pssm-ID: 455393  Cd Length: 109  Bit Score: 116.30  E-value: 3.37e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840  123 FSYAEWNRCNSDWSGGAVSASTArfnALVSMWKLQAMRRAMGnAPLYLSSGFRSYSCNSAVGGASNSRHLYGDGIDL-VG 201
Cdd:pfam08291   3 FTYAELARSDGAVRQGCDNAPTA---IVKLLAKLQAVRAHYG-LPIVVTSGYRSSVVNRRVGGASQSQHLTGLAADItVG 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 328809840  202 SHSFCALAQQARNHGFTnilGPGYPGHNDHTHL 234
Cdd:pfam08291  79 GVNFEELAQILRNAGPT---GVGIYRHNRFVHV 108
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 45-112 7.60e-20

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 80.34  E-value: 7.60e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328809840  45 RTLSSGMTGEDVRQLQIRVSGYpGYgAVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQTFNQIYA 112
Cdd:COG3409    4 PTLRLGDSGEDVRELQQRLNAL-GY-YPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALRA 69
 
Name Accession Description Interval E-value
Peptidase_M15_3 pfam08291
Peptidase M15;
123-234 3.37e-33

Peptidase M15;


Pssm-ID: 429903  Cd Length: 109  Bit Score: 116.30  E-value: 3.37e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840  123 FSYAEWNRCNSDWSGGAVSASTArfnALVSMWKLQAMRRAMGnAPLYLSSGFRSYSCNSAVGGASNSRHLYGDGIDL-VG 201
Cdd:pfam08291   3 FTYAELARSDGAVRQGCDNAPTA---IVKLLAKLQAVRAHYG-LPIVVTSGYRSSVVNRRVGGASQSQHLTGLAADItVG 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 328809840  202 SHSFCALAQQARNHGFTnilGPGYPGHNDHTHL 234
Cdd:pfam08291  79 GVNFEELAQILRNAGPT---GVGIYRHNRFVHV 108
Zn-DD-carboxypeptidase_like cd14844
Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala ...
 140-242 1.54e-29

Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala carboxypeptidase (Streptomyces-type) (also known as D-alanyl-D-alanine hydrolase; D-alanyl-D-alanine-cleaving carboxypeptidase; DD-carboxypeptidase; DD-carboxypeptidase-transpeptidase; Zn2+ G peptidase; G enzyme; EC 3.4.17.14) is a zinc enzyme that belongs to the peptidase M15 subfamily A. The enzyme catalyzes carboxypeptidation but not transpeptidation reactions involved in bacterial cell wall metabolism. Its specificity with substrates of the type Xaa-Yaa-Zaa shows that the enzyme requires the substrate N-terminus to be blocked and C-terminus to be free, and Yaa and Zaa should be in the D-configuration. It is weakly inhibited by beta-lactams most likely caused by the enzyme active site geometry.


Pssm-ID: 350619  Cd Length: 108  Bit Score: 107.07  E-value: 1.54e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840 140 VSASTARFNALVSMWKLQAMRRAMGN-APLYLSSGFRSYSCNSAV-----GGASNSRHLYGDGIDLvgSHSFCALAQQAR 213
Cdd:cd14844    2 FRTAEARRIDPRLMDQLYALRHKLGSdKPIQIISGYRSPKTNAMLrktsgGVAKKSLHMYGQAIDI--RLPGVSLAHLRK 79

                         90       100
                 ....*....|....*....|....*....
gi 328809840 214 NHGFTNILGPGYPGHNDHTHLGNTPSRSW 242
Cdd:cd14844   80 AAGFLEIGGVGYYPHSDFVHIDTGPVRFW 108
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 45-112 7.60e-20

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 80.34  E-value: 7.60e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328809840  45 RTLSSGMTGEDVRQLQIRVSGYpGYgAVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQTFNQIYA 112
Cdd:COG3409    4 PTLRLGDSGEDVRELQQRLNAL-GY-YPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALRA 69
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 52-110 2.91e-16

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 70.62  E-value: 2.91e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 328809840   52 TGEDVRQLQIRVSGYpGYGaVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQTFNQI 110
Cdd:pfam01471   1 SGEDVKELQRYLNRL-GYY-PGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
155-244 5.16e-09

Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];


Pssm-ID: 442342  Cd Length: 138  Bit Score: 53.38  E-value: 5.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840 155 KLQAMRRAMG-NAPLYLSSGFRSYSCNSAV-----GGASNSRHLYGDGIDL-VGSHSFCALAQQARNHGFTnilGPGYPG 227
Cdd:COG3108   45 LLWALRRRLGsPEPIQIISGYRSPATNAMLrrrsrGVAKNSLHMLGKAADIrIPGVSLSQLRRAALALGRG---GVGYYP 121

                         90
                 ....*....|....*..
gi 328809840 228 HNDHTHLGNTPSRSWSA 244
Cdd:COG3108  122 RSGFVHVDTGPVRSWGG 138
PRK10594 PRK10594
murein L,D-transpeptidase; Provisional
 49-106 4.95e-03

murein L,D-transpeptidase; Provisional


Pssm-ID: 236723 [Multi-domain]  Cd Length: 608  Bit Score: 37.79  E-value: 4.95e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 328809840  49 SGMTGEDVRQLQIRVSGYPGYGAVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQT 106
Cdd:PRK10594 279 SAVTVETAETKPMDKQTTSRSKPAPAVRAAYDNELVEAVKRFQAWQGLGADGVIGPRT 336
 
Name Accession Description Interval E-value
Peptidase_M15_3 pfam08291
Peptidase M15;
123-234 3.37e-33

Peptidase M15;


