NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|530377307|ref|XP_005262864|]
View 

tigger transposable element-derived protein 4 isoform X1 [Homo sapiens]

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
DDE_3 super family cl46863
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 211-372 5.44e-32

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 pfam03184:

Pssm-ID: 481203  Cd Length: 177  Bit Score: 120.96  E-value: 5.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377307  211 KDRITLVVGTNMDGSEKLPLLVIGKKRTPHCFKGLK---SLPVCYEANRMAWMTSDVFEQWmrkLDEEFQAQ-----QRR 282
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEKtpkPLPVEYKSNGKAWMTTSIFEEW---LQKWFDPRmrespGRK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377307  283 VVIFVESFPAHPEVKNLKS-----IELAFFPSCLSSKCIAMKQGVIKSLKIKYRHCLIKKFLSSVEGSKEF--TFSLLDA 355
Cdd:pfam03184  78 VLLLLDGSGSHPTVELIRScglqnIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSPPwkKLTLLDA 157

                         170
                  ....*....|....*..
gi 530377307  356 VDTLHLCWRAVTPETIV 372
Cdd:pfam03184 158 LKWIAKAWNAVSPSTIT 174
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
84-143 2.00e-20

Tc5 transposase DNA-binding domain;


:

Pssm-ID: 460850  Cd Length: 63  Bit Score: 84.99  E-value: 2.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530377307   84 YTDLEEALMRWYRIAQCLNVPVNGPMLRLKANDFAQK---LGHNDFKCSNGWLDRFKSRYGLV 143
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQLaadLGEPDFKASKGWLDRFKKRHGIK 63
CENP-B_N super family cl47877
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 16-67 4.60e-08

CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.


The actual alignment was detected with superfamily member pfam04218:

Pssm-ID: 461229  Cd Length: 53  Bit Score: 49.33  E-value: 4.60e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 530377307   16 KKKKSLSIEEKIDIINAVESGKKKAEIAAEYGIKKNSLSSIMKNKDKVLEAF 67
Cdd:pfam04218   2 RKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
CENP-B_dimeriz super family cl07586
Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization ...
 427-504 1.96e-05

Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization domain is composed of two alpha-helices, which are folded into an antiparallel configuration. dimerization of CENP-B is mediated by this domain, in which monomers dimerize to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation.


The actual alignment was detected with superfamily member pfam09026:

Pssm-ID: 462657  Cd Length: 100  Bit Score: 43.60  E-value: 1.96e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530377307  427 LETCEAAPNGDSICTKESKSDETGFYTSDEEDDDGspGTELPLPSKSEAITALDTLKKFLRSQDMNDGLQNSLADLEN 504
Cdd:pfam09026   3 PKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNI--PPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLE 78
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 211-372 5.44e-32

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. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere.


Pssm-ID: 367380  Cd Length: 177  Bit Score: 120.96  E-value: 5.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377307  211 KDRITLVVGTNMDGSEKLPLLVIGKKRTPHCFKGLK---SLPVCYEANRMAWMTSDVFEQWmrkLDEEFQAQ-----QRR 282
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEKtpkPLPVEYKSNGKAWMTTSIFEEW---LQKWFDPRmrespGRK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377307  283 VVIFVESFPAHPEVKNLKS-----IELAFFPSCLSSKCIAMKQGVIKSLKIKYRHCLIKKFLSSVEGSKEF--TFSLLDA 355
Cdd:pfam03184  78 VLLLLDGSGSHPTVELIRScglqnIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSPPwkKLTLLDA 157

                         170
                  ....*....|....*..
gi 530377307  356 VDTLHLCWRAVTPETIV 372
Cdd:pfam03184 158 LKWIAKAWNAVSPSTIT 174
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
84-143 2.00e-20

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 84.99  E-value: 2.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530377307   84 YTDLEEALMRWYRIAQCLNVPVNGPMLRLKANDFAQK---LGHNDFKCSNGWLDRFKSRYGLV 143
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQLaadLGEPDFKASKGWLDRFKKRHGIK 63
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
84-145 1.04e-15

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


Pssm-ID: 197828  Cd Length: 66  Bit Score: 71.55  E-value: 1.04e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530377307    84 YTDLEEALMRWYRIAQCLNVPVNGPMLRLKANDFAQKLGHNDFKCSNGWLDRFKSRYGLVFR 145
Cdd:smart00674   4 YPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLENFKASKGWLTRFKKRHNIVKT 65
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 16-67 4.60e-08

CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.


