NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|578816225|ref|XP_006716740|]
View 

jerky protein homolog isoform X1 [Homo sapiens]

Protein Classification

CENP-B_N and DDE_1 domain-containing protein( domain architecture ID 10514952)

protein containing domains CENP-B_N, CENPB, and DDE_1

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_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 213-382 2.44e-65

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: 210.71  E-value: 2.44e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578816225  213 KDRLTVLMCANATGSHRLKPLAIGKCSGPRAFKGI---QHLPVAYKAQGNAWVDKEIFSDWFHHIFVPSVREhfrtiglP 289
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEktpKPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRE-------S 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578816225  290 EDSKAVLLLDSSRAHPQE---AELVSSNVFTIFLPASVASLVQPMEQGI--------RRDFMRNFINPPVPLQGPHARYN 358
Cdd:pfam03184  74 PGRKVLLLLDGSGSHPTVeliRSCGLQNIFLVFLPANSTSILQPLDQGVvstfkanyRRQWLQYLLAGNNLLSPPWKKLT 153

                         170       180
                  ....*....|....*....|....
gi 578816225  359 MNDAIFSVACAWNAVPSHVFRRAW 382
Cdd:pfam03184 154 LLDALKWIAKAWNAVSPSTITSGF 177
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 14-66 3.30e-20

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: 84.00  E-value: 3.30e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578816225   14 KRKRVVLTLKEKIDICTRLEKGESRKALMQEYNVGMSTLYDIRAHKAQLLRFF 66
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
83-147 7.54e-19

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


:

Pssm-ID: 197828  Cd Length: 66  Bit Score: 80.41  E-value: 7.54e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578816225    83 TPKLEHLDRVLYEWFLGKRSEGVPVSGPMLIEKAKDFYEQMQLtEPCVFSGGWLWRFKARHGIKK 147
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGL-ENFKASKGWLTRFKKRHNIVK 64
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 213-382 2.44e-65

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: 210.71  E-value: 2.44e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578816225  213 KDRLTVLMCANATGSHRLKPLAIGKCSGPRAFKGI---QHLPVAYKAQGNAWVDKEIFSDWFHHIFVPSVREhfrtiglP 289
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEktpKPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRE-------S 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578816225  290 EDSKAVLLLDSSRAHPQE---AELVSSNVFTIFLPASVASLVQPMEQGI--------RRDFMRNFINPPVPLQGPHARYN 358
Cdd:pfam03184  74 PGRKVLLLLDGSGSHPTVeliRSCGLQNIFLVFLPANSTSILQPLDQGVvstfkanyRRQWLQYLLAGNNLLSPPWKKLT 153

                         170       180
                  ....*....|....*....|....
gi 578816225  359 MNDAIFSVACAWNAVPSHVFRRAW 382
Cdd:pfam03184 154 LLDALKWIAKAWNAVSPSTITSGF 177
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 14-66 3.30e-20

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: 84.00  E-value: 3.30e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578816225   14 KRKRVVLTLKEKIDICTRLEKGESRKALMQEYNVGMSTLYDIRAHKAQLLRFF 66
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
83-147 7.54e-19

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 80.41  E-value: 7.54e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578816225    83 TPKLEHLDRVLYEWFLGKRSEGVPVSGPMLIEKAKDFYEQMQLtEPCVFSGGWLWRFKARHGIKK 147
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGL-ENFKASKGWLTRFKKRHNIVK 64
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-146 3.88e-16

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 72.66  E-value: 3.88e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578816225   87 EHLDRVLYEWFLGKRSEGVPVSGPMLIEKAKDFYEQMQL--TEPCVFSGGWLWRFKARHGIK 146
Cdd:pfam03221   2 PDLEKALYEWILQLRARGIPITGPMIREKALELAQLAADlgEPDFKASKGWLDRFKKRHGIK 63
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 15-53 6.28e-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: 34.61  E-value: 6.28e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 578816225  15 RKRVvLTLKEKIDICTRLEKGESRKALMQEYNVGMSTLY 53
Cdd:cd00569    2 RPPK-LTPEQIAEARRLLAAGESVAEIARELGVSRSTLY 39
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 213-382 2.44e-65

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: 210.71  E-value: 2.44e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578816225  213 KDRLTVLMCANATGSHRLKPLAIGKCSGPRAFKGI---QHLPVAYKAQGNAWVDKEIFSDWFHHIFVPSVREhfrtiglP 289
Cdd:pfam03184   1 KERLTVMLCCNAAGSEKLPPLVIGKGKNPRAFKNEktpKPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRE-------S 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578816225  290 EDSKAVLLLDSSRAHPQE---AELVSSNVFTIFLPASVASLVQPMEQGI--------RRDFMRNFINPPVPLQGPHARYN 358
Cdd:pfam03184  74 PGRKVLLLLDGSGSHPTVeliRSCGLQNIFLVFLPANSTSILQPLDQGVvstfkanyRRQWLQYLLAGNNLLSPPWKKLT 153

                         170       180
                  ....*....|....*....|....
gi 578816225  359 MNDAIFSVACAWNAVPSHVFRRAW 382
Cdd:pfam03184 154 LLDALKWIAKAWNAVSPSTITSGF 177
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 14-66 3.30e-20

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: 84.00  E-value: 3.30e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578816225   14 KRKRVVLTLKEKIDICTRLEKGESRKALMQEYNVGMSTLYDIRAHKAQLLRFF 66
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
83-147 7.54e-19

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 80.41  E-value: 7.54e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578816225    83 TPKLEHLDRVLYEWFLGKRSEGVPVSGPMLIEKAKDFYEQMQLtEPCVFSGGWLWRFKARHGIKK 147
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGL-ENFKASKGWLTRFKKRHNIVK 64
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-146 3.88e-16

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 72.66  E-value: 3.88e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578816225   87 EHLDRVLYEWFLGKRSEGVPVSGPMLIEKAKDFYEQMQL--TEPCVFSGGWLWRFKARHGIK 146
Cdd:pfam03221   2 PDLEKALYEWILQLRARGIPITGPMIREKALELAQLAADlgEPDFKASKGWLDRFKKRHGIK 63
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 15-53 6.28e-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: 34.61  E-value: 6.28e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 578816225  15 RKRVvLTLKEKIDICTRLEKGESRKALMQEYNVGMSTLY 53
Cdd:cd00569    2 RPPK-LTPEQIAEARRLLAAGESVAEIARELGVSRSTLY 39
 
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