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Conserved domains on  [gi|931374052|gb|KPJ64928|]
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hypothetical protein AMK68_00025 [candidate division KD3-62 bacterium DG_56]

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 ...
 1-47 9.78e-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: 54.27  E-value: 9.78e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 931374052   1 MPVFEYRCHACGRRFAWLEGvVDDRTKPACPHCGGTDIKRLISRFAV 47
Cdd:TIGR02605  1 MPIYEYRCTACGHRFEVLQK-MSDDPLATCPACGGTKLRRLLSAAGF 46
 
Name Accession Description Interval E-value
CxxC_CxxC_SSSS TIGR02605
putative regulatory protein, FmdB family; This model represents a region of about 50 amino ...
 1-47 9.78e-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: 54.27  E-value: 9.78e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 931374052   1 MPVFEYRCHACGRRFAWLEGvVDDRTKPACPHCGGTDIKRLISRFAV 47
Cdd:TIGR02605  1 MPIYEYRCTACGHRFEVLQK-MSDDPLATCPACGGTKLRRLLSAAGF 46
COG2331 COG2331
Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction ...
 1-50 4.02e-10

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


Pssm-ID: 441902  Cd Length: 77  Bit Score: 50.81  E-value: 4.02e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 931374052  1 MPVFEYRCHACGRRFAWLEGVVDDRTKpACPHCGGtDIKRLISRFAVSRS 50
Cdd:COG2331   1 MPIYEYRCESCGHEFEVLQKMSDDPLT-VCPECGG-PLRRLISAPGFVFK 48
Zn-ribbon_8 pfam09723
Zinc ribbon domain; This entry represents a region of about 41 amino acids found in a number ...
 1-42 1.59e-09

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: 48.37  E-value: 1.59e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 931374052   1 MPVFEYRCHACGRRFawlEGVV--DDRTKPACPHCGGTDIKRLI 42
Cdd:pfam09723  1 MPIYEYRCEECGHEF---EVLQkiSDPPLTTCPECGSGDVRRLI 41
CxxC_CXXC_SSSS smart00834
Putative regulatory protein; CxxC_CXXC_SSSS represents a region of about 41 amino acids found ...
 1-43 1.22e-07

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: 43.31  E-value: 1.22e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 931374052    1 MPVFEYRCHACGRRFAWLEGVVDDrTKPACPHCGGtDIKRLIS 43
Cdd:smart00834  1 MPIYEYRCEDCGHTFEVLQKISDD-PLTTCPECGG-DVRRLIS 41
PRK07111 PRK07111
anaerobic ribonucleoside triphosphate reductase; Provisional
 7-44 8.75e-04

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 235937 [Multi-domain]  Cd Length: 735  Bit Score: 36.08  E-value: 8.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 931374052   7 RCHACGrrfawLEGVVDDrtkpACPHCGGTDIKRlISR 44
Cdd:PRK07111 682 RCPVCG-----YLGVIED----KCPKCGSTNIQR-IRR 709
 
Name Accession Description Interval E-value
CxxC_CxxC_SSSS TIGR02605
putative regulatory protein, FmdB family; This model represents a region of about 50 amino ...
 1-47 9.78e-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: 54.27  E-value: 9.78e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 931374052   1 MPVFEYRCHACGRRFAWLEGvVDDRTKPACPHCGGTDIKRLISRFAV 47
Cdd:TIGR02605  1 MPIYEYRCTACGHRFEVLQK-MSDDPLATCPACGGTKLRRLLSAAGF 46
COG2331 COG2331
Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction ...
 1-50 4.02e-10

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


Pssm-ID: 441902  Cd Length: 77  Bit Score: 50.81  E-value: 4.02e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 931374052  1 MPVFEYRCHACGRRFAWLEGVVDDRTKpACPHCGGtDIKRLISRFAVSRS 50
Cdd:COG2331   1 MPIYEYRCESCGHEFEVLQKMSDDPLT-VCPECGG-PLRRLISAPGFVFK 48
Zn-ribbon_8 pfam09723
Zinc ribbon domain; This entry represents a region of about 41 amino acids found in a number ...
 1-42 1.59e-09

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: 48.37  E-value: 1.59e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 931374052   1 MPVFEYRCHACGRRFawlEGVV--DDRTKPACPHCGGTDIKRLI 42
Cdd:pfam09723  1 MPIYEYRCEECGHEF---EVLQkiSDPPLTTCPECGSGDVRRLI 41
CxxC_CXXC_SSSS smart00834
Putative regulatory protein; CxxC_CXXC_SSSS represents a region of about 41 amino acids found ...
 1-43 1.22e-07

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: 43.31  E-value: 1.22e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 931374052    1 MPVFEYRCHACGRRFAWLEGVVDDrTKPACPHCGGtDIKRLIS 43
Cdd:smart00834  1 MPIYEYRCEDCGHTFEVLQKISDD-PLTTCPECGG-DVRRLIS 41
SIR2 COG0846
NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein ...
 3-35 7.58e-04

NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440607  Cd Length: 243  Bit Score: 35.91  E-value: 7.58e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 931374052   3 VFEYRCHACGRRFAWlEGVVDDRTK---PACPHCGG 35
Cdd:COG0846  121 LHRLRCTKCGKRYDL-EDVLEDLEGelpPRCPKCGG 155
PRK07111 PRK07111
anaerobic ribonucleoside triphosphate reductase; Provisional
 7-44 8.75e-04

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 235937 [Multi-domain]  Cd Length: 735  Bit Score: 36.08  E-value: 8.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 931374052   7 RCHACGrrfawLEGVVDDrtkpACPHCGGTDIKRlISR 44
Cdd:PRK07111 682 RCPVCG-----YLGVIED----KCPKCGSTNIQR-IRR 709
NOB1_Zn_bind pfam08772
Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found ...
 4-40 6.30e-03

Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 (Nin one binding).


Pssm-ID: 462597  Cd Length: 72  Bit Score: 32.10  E-value: 6.30e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 931374052   4 FEYRCHACGRrfawlegVVDDRTKPACPHCGGTDIKR 40
Cdd:pfam08772  7 WVLRCHACFK-------VTKDMTKQFCPKCGNATLRR 36
COG5319 COG5319
Uncharacterized conserved protein, DUF1178 domain [Function unknown];
29-50 8.38e-03

Uncharacterized conserved protein, DUF1178 domain [Function unknown];


Pssm-ID: 444112  Cd Length: 150  Bit Score: 32.90  E-value: 8.38e-03
                         10        20
                 ....*....|....*....|..
gi 931374052  29 ACPHCGGTDIKRLISRFAVSRS 50
Cdd:COG5319   34 SCPVCGSTKVEKALMAPRVATS 55
PTZ00408 PTZ00408
NAD-dependent deacetylase; Provisional
 3-40 8.44e-03

NAD-dependent deacetylase; Provisional


Pssm-ID: 240405  Cd Length: 242  Bit Score: 33.26  E-value: 8.44e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 931374052   3 VFEYRCHACGRRFAWLEGVVDDRTKpaCPHCGGTDIKR 40
Cdd:PTZ00408 115 LLKVRCTATGHVFDWTEDVVHGSSR--CKCCGCVGTLR 150
 
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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