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Conserved domains on  [gi|544679879|ref|WP_021112051|]
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YcbK family protein [Glaesserella parasuis]

Protein Classification

YcbK family protein( domain architecture ID 11459704)

YcbK family protein similar to Escherichia coli DUF882 domain-containing protein YcbK

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_M15_3 super family cl42048
Peptidase M15;
33-182 9.40e-64

Peptidase M15;


The actual alignment was detected with superfamily member pfam05951:

Pssm-ID: 455393  Cd Length: 152  Bit Score: 193.43  E-value: 9.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879   33 STPKPLILRLKRLSTGETLSANYHTNG-FVTKDLNRLNHIMRDVHINRIKRIDPKLFVKLTQIQARLGLRKsEILIVSGY 111
Cdd:pfam05951   1 AAAKPRELKLYNIHTGEKAEITYKRNGrYVSDGLKRLNHLLRDWRRNEPHRMDPRLFDLLWQVYRSLGSRD-YIHVVSGY 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544679879  112 RSAQTNARLRRRSRGVASNSYHILGKAIDFRIEGVPLARIKAAAESLNNGGVGYYPHSN--FVHVDTGPVRTW 182
Cdd:pfam05951  80 RSPATNAMLRSRSKGVAKKSYHMLGKAMDFRIPGVPLKKLREAAMSLQVGGVGYYPTSGspFVHVDVGPVRHW 152
 
Name Accession Description Interval E-value
Peptidase_M15_2 pfam05951
Bacterial protein of unknown function (DUF882); This family consists of a series of ...
 33-182 9.40e-64

Bacterial protein of unknown function (DUF882); This family consists of a series of hypothetical bacterial proteins of unknown function.


Pssm-ID: 428687  Cd Length: 152  Bit Score: 193.43  E-value: 9.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879   33 STPKPLILRLKRLSTGETLSANYHTNG-FVTKDLNRLNHIMRDVHINRIKRIDPKLFVKLTQIQARLGLRKsEILIVSGY 111
Cdd:pfam05951   1 AAAKPRELKLYNIHTGEKAEITYKRNGrYVSDGLKRLNHLLRDWRRNEPHRMDPRLFDLLWQVYRSLGSRD-YIHVVSGY 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544679879  112 RSAQTNARLRRRSRGVASNSYHILGKAIDFRIEGVPLARIKAAAESLNNGGVGYYPHSN--FVHVDTGPVRTW 182
Cdd:pfam05951  80 RSPATNAMLRSRSKGVAKKSYHMLGKAMDFRIPGVPLKKLREAAMSLQVGGVGYYPTSGspFVHVDVGPVRHW 152
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
59-184 4.72e-63

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


Pssm-ID: 442342  Cd Length: 138  Bit Score: 190.90  E-value: 4.72e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879  59 GFVTKDLNRLNHIMRDVHINRIKRIDPKLFVKLTQIQARLGLRKsEILIVSGYRSAQTNARLRRRSRGVASNSYHILGKA 138
Cdd:COG3108   14 AAAALALKRLNFFLRDWRTNEVAPIDPRLLDLLWALRRRLGSPE-PIQIISGYRSPATNAMLRRRSRGVAKNSLHMLGKA 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 544679879 139 IDFRIEGVPLARIKAAAESLNNGGVGYYPHSNFVHVDTGPVRTWRG 184
Cdd:COG3108   93 ADIRIPGVSLSQLRRAALALGRGGVGYYPRSGFVHVDTGPVRSWGG 138
Zn-DD-carboxypeptidase_like cd14844
Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala ...
 74-182 2.30e-46

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: 147.90  E-value: 2.30e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879  74 DVHINRIKRIDPKLFVKLTQIQARLGLRKSeILIVSGYRSAQTNARLRRRSRGVASNSYHILGKAIDFRIEGVPLARIKA 153
Cdd:cd14844    1 DFRTAEARRIDPRLMDQLYALRHKLGSDKP-IQIISGYRSPKTNAMLRKTSGGVAKKSLHMYGQAIDIRLPGVSLAHLRK 79

                         90       100
                 ....*....|....*....|....*....
gi 544679879 154 AAESLNNGGVGYYPHSNFVHVDTGPVRTW 182
Cdd:cd14844   80 AAGFLEIGGVGYYPHSDFVHIDTGPVRFW 108
 
Name Accession Description Interval E-value
Peptidase_M15_2 pfam05951
Bacterial protein of unknown function (DUF882); This family consists of a series of ...
 33-182 9.40e-64

Bacterial protein of unknown function (DUF882); This family consists of a series of hypothetical bacterial proteins of unknown function.


