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Conserved domains on  [gi|1308675547|gb|PKM47458|]
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zinc ribbon domain-containing protein [Firmicutes bacterium HGW-Firmicutes-8]

Protein Classification

zinc ribbon domain-containing protein( domain architecture ID 10021090)

zinc ribbon domain-containing protein similar to Methylophilus methylotrophus regulatory protein FmdB that may be a positive regulator of formamidase

Gene Ontology:  GO:0008270
PubMed:  32851833

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CxxC_CxxC_SSSS TIGR02605
putative regulatory protein, FmdB family; This model represents a region of about 50 amino ...
 1-51 2.80e-12

putative regulatory protein, FmdB family; This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors. [Regulatory functions, DNA interactions]


:

Pssm-ID: 274226  Cd Length: 52  Bit Score: 55.04  E-value: 2.80e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQLFTPFAVTVKSG 51
Cdd:TIGR02605  1 MPIYEYRCTACGHRFEVLQKMSDDPLATCPACGGTKLRRLLSAAGFALKGS 51
 
Name Accession Description Interval E-value
CxxC_CxxC_SSSS TIGR02605
putative regulatory protein, FmdB family; This model represents a region of about 50 amino ...
 1-51 2.80e-12

putative regulatory protein, FmdB family; This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors. [Regulatory functions, DNA interactions]


Pssm-ID: 274226  Cd Length: 52  Bit Score: 55.04  E-value: 2.80e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQLFTPFAVTVKSG 51
Cdd:TIGR02605  1 MPIYEYRCTACGHRFEVLQKMSDDPLATCPACGGTKLRRLLSAAGFALKGS 51
COG2331 COG2331
Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction ...
 1-65 6.59e-12

Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only];


Pssm-ID: 441902  Cd Length: 77  Bit Score: 54.67  E-value: 6.59e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDsSSVQQLFTPFAVTVKSGDSHSCDLSCGSKTK 65
Cdd:COG2331    1 MPIYEYRCESCGHEFEVLQKMSDDPLTVCPECG-GPLRRLISAPGFVFKGSGFYVTDSRSGSKKS 64
Zn-ribbon_8 pfam09723
Zinc ribbon domain; This entry represents a region of about 41 amino acids found in a number ...
 1-41 5.22e-10

Zinc ribbon domain; This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.


Pssm-ID: 462856  Cd Length: 41  Bit Score: 48.75  E-value: 5.22e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQLF 41
Cdd:pfam09723  1 MPIYEYRCEECGHEFEVLQKISDPPLTTCPECGSGDVRRLI 41
CxxC_CXXC_SSSS smart00834
Putative regulatory protein; CxxC_CXXC_SSSS represents a region of about 41 amino acids found ...
 1-40 4.09e-09

Putative regulatory protein; CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.


Pssm-ID: 197903  Cd Length: 41  Bit Score: 46.78  E-value: 4.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1308675547   1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQL 40
Cdd:smart00834  1 MPIYEYRCEDCGHTFEVLQKISDDPLTTCPECGGDVRRLI 40
 
Name Accession Description Interval E-value
CxxC_CxxC_SSSS TIGR02605
putative regulatory protein, FmdB family; This model represents a region of about 50 amino ...
 1-51 2.80e-12

putative regulatory protein, FmdB family; This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors. [Regulatory functions, DNA interactions]


Pssm-ID: 274226  Cd Length: 52  Bit Score: 55.04  E-value: 2.80e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQLFTPFAVTVKSG 51
Cdd:TIGR02605  1 MPIYEYRCTACGHRFEVLQKMSDDPLATCPACGGTKLRRLLSAAGFALKGS 51
COG2331 COG2331
Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction ...
 1-65 6.59e-12

Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only];


Pssm-ID: 441902  Cd Length: 77  Bit Score: 54.67  E-value: 6.59e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDsSSVQQLFTPFAVTVKSGDSHSCDLSCGSKTK 65
Cdd:COG2331    1 MPIYEYRCESCGHEFEVLQKMSDDPLTVCPECG-GPLRRLISAPGFVFKGSGFYVTDSRSGSKKS 64
Zn-ribbon_8 pfam09723
Zinc ribbon domain; This entry represents a region of about 41 amino acids found in a number ...
 1-41 5.22e-10

Zinc ribbon domain; This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.


Pssm-ID: 462856  Cd Length: 41  Bit Score: 48.75  E-value: 5.22e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1308675547  1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQLF 41
Cdd:pfam09723  1 MPIYEYRCEECGHEFEVLQKISDPPLTTCPECGSGDVRRLI 41
CxxC_CXXC_SSSS smart00834
Putative regulatory protein; CxxC_CXXC_SSSS represents a region of about 41 amino acids found ...
 1-40 4.09e-09

Putative regulatory protein; CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.


Pssm-ID: 197903  Cd Length: 41  Bit Score: 46.78  E-value: 4.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1308675547   1 MPAYDFRCKRCENKFTVRISISERDKVRCPECDSSSVQQL 40
Cdd:smart00834  1 MPIYEYRCEDCGHTFEVLQKISDDPLTTCPECGGDVRRLI 40
 
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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