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Conserved domains on  [gi|21735415|ref|NP_001801|]
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major centromere autoantigen B [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 222-384 4.09e-55

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: 184.52  E-value: 4.09e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   222 TQRLSVLLCANADGSEKLPPLVAGKSAKPRAGQAG-----LPCDYTANSKGGVTTQALAKYL-KALDTRMA-AESRRVLL 294
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEktpkpLPVEYKSNGKAWMTTSIFEEWLqKWFDPRMReSPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   295 LAGRLAAQSLDTS----GLRHVQLAFFPPGT---VHPLERGVVQQVKGHYRQAMLLKAMAALEGQDPSGLQLGLTEALHF 367
Cdd:pfam03184  81 LLDGSGSHPTVELirscGLQNIFLVFLPANStsiLQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSPPWKKLTLLDALKW 160

                         170
                  ....*....|....*..
gi 21735415   368 VAAAWQAVEPSDIAACF 384
Cdd:pfam03184 161 IAKAWNAVSPSTITSGF 177
CENP-B_dimeriz super family cl07586
Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization ...
 539-598 2.92e-39

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: 139.13  E-value: 2.92e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   539 VPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKNHARQAGVRGLGHQ 598
Cdd:pfam09026  41 TLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIIL 100
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
74-135 4.46e-20

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


:

Pssm-ID: 197828  Cd Length: 66  Bit Score: 84.27  E-value: 4.46e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21735415     74 YDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRHGVVSC 135
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 ...
 2-56 1.36e-19

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: 82.46  E-value: 1.36e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 21735415     2 GPKRRQLTFREKSRIIQEVEENPdlRKGEIARRFNIPPSTLSTILKNKRAILASE 56
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGE--SKASLARRFGVPASTLRRILKNKKKLLQQL 53
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 222-384 4.09e-55

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: 184.52  E-value: 4.09e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   222 TQRLSVLLCANADGSEKLPPLVAGKSAKPRAGQAG-----LPCDYTANSKGGVTTQALAKYL-KALDTRMA-AESRRVLL 294
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEktpkpLPVEYKSNGKAWMTTSIFEEWLqKWFDPRMReSPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   295 LAGRLAAQSLDTS----GLRHVQLAFFPPGT---VHPLERGVVQQVKGHYRQAMLLKAMAALEGQDPSGLQLGLTEALHF 367
Cdd:pfam03184  81 LLDGSGSHPTVELirscGLQNIFLVFLPANStsiLQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSPPWKKLTLLDALKW 160

                         170
                  ....*....|....*..
gi 21735415   368 VAAAWQAVEPSDIAACF 384
Cdd:pfam03184 161 IAKAWNAVSPSTITSGF 177
CENP-B_dimeriz pfam09026
Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization ...
 539-598 2.92e-39

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: 139.13  E-value: 2.92e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   539 VPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKNHARQAGVRGLGHQ 598
Cdd:pfam09026  41 TLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIIL 100
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
74-135 4.46e-20

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 84.27  E-value: 4.46e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21735415     74 YDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRHGVVSC 135
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 ...
 2-56 1.36e-19

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: 82.46  E-value: 1.36e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 21735415     2 GPKRRQLTFREKSRIIQEVEENPdlRKGEIARRFNIPPSTLSTILKNKRAILASE 56
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGE--SKASLARRFGVPASTLRRILKNKKKLLQQL 53
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
74-133 7.67e-18

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 77.67  E-value: 7.67e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21735415    74 YDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAE---ELGMDDFTASNGWLDRFRRRHGVV 133
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQlaaDLGEPDFKASKGWLDRFKKRHGIK 63
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
1-44 2.91e-03

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


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 37.21  E-value: 2.91e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21735415   1 MGPKRRQLTFREKSRIIQEVEEnPDLRKGEIARRFNIPPSTLST 44
Cdd:COG2963   1 MSKKRRRYSPEFKAEAVRLVLE-GGASVAEVARELGISPSTLYR 43
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 222-384 4.09e-55

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: 184.52  E-value: 4.09e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   222 TQRLSVLLCANADGSEKLPPLVAGKSAKPRAGQAG-----LPCDYTANSKGGVTTQALAKYL-KALDTRMA-AESRRVLL 294
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEktpkpLPVEYKSNGKAWMTTSIFEEWLqKWFDPRMReSPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   295 LAGRLAAQSLDTS----GLRHVQLAFFPPGT---VHPLERGVVQQVKGHYRQAMLLKAMAALEGQDPSGLQLGLTEALHF 367
Cdd:pfam03184  81 LLDGSGSHPTVELirscGLQNIFLVFLPANStsiLQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSPPWKKLTLLDALKW 160

                         170
                  ....*....|....*..
gi 21735415   368 VAAAWQAVEPSDIAACF 384
Cdd:pfam03184 161 IAKAWNAVSPSTITSGF 177
CENP-B_dimeriz pfam09026
Centromere protein B dimerization domain; The centromere protein B (CENP-B) dimerization ...
 539-598 2.92e-39

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: 139.13  E-value: 2.92e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 21735415   539 VPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKNHARQAGVRGLGHQ 598
Cdd:pfam09026  41 TLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIIL 100
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
74-135 4.46e-20

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 84.27  E-value: 4.46e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21735415     74 YDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRHGVVSC 135
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 ...
 2-56 1.36e-19

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: 82.46  E-value: 1.36e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 21735415     2 GPKRRQLTFREKSRIIQEVEENPdlRKGEIARRFNIPPSTLSTILKNKRAILASE 56
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGE--SKASLARRFGVPASTLRRILKNKKKLLQQL 53
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
74-133 7.67e-18

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 77.67  E-value: 7.67e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21735415    74 YDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAE---ELGMDDFTASNGWLDRFRRRHGVV 133
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQlaaDLGEPDFKASKGWLDRFKKRHGIK 63
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
15-48 2.12e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 36.26  E-value: 2.12e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 21735415    15 RIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN 48
Cdd:pfam13412   5 KILNLLQENPRISQRELAERLGLSPSTVNRRLKR 38
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
1-44 2.91e-03

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


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 37.21  E-value: 2.91e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21735415   1 MGPKRRQLTFREKSRIIQEVEEnPDLRKGEIARRFNIPPSTLST 44
Cdd:COG2963   1 MSKKRRRYSPEFKAEAVRLVLE-GGASVAEVARELGISPSTLYR 43
 
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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