Pssm-ID: 429903  Cd Length: 109  Bit Score: 116.30  E-value: 3.37e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840  123 FSYAEWNRCNSDWSGGAVSASTArfnALVSMWKLQAMRRAMGnAPLYLSSGFRSYSCNSAVGGASNSRHLYGDGIDL-VG 201
Cdd:pfam08291   3 FTYAELARSDGAVRQGCDNAPTA---IVKLLAKLQAVRAHYG-LPIVVTSGYRSSVVNRRVGGASQSQHLTGLAADItVG 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 328809840  202 SHSFCALAQQARNHGFTnilGPGYPGHNDHTHL 234
Cdd:pfam08291  79 GVNFEELAQILRNAGPT---GVGIYRHNRFVHV 108
Zn-DD-carboxypeptidase_like cd14844
Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala ...
 140-242 1.54e-29

Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala carboxypeptidase (Streptomyces-type) (also known as D-alanyl-D-alanine hydrolase; D-alanyl-D-alanine-cleaving carboxypeptidase; DD-carboxypeptidase; DD-carboxypeptidase-transpeptidase; Zn2+ G peptidase; G enzyme; EC 3.4.17.14) is a zinc enzyme that belongs to the peptidase M15 subfamily A. The enzyme catalyzes carboxypeptidation but not transpeptidation reactions involved in bacterial cell wall metabolism. Its specificity with substrates of the type Xaa-Yaa-Zaa shows that the enzyme requires the substrate N-terminus to be blocked and C-terminus to be free, and Yaa and Zaa should be in the D-configuration. It is weakly inhibited by beta-lactams most likely caused by the enzyme active site geometry.


Pssm-ID: 350619  Cd Length: 108  Bit Score: 107.07  E-value: 1.54e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840 140 VSASTARFNALVSMWKLQAMRRAMGN-APLYLSSGFRSYSCNSAV-----GGASNSRHLYGDGIDLvgSHSFCALAQQAR 213
Cdd:cd14844    2 FRTAEARRIDPRLMDQLYALRHKLGSdKPIQIISGYRSPKTNAMLrktsgGVAKKSLHMYGQAIDI--RLPGVSLAHLRK 79

                         90       100
                 ....*....|....*....|....*....
gi 328809840 214 NHGFTNILGPGYPGHNDHTHLGNTPSRSW 242
Cdd:cd14844   80 AAGFLEIGGVGYYPHSDFVHIDTGPVRFW 108
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 45-112 7.60e-20

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 80.34  E-value: 7.60e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328809840  45 RTLSSGMTGEDVRQLQIRVSGYpGYgAVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQTFNQIYA 112
Cdd:COG3409    4 PTLRLGDSGEDVRELQQRLNAL-GY-YPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALRA 69
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 52-110 2.91e-16

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 70.62  E-value: 2.91e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 328809840   52 TGEDVRQLQIRVSGYpGYGaVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQTFNQI 110
Cdd:pfam01471   1 SGEDVKELQRYLNRL-GYY-PGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
YcbB COG2989
Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];
44-110 8.76e-10

Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442228 [Multi-domain]  Cd Length: 529  Bit Score: 58.42  E-value: 8.76e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 328809840  44 GRTLSSGMTGEDVRQLQ--IRVSGYPGYGAVlTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQTFNQI 110
Cdd:COG2989  201 GPTLRPGDSDPRVPALRerLAALGDLPADAP-SDSDVYDAELVEAVKRFQARHGLKADGVIGPATLAAL 268
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
155-244 5.16e-09

Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];


Pssm-ID: 442342  Cd Length: 138  Bit Score: 53.38  E-value: 5.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840 155 KLQAMRRAMG-NAPLYLSSGFRSYSCNSAV-----GGASNSRHLYGDGIDL-VGSHSFCALAQQARNHGFTnilGPGYPG 227
Cdd:COG3108   45 LLWALRRRLGsPEPIQIISGYRSPATNAMLrrrsrGVAKNSLHMLGKAADIrIPGVSLSQLRRAALALGRG---GVGYYP 121

                         90
                 ....*....|....*..
gi 328809840 228 HNDHTHLGNTPSRSWSA 244
Cdd:COG3108  122 RSGFVHVDTGPVRSWGG 138
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 153-233 2.30e-06

Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins; This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism.


Pssm-ID: 350615 [Multi-domain]  Cd Length: 111  Bit Score: 45.12  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328809840 153 MWKLQAMRRAMG--NAPLYLSSGFRSYSCNSAVGGA--------------SNSRHLYGDGIDL------VGSHSFCALAQ 210
Cdd:cd14814    4 AEALARMIAAAGaeGRTLTINSGYRTYAQQLRLFAAkgkgsggrrwaappGTSNHQWGLAIDLgdgggwRETQGYRWLKA 83

                         90       100
                 ....*....|....*....|....
gi 328809840 211 QARNHGFTNILGPGY-PGHNDHTH 233
Cdd:cd14814   84 NAPRYGFDNPGGARRgGAFQEPWH 107
PRK10594 PRK10594
murein L,D-transpeptidase; Provisional
 49-106 4.95e-03

murein L,D-transpeptidase; Provisional


Pssm-ID: 236723 [Multi-domain]  Cd Length: 608  Bit Score: 37.79  E-value: 4.95e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 328809840  49 SGMTGEDVRQLQIRVSGYPGYGAVLTLDGAYGPATRSAVIRFQQAYGLAADGVAGAQT 106
Cdd:PRK10594 279 SAVTVETAETKPMDKQTTSRSKPAPAVRAAYDNELVEAVKRFQAWQGLGADGVIGPRT 336
 
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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