Pssm-ID: 461229  Cd Length: 53  Bit Score: 49.33  E-value: 4.60e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 530377307   16 KKKKSLSIEEKIDIINAVESGKKKAEIAAEYGIKKNSLSSIMKNKDKVLEAF 67
Cdd:pfam04218   2 RKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
CENP-B_dimeriz pfam09026
Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization ...
 427-504 1.96e-05

Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization domain is composed of two alpha-helices, which are folded into an antiparallel configuration. dimerization of CENP-B is mediated by this domain, in which monomers dimerize to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation.


Pssm-ID: 462657  Cd Length: 100  Bit Score: 43.60  E-value: 1.96e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530377307  427 LETCEAAPNGDSICTKESKSDETGFYTSDEEDDDGspGTELPLPSKSEAITALDTLKKFLRSQDMNDGLQNSLADLEN 504
Cdd:pfam09026   3 PKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNI--PPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLE 78
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
16-54 6.27e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.06  E-value: 6.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 530377307  16 KKKKSLSIEEKIDIINAV-ESGKKKAEIAAEYGIKKNSLS 54
Cdd:COG2963    3 KKRRRYSPEFKAEAVRLVlEGGASVAEVARELGISPSTLY 42
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 211-372 5.44e-32

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. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere.


Pssm-ID: 367380  Cd Length: 177  Bit Score: 120.96  E-value: 5.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377307  211 KDRITLVVGTNMDGSEKLPLLVIGKKRTPHCFKGLK---SLPVCYEANRMAWMTSDVFEQWmrkLDEEFQAQ-----QRR 282
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEKtpkPLPVEYKSNGKAWMTTSIFEEW---LQKWFDPRmrespGRK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377307  283 VVIFVESFPAHPEVKNLKS-----IELAFFPSCLSSKCIAMKQGVIKSLKIKYRHCLIKKFLSSVEGSKEF--TFSLLDA 355
Cdd:pfam03184  78 VLLLLDGSGSHPTVELIRScglqnIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSPPwkKLTLLDA 157

                         170
                  ....*....|....*..
gi 530377307  356 VDTLHLCWRAVTPETIV 372
Cdd:pfam03184 158 LKWIAKAWNAVSPSTIT 174
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
84-143 2.00e-20

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 84.99  E-value: 2.00e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530377307   84 YTDLEEALMRWYRIAQCLNVPVNGPMLRLKANDFAQK---LGHNDFKCSNGWLDRFKSRYGLV 143
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQLaadLGEPDFKASKGWLDRFKKRHGIK 63
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
84-145 1.04e-15

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


Pssm-ID: 197828  Cd Length: 66  Bit Score: 71.55  E-value: 1.04e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530377307    84 YTDLEEALMRWYRIAQCLNVPVNGPMLRLKANDFAQKLGHNDFKCSNGWLDRFKSRYGLVFR 145
Cdd:smart00674   4 YPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLENFKASKGWLTRFKKRHNIVKT 65
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 16-67 4.60e-08

CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.


Pssm-ID: 461229  Cd Length: 53  Bit Score: 49.33  E-value: 4.60e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 530377307   16 KKKKSLSIEEKIDIINAVESGKKKAEIAAEYGIKKNSLSSIMKNKDKVLEAF 67
Cdd:pfam04218   2 RKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
CENP-B_dimeriz pfam09026
Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization ...
 427-504 1.96e-05

Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization domain is composed of two alpha-helices, which are folded into an antiparallel configuration. dimerization of CENP-B is mediated by this domain, in which monomers dimerize to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation.


Pssm-ID: 462657  Cd Length: 100  Bit Score: 43.60  E-value: 1.96e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530377307  427 LETCEAAPNGDSICTKESKSDETGFYTSDEEDDDGspGTELPLPSKSEAITALDTLKKFLRSQDMNDGLQNSLADLEN 504
Cdd:pfam09026   3 PKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNI--PPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLE 78
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
16-54 6.27e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.06  E-value: 6.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 530377307  16 KKKKSLSIEEKIDIINAV-ESGKKKAEIAAEYGIKKNSLS 54
Cdd:COG2963    3 KKRRRYSPEFKAEAVRLVlEGGASVAEVARELGISPSTLY 42
 
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