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Conserved domains on  [gi|255290428|emb|CBA12814|]
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unnamed protein product [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DDE_Tnp_4 super family cl48181
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 183-348 3.40e-16

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


The actual alignment was detected with superfamily member pfam13359:

Pssm-ID: 463855 [Multi-domain]  Cd Length: 158  Bit Score: 75.39  E-value: 3.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255290428  183 IDTTHIIMTLPAVQASDD--WCDQEKNYSMFLQGVFDHEMRFLNMVTGWPGGMTVSKLLKFSGFFKLcenaqildgnpkt 260
Cdd:pfam13359   1 VDGTEIPIQRPSNLEARGqtYSNYKHHNTLKVLIVVTPNGKIIFVSKGYPGSVSDKSILENSGLLKA------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255290428  261 LSQGAQIREYVVGGISYPLLPWLITPHDSDH---PSDSMVAFNERHEKVRSVAATAFQQLKGSWRILSKVMWRPDRRKLP 337
Cdd:pfam13359  68 LNLAFGPGDYILADKGFPISDWLLVPYKKPGgaqLSPEEVEFNRRIASARIHVERVIGRLKGRFRILRGRLPISLPERLD 147

                         170
                  ....*....|.
gi 255290428  338 SIILVCCLLHN 348
Cdd:pfam13359 148 KIVTVCCVLHN 158
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 90-136 6.42e-03

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member cd00569:

Pssm-ID: 481199 [Multi-domain]  Cd Length: 42  Bit Score: 34.22  E-value: 6.42e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 255290428  90 RPPSgliniegrlLSvEKQVAIALRRLASGDSQVSVGAAFGVGQSTV 136
Cdd:cd00569    2 RPPK---------LT-PEQIAEARRLLAAGESVAEIARELGVSRSTL 38
 
Name Accession Description Interval E-value
DDE_Tnp_4 pfam13359
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 183-348 3.40e-16

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


Pssm-ID: 463855 [Multi-domain]  Cd Length: 158  Bit Score: 75.39  E-value: 3.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255290428  183 IDTTHIIMTLPAVQASDD--WCDQEKNYSMFLQGVFDHEMRFLNMVTGWPGGMTVSKLLKFSGFFKLcenaqildgnpkt 260
Cdd:pfam13359   1 VDGTEIPIQRPSNLEARGqtYSNYKHHNTLKVLIVVTPNGKIIFVSKGYPGSVSDKSILENSGLLKA------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255290428  261 LSQGAQIREYVVGGISYPLLPWLITPHDSDH---PSDSMVAFNERHEKVRSVAATAFQQLKGSWRILSKVMWRPDRRKLP 337
Cdd:pfam13359  68 LNLAFGPGDYILADKGFPISDWLLVPYKKPGgaqLSPEEVEFNRRIASARIHVERVIGRLKGRFRILRGRLPISLPERLD 147

                         170
                  ....*....|.
gi 255290428  338 SIILVCCLLHN 348
Cdd:pfam13359 148 KIVTVCCVLHN 158
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 90-136 6.42e-03

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 34.22  E-value: 6.42e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 255290428  90 RPPSgliniegrlLSvEKQVAIALRRLASGDSQVSVGAAFGVGQSTV 136
Cdd:cd00569    2 RPPK---------LT-PEQIAEARRLLAAGESVAEIARELGVSRSTL 38
 
Name Accession Description Interval E-value
DDE_Tnp_4 pfam13359
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 183-348 3.40e-16

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


Pssm-ID: 463855 [Multi-domain]  Cd Length: 158  Bit Score: 75.39  E-value: 3.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255290428  183 IDTTHIIMTLPAVQASDD--WCDQEKNYSMFLQGVFDHEMRFLNMVTGWPGGMTVSKLLKFSGFFKLcenaqildgnpkt 260
Cdd:pfam13359   1 VDGTEIPIQRPSNLEARGqtYSNYKHHNTLKVLIVVTPNGKIIFVSKGYPGSVSDKSILENSGLLKA------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255290428  261 LSQGAQIREYVVGGISYPLLPWLITPHDSDH---PSDSMVAFNERHEKVRSVAATAFQQLKGSWRILSKVMWRPDRRKLP 337
Cdd:pfam13359  68 LNLAFGPGDYILADKGFPISDWLLVPYKKPGgaqLSPEEVEFNRRIASARIHVERVIGRLKGRFRILRGRLPISLPERLD 147

                         170
                  ....*....|.
gi 255290428  338 SIILVCCLLHN 348
Cdd:pfam13359 148 KIVTVCCVLHN 158
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 90-136 6.42e-03

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 34.22  E-value: 6.42e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 255290428  90 RPPSgliniegrlLSvEKQVAIALRRLASGDSQVSVGAAFGVGQSTV 136
Cdd:cd00569    2 RPPK---------LT-PEQIAEARRLLAAGESVAEIARELGVSRSTL 38
 
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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