Pssm-ID: 428687  Cd Length: 152  Bit Score: 193.43  E-value: 9.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879   33 STPKPLILRLKRLSTGETLSANYHTNG-FVTKDLNRLNHIMRDVHINRIKRIDPKLFVKLTQIQARLGLRKsEILIVSGY 111
Cdd:pfam05951   1 AAAKPRELKLYNIHTGEKAEITYKRNGrYVSDGLKRLNHLLRDWRRNEPHRMDPRLFDLLWQVYRSLGSRD-YIHVVSGY 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544679879  112 RSAQTNARLRRRSRGVASNSYHILGKAIDFRIEGVPLARIKAAAESLNNGGVGYYPHSN--FVHVDTGPVRTW 182
Cdd:pfam05951  80 RSPATNAMLRSRSKGVAKKSYHMLGKAMDFRIPGVPLKKLREAAMSLQVGGVGYYPTSGspFVHVDVGPVRHW 152
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
59-184 4.72e-63

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


Pssm-ID: 442342  Cd Length: 138  Bit Score: 190.90  E-value: 4.72e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879  59 GFVTKDLNRLNHIMRDVHINRIKRIDPKLFVKLTQIQARLGLRKsEILIVSGYRSAQTNARLRRRSRGVASNSYHILGKA 138
Cdd:COG3108   14 AAAALALKRLNFFLRDWRTNEVAPIDPRLLDLLWALRRRLGSPE-PIQIISGYRSPATNAMLRRRSRGVAKNSLHMLGKA 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 544679879 139 IDFRIEGVPLARIKAAAESLNNGGVGYYPHSNFVHVDTGPVRTWRG 184
Cdd:COG3108   93 ADIRIPGVSLSQLRRAALALGRGGVGYYPRSGFVHVDTGPVRSWGG 138
Zn-DD-carboxypeptidase_like cd14844
Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala ...
 74-182 2.30e-46

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: 147.90  E-value: 2.30e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879  74 DVHINRIKRIDPKLFVKLTQIQARLGLRKSeILIVSGYRSAQTNARLRRRSRGVASNSYHILGKAIDFRIEGVPLARIKA 153
Cdd:cd14844    1 DFRTAEARRIDPRLMDQLYALRHKLGSDKP-IQIISGYRSPKTNAMLRKTSGGVAKKSLHMYGQAIDIRLPGVSLAHLRK 79

                         90       100
                 ....*....|....*....|....*....
gi 544679879 154 AAESLNNGGVGYYPHSNFVHVDTGPVRTW 182
Cdd:cd14844   80 AAGFLEIGGVGYYPHSDFVHIDTGPVRFW 108
Peptidase_M15_3 pfam08291
Peptidase M15;
85-175 4.53e-16

Peptidase M15;


Pssm-ID: 429903  Cd Length: 109  Bit Score: 70.07  E-value: 4.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544679879   85 PKLFVKLTQIQARLGLrksEILIVSGYRSAQTNarlrrRSRGVASNSYHILGKAIDFRIEGVPLARIKAAAESLNNGGVG 164
Cdd:pfam08291  27 VKLLAKLQAVRAHYGL---PIVVTSGYRSSVVN-----RRVGGASQSQHLTGLAADITVGGVNFEELAQILRNAGPTGVG 98

                          90
                  ....*....|.
gi 544679879  165 YYPHSNFVHVD 175
Cdd:pfam08291  99 IYRHNRFVHVD 109
L-Ala-D-Glu_peptidase_like cd14845
L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu ...
 78-143 6.63e-06

L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu peptidase family includes L-alanyl-D-glutamate peptidase (bacteriophage T5) (also known as L-alanoyl-D-glutamate endopeptidase), and Ply118 and Ply500 L-Ala-D-Glu peptidase. Bacteriophage endolysin degrades the peptidoglycan of the bacterial host from within, leading to cell lysis and release of progeny virions. The bacteriophage endolysin Ply118 cleaves between L-Ala and D-Glu residues of Listeria cell wall peptidoglycan. This family belongs to the MEROPS peptidase M15 subfamily C.


Pssm-ID: 350620 [Multi-domain]  Cd Length: 126  Bit Score: 43.50  E-value: 6.63e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544679879  78 NRIKRIDPKLFVKLTQIQARLGLRKSEILIVSGYRSAQTNARLRRRSRGV---------ASNSYHILGKAIDFRI 143
Cdd:cd14845    3 RRIAGLHPEVRAVVKELIELAEEEGIDFRITEGYRSPARQAALYAQGRTKpglivtnarGGQSYHNYGLAVDIVP 77
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 85-141 3.69e-03

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: 35.49  E-value: 3.69e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544679879  85 PKLFVKLTQIQARLGLRKSEILIVSGYRS-------AQTNARLRRRSRGVA--SNSYHILGKAIDF 141
Cdd:cd14814    1 PDAAEALARMIAAAGAEGRTLTINSGYRTyaqqlrlFAAKGKGSGGRRWAAppGTSNHQWGLAIDL 66
 
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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