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Conserved domains on  [gi|1232713478|gb|OYZ42459.1|]
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hypothetical protein B7Y18_00650 [Thiotrichales bacterium 24-47-4]

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
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
56-171 6.96e-27

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


:

Pssm-ID: 442342  Cd Length: 138  Bit Score: 98.83  E-value: 6.96e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  56 AYRQICHVMRDVKADQASVIDVRLLDIMDGIRVALtqaGVLNPtFLVHSAFRTWQTNREV-----GGALQSYHMKGQAID 130
Cdd:COG3108    19 ALKRLNFFLRDWRTNEVAPIDPRLLDLLWALRRRL---GSPEP-IQIISGYRSPATNAMLrrrsrGVAKNSLHMLGKAAD 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1232713478 131 FHIPGVPTDVLFSWMKQVKFhegVGMGFYGGTpNWMHLDSR 171
Cdd:COG3108    95 IRIPGVSLSQLRRAALALGR---GGVGYYPRS-GFVHVDTG 131
 
Name Accession Description Interval E-value
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
56-171 6.96e-27

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


Pssm-ID: 442342  Cd Length: 138  Bit Score: 98.83  E-value: 6.96e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  56 AYRQICHVMRDVKADQASVIDVRLLDIMDGIRVALtqaGVLNPtFLVHSAFRTWQTNREV-----GGALQSYHMKGQAID 130
Cdd:COG3108    19 ALKRLNFFLRDWRTNEVAPIDPRLLDLLWALRRRL---GSPEP-IQIISGYRSPATNAMLrrrsrGVAKNSLHMLGKAAD 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1232713478 131 FHIPGVPTDVLFSWMKQVKFhegVGMGFYGGTpNWMHLDSR 171
Cdd:COG3108    95 IRIPGVSLSQLRRAALALGR---GGVGYYPRS-GFVHVDTG 131
Peptidase_M15_2 pfam05951
Bacterial protein of unknown function (DUF882); This family consists of a series of ...
 29-137 1.29e-18

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: 77.87  E-value: 1.29e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  29 RWLNLKRPQSGEVLSVVYKRNGVLDERAYRQICHVMRDVKADQASVIDVRLLDIMDGIRVALTQAGvlnpTFLVHSAFRT 108
Cdd:pfam05951   6 RELKLYNIHTGEKAEITYKRNGRYVSDGLKRLNHLLRDWRRNEPHRMDPRLFDLLWQVYRSLGSRD----YIHVVSGYRS 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1232713478 109 WQTN-----REVGGALQSYHMKGQAIDFHIPGVP 137
Cdd:pfam05951  82 PATNamlrsRSKGVAKKSYHMLGKAMDFRIPGVP 115
Zn-DD-carboxypeptidase_like cd14844
Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala ...
 66-170 4.89e-13

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: 62.00  E-value: 4.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  66 DVKADQASVIDVRLLDIMDGIRVALtqaGVLNPtFLVHSAFRTWQTN-----REVGGALQSYHMKGQAIDFHIPGVPtdv 140
Cdd:cd14844     1 DFRTAEARRIDPRLMDQLYALRHKL---GSDKP-IQIISGYRSPKTNamlrkTSGGVAKKSLHMYGQAIDIRLPGVS--- 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 1232713478 141 LFSWMKQVKFHEGVGMGFYGGTpNWMHLDS 170
Cdd:cd14844    74 LAHLRKAAGFLEIGGVGYYPHS-DFVHIDT 102
 
Name Accession Description Interval E-value
YcbK COG3108
Uncharacterized conserved protein YcbK, DUF882 family [Function unknown];
56-171 6.96e-27

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


Pssm-ID: 442342  Cd Length: 138  Bit Score: 98.83  E-value: 6.96e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  56 AYRQICHVMRDVKADQASVIDVRLLDIMDGIRVALtqaGVLNPtFLVHSAFRTWQTNREV-----GGALQSYHMKGQAID 130
Cdd:COG3108    19 ALKRLNFFLRDWRTNEVAPIDPRLLDLLWALRRRL---GSPEP-IQIISGYRSPATNAMLrrrsrGVAKNSLHMLGKAAD 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1232713478 131 FHIPGVPTDVLFSWMKQVKFhegVGMGFYGGTpNWMHLDSR 171
Cdd:COG3108    95 IRIPGVSLSQLRRAALALGR---GGVGYYPRS-GFVHVDTG 131
Peptidase_M15_2 pfam05951
Bacterial protein of unknown function (DUF882); This family consists of a series of ...
 29-137 1.29e-18

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: 77.87  E-value: 1.29e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  29 RWLNLKRPQSGEVLSVVYKRNGVLDERAYRQICHVMRDVKADQASVIDVRLLDIMDGIRVALTQAGvlnpTFLVHSAFRT 108
Cdd:pfam05951   6 RELKLYNIHTGEKAEITYKRNGRYVSDGLKRLNHLLRDWRRNEPHRMDPRLFDLLWQVYRSLGSRD----YIHVVSGYRS 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1232713478 109 WQTN-----REVGGALQSYHMKGQAIDFHIPGVP 137
Cdd:pfam05951  82 PATNamlrsRSKGVAKKSYHMLGKAMDFRIPGVP 115
Peptidase_M15_3 pfam08291
Peptidase M15;
69-169 2.32e-13

Peptidase M15;


Pssm-ID: 429903  Cd Length: 109  Bit Score: 63.14  E-value: 2.32e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  69 ADQASVIDVRLLDIMDGIRVALTQAGVLNptflvhSAFRTWQTNREVGGALQSYHMKGQAIDFHIPGVPTDVLFSWMKQV 148
Cdd:pfam08291  19 CDNAPTAIVKLLAKLQAVRAHYGLPIVVT------SGYRSSVVNRRVGGASQSQHLTGLAADITVGGVNFEELAQILRNA 92

                          90       100
                  ....*....|....*....|.
gi 1232713478 149 KFHegvGMGFYGGTpNWMHLD 169
Cdd:pfam08291  93 GPT---GVGIYRHN-RFVHVD 109
Zn-DD-carboxypeptidase_like cd14844
Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase; The zinc D-Ala-D-Ala ...
 66-170 4.89e-13

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: 62.00  E-value: 4.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232713478  66 DVKADQASVIDVRLLDIMDGIRVALtqaGVLNPtFLVHSAFRTWQTN-----REVGGALQSYHMKGQAIDFHIPGVPtdv 140
Cdd:cd14844     1 DFRTAEARRIDPRLMDQLYALRHKL---GSDKP-IQIISGYRSPKTNamlrkTSGGVAKKSLHMYGQAIDIRLPGVS--- 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 1232713478 141 LFSWMKQVKFHEGVGMGFYGGTpNWMHLDS 170
Cdd:cd14844    74 LAHLRKAAGFLEIGGVGYYPHS-DFVHIDT 102
 
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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