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Conserved domains on  [gi|1490377451|gb|RLA24706|]
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DNA-binding protein [Gammaproteobacteria bacterium]

Protein Classification

Zn-ribbon domain-containing OB-fold protein( domain architecture ID 11446204)

Zn-ribbon domain-containing OB-fold protein may bind nucleic acids; similar to Pseudomonas protegens 2,4-diacetylphloroglucinol biosynthesis protein PhlB

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
PubMed:  12504685|12769718|12598368|8458342

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG1545 COG1545
Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only];
17-127 1.85e-38

Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only];


:

Pssm-ID: 441154 [Multi-domain]  Cd Length: 116  Bit Score: 125.77  E-value: 1.85e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490377451  17 YADYLKKEVFALPKCKKCGEFHFFPRIVCPHCGSFELEWQPLSGKGEVYSTTTIRRKP---ERGGNYNVCLVTLEEGPRL 93
Cdd:COG1545     1 FWRALAEGRLLGQRCPACGTVYFPPRPVCPHCGSEDLEWVELSGRGTVYSYTVVHRPPppfEDEVPYVVALVELDEGVRV 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1490377451  94 MSRVEGIEAEAVKIGAQVCAQI--NNDSDEPFVVFT 127
Cdd:COG1545    81 LGRLVGVDPEDVRIGMRVRVVFrpIDEDGRTLPVFR 116
 
Name Accession Description Interval E-value
COG1545 COG1545
Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only];
17-127 1.85e-38

Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only];


Pssm-ID: 441154 [Multi-domain]  Cd Length: 116  Bit Score: 125.77  E-value: 1.85e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490377451  17 YADYLKKEVFALPKCKKCGEFHFFPRIVCPHCGSFELEWQPLSGKGEVYSTTTIRRKP---ERGGNYNVCLVTLEEGPRL 93
Cdd:COG1545     1 FWRALAEGRLLGQRCPACGTVYFPPRPVCPHCGSEDLEWVELSGRGTVYSYTVVHRPPppfEDEVPYVVALVELDEGVRV 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1490377451  94 MSRVEGIEAEAVKIGAQVCAQI--NNDSDEPFVVFT 127
Cdd:COG1545    81 LGRLVGVDPEDVRIGMRVRVVFrpIDEDGRTLPVFR 116
OB_aCoA_assoc pfam01796
DUF35 OB-fold domain, acyl-CoA-associated; The structure of a DUF35 representative reveals two ...
 55-111 1.78e-16

DUF35 OB-fold domain, acyl-CoA-associated; The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA (Topsan http://www.topsan.org/). Genomic context shows it to be adjacent to acyl-CoA transferase (http:/www.microbesonline.org/).


Pssm-ID: 460333  Cd Length: 65  Bit Score: 68.40  E-value: 1.78e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490377451  55 WQPLSGKGEVYSTTTIRRKPERGGN---YNVCLVTLEEGPRLMSRVEGIEAEAVKIGAQV 111
Cdd:pfam01796   1 WVELSGRGTVYSYTVVHRPPPGFADdvpYVVGLVELDEGPRVMARLVGVDPDEVRIGMRV 60
 
Name Accession Description Interval E-value
COG1545 COG1545
Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only];
17-127 1.85e-38

Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only];


Pssm-ID: 441154 [Multi-domain]  Cd Length: 116  Bit Score: 125.77  E-value: 1.85e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490377451  17 YADYLKKEVFALPKCKKCGEFHFFPRIVCPHCGSFELEWQPLSGKGEVYSTTTIRRKP---ERGGNYNVCLVTLEEGPRL 93
Cdd:COG1545     1 FWRALAEGRLLGQRCPACGTVYFPPRPVCPHCGSEDLEWVELSGRGTVYSYTVVHRPPppfEDEVPYVVALVELDEGVRV 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1490377451  94 MSRVEGIEAEAVKIGAQVCAQI--NNDSDEPFVVFT 127
Cdd:COG1545    81 LGRLVGVDPEDVRIGMRVRVVFrpIDEDGRTLPVFR 116
OB_aCoA_assoc pfam01796
DUF35 OB-fold domain, acyl-CoA-associated; The structure of a DUF35 representative reveals two ...
 55-111 1.78e-16

DUF35 OB-fold domain, acyl-CoA-associated; The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA (Topsan http://www.topsan.org/). Genomic context shows it to be adjacent to acyl-CoA transferase (http:/www.microbesonline.org/).


Pssm-ID: 460333  Cd Length: 65  Bit Score: 68.40  E-value: 1.78e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490377451  55 WQPLSGKGEVYSTTTIRRKPERGGN---YNVCLVTLEEGPRLMSRVEGIEAEAVKIGAQV 111
Cdd:pfam01796   1 WVELSGRGTVYSYTVVHRPPPGFADdvpYVVGLVELDEGPRVMARLVGVDPDEVRIGMRV 60
DUF35_N pfam12172
Rubredoxin-like zinc ribbon domain (DUF35_N); This domain has no known function and is found ...
 21-54 3.52e-09

Rubredoxin-like zinc ribbon domain (DUF35_N); This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in Swiss:O53566. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment.


Pssm-ID: 463482  Cd Length: 37  Bit Score: 48.86  E-value: 3.52e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1490377451  21 LKKEVFALPKCKKCGEFHFFPRIVCPHCGSFELE 54
Cdd:pfam12172   4 LAEGRLVGQRCPDCGTVRFPPRAVCPHCGSRDLE 37
 
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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