NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2410729438|ref|WP_268541845|]
View 

zinc finger domain-containing protein [Candidatus Nitrosotenuis cloacae]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HVO_2753_ZBP super family cl46982
Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many ...
 8-59 2.81e-12

Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many archaeal proteins, including HVO_2753 (also known as Small CPxCG-related zinc finger protein) from Haloferax volcanii. NMR 3D structure analysis revealed the content of four C(P)XCG motifs, suggesting the presence of two zinc-binding pockets (ZBPs). However, only C(P)XCG motifs 2 and 4 (comprising Cys-32 to Cys-35 and Cys-50 to Cys-53) form a ZBP and binds one zinc atom, while C(P)XCG motifs 1 and 3 (comprising Cys-12 to Cys-15 and Cys-39 to Cys-42) form a four-Cys cluster that do not bind zinc. The four C(P)XCG motifs are critical for protein stability, folding and functionality. This domain can also be present in small zinc finger proteins from bacteria and eukaryotes.


The actual alignment was detected with superfamily member PRK14890:

Pssm-ID: 481322 [Multi-domain]  Cd Length: 59  Bit Score: 54.59  E-value: 2.81e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2410729438  8 PVCSCCHKHIMPNDKCVKFNCPECGAVLIWRCESCREAARSFTCSSCNFSGP 59
Cdd:PRK14890   8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFEGP 59
 
Name Accession Description Interval E-value
PRK14890 PRK14890
putative Zn-ribbon RNA-binding protein; Provisional
 8-59 2.81e-12

putative Zn-ribbon RNA-binding protein; Provisional


Pssm-ID: 184884 [Multi-domain]  Cd Length: 59  Bit Score: 54.59  E-value: 2.81e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2410729438  8 PVCSCCHKHIMPNDKCVKFNCPECGAVLIWRCESCREAARSFTCSSCNFSGP 59
Cdd:PRK14890   8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFEGP 59
COG2888 COG2888
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ...
 8-59 1.69e-08

Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only];


Pssm-ID: 442134 [Multi-domain]  Cd Length: 52  Bit Score: 45.11  E-value: 1.69e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 2410729438  8 PVCSCCHKHIMPnDKCVKFNCPECGAVLIWRCESCREAARSF-TCSSCNFSGP 59
Cdd:COG2888    1 PVCPSCGREIAP-EGGVAFYCPNCGEALIIRCPKCRKQSNALyFCPKCGFEGP 52
HVO_2753_ZBP pfam07754
Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many ...
 10-54 4.79e-07

Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many archaeal proteins, including HVO_2753 (also known as Small CPxCG-related zinc finger protein) from Haloferax volcanii. NMR 3D structure analysis revealed the content of four C(P)XCG motifs, suggesting the presence of two zinc-binding pockets (ZBPs). However, only C(P)XCG motifs 2 and 4 (comprising Cys-32 to Cys-35 and Cys-50 to Cys-53) form a ZBP and binds one zinc atom, while C(P)XCG motifs 1 and 3 (comprising Cys-12 to Cys-15 and Cys-39 to Cys-42) form a four-Cys cluster that do not bind zinc. The four C(P)XCG motifs are critical for protein stability, folding and functionality. This domain can also be present in small zinc finger proteins from bacteria and eukaryotes.


Pssm-ID: 429637  Cd Length: 46  Bit Score: 41.26  E-value: 4.79e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2410729438 10 CSCCHKHIMPNDKCVKFNCPECGAVLIWRCESCREAARSFTCSSC 54
Cdd:pfam07754  1 CTSCGAEIAPRERAVVFPCPNCGEAVIIRCEKCRKLSNPYVCPKC 45
 
Name Accession Description Interval E-value
PRK14890 PRK14890
putative Zn-ribbon RNA-binding protein; Provisional
 8-59 2.81e-12

putative Zn-ribbon RNA-binding protein; Provisional


Pssm-ID: 184884 [Multi-domain]  Cd Length: 59  Bit Score: 54.59  E-value: 2.81e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2410729438  8 PVCSCCHKHIMPNDKCVKFNCPECGAVLIWRCESCREAARSFTCSSCNFSGP 59
Cdd:PRK14890   8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFEGP 59
COG2888 COG2888
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ...
 8-59 1.69e-08

Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only];


Pssm-ID: 442134 [Multi-domain]  Cd Length: 52  Bit Score: 45.11  E-value: 1.69e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 2410729438  8 PVCSCCHKHIMPnDKCVKFNCPECGAVLIWRCESCREAARSF-TCSSCNFSGP 59
Cdd:COG2888    1 PVCPSCGREIAP-EGGVAFYCPNCGEALIIRCPKCRKQSNALyFCPKCGFEGP 52
HVO_2753_ZBP pfam07754
Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many ...
 10-54 4.79e-07

Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many archaeal proteins, including HVO_2753 (also known as Small CPxCG-related zinc finger protein) from Haloferax volcanii. NMR 3D structure analysis revealed the content of four C(P)XCG motifs, suggesting the presence of two zinc-binding pockets (ZBPs). However, only C(P)XCG motifs 2 and 4 (comprising Cys-32 to Cys-35 and Cys-50 to Cys-53) form a ZBP and binds one zinc atom, while C(P)XCG motifs 1 and 3 (comprising Cys-12 to Cys-15 and Cys-39 to Cys-42) form a four-Cys cluster that do not bind zinc. The four C(P)XCG motifs are critical for protein stability, folding and functionality. This domain can also be present in small zinc finger proteins from bacteria and eukaryotes.


Pssm-ID: 429637  Cd Length: 46  Bit Score: 41.26  E-value: 4.79e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2410729438 10 CSCCHKHIMPNDKCVKFNCPECGAVLIWRCESCREAARSFTCSSC 54
Cdd:pfam07754  1 CTSCGAEIAPRERAVVFPCPNCGEAVIIRCEKCRKLSNPYVCPKC 45
PolC_DP2 pfam03833
DNA polymerase II large subunit DP2;
25-55 3.01e-03

DNA polymerase II large subunit DP2;


Pssm-ID: 427537  Cd Length: 866  Bit Score: 33.28  E-value: 3.01e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2410729438  25 KFNCPECGA--VLIWRCESCREAARSFTCSSCN 55
Cdd:pfam03833 632 ENRCPDCGAhtEPVYVCPKCGIEVEDEKCPKCG 664
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH