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Conserved domains on  [gi|298351597|sp|B2RD01|]
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PUTATIVE PSEUDOGENE: RecName: Full=Putative CENPB DNA-binding domain-containing protein 1

Protein Classification

HTH and HTH_Tnp_Tc5 domain-containing protein( domain architecture ID 10405118)

HTH and HTH_Tnp_Tc5 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-151 5.83e-10

Tc5 transposase DNA-binding domain;


:

Pssm-ID: 460850  Cd Length: 63  Bit Score: 53.02  E-value: 5.83e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 298351597   87 MESMEQLLSLWLEDQSQPNATLSAAIVQEKAEFddLqREHGEGSQTERFHASQGWLVRFKECHCL 151
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALE--L-AQLAADLGEPDFKASKGWLDRFKKRHGI 62
CENP-B_N super family cl47877
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 16-68 1.58e-04

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: 38.16  E-value: 1.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 298351597   16 KRERKAITLDLKLEVLRRFEAGEKLSQIAKALDLAISTVATIRDSKEKIKASS 68
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
 
Name Accession Description Interval E-value
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-151 5.83e-10

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 53.02  E-value: 5.83e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 298351597   87 MESMEQLLSLWLEDQSQPNATLSAAIVQEKAEFddLqREHGEGSQTERFHASQGWLVRFKECHCL 151
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALE--L-AQLAADLGEPDFKASKGWLDRFKKRHGI 62
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
87-151 1.17e-04

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 38.81  E-value: 1.17e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 298351597    87 MESMEQLLSLWLEDQSQPNATLSAAIVQEKAEfdDLQREHGEGSqterFHASQGWLVRFKECHCL 151
Cdd:smart00674   4 YPLLEKALYEWILRQEALGIPISGEDIREKAL--EILQRLGLEN----FKASKGWLTRFKKRHNI 62
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 16-68 1.58e-04

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: 38.16  E-value: 1.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 298351597   16 KRERKAITLDLKLEVLRRFEAGEKLSQIAKALDLAISTVATIRDSKEKIKASS 68
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
 
Name Accession Description Interval E-value
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-151 5.83e-10

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 53.02  E-value: 5.83e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 298351597   87 MESMEQLLSLWLEDQSQPNATLSAAIVQEKAEFddLqREHGEGSQTERFHASQGWLVRFKECHCL 151
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALE--L-AQLAADLGEPDFKASKGWLDRFKKRHGI 62
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
87-151 1.17e-04

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 38.81  E-value: 1.17e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 298351597    87 MESMEQLLSLWLEDQSQPNATLSAAIVQEKAEfdDLQREHGEGSqterFHASQGWLVRFKECHCL 151
Cdd:smart00674   4 YPLLEKALYEWILRQEALGIPISGEDIREKAL--EILQRLGLEN----FKASKGWLTRFKKRHNI 62
CENP-B_N pfam04218
CENP-B N-terminal DNA-binding domain; Centromere Protein B (CENP-B) is a DNA-binding protein ...
 16-68 1.58e-04

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: 38.16  E-value: 1.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 298351597   16 KRERKAITLDLKLEVLRRFEAGEKLSQIAKALDLAISTVATIRDSKEKIKASS 68
Cdd:pfam04218   1 RRKRRSLTLREKIAIIQRYEEGESKASLARRFGVPASTLRRILKNKKKLLQQL 53
 
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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