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Conserved domains on  [gi|1907094792|ref|XP_036014130|]
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uncharacterized protein Gm53778 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 52-126 8.24e-21

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 81.21  E-value: 8.24e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907094792  52 PGTHWEIDFTEVR-PGLYGHKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFVSQ 126
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSK 77
zf-H2C2 super family cl07828
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1-39 5.99e-13

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


The actual alignment was detected with superfamily member pfam16721:

Pssm-ID: 447530  Cd Length: 96  Bit Score: 60.90  E-value: 5.99e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907094792   1 MRALLDRKESPYYMLNKDKILHEVAESCQACVQVNASKA 39
Cdd:pfam16721  58 MKALLERSHSPYYMLNRDRTLKNITETCKACAQVNASKS 96
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 52-126 8.24e-21

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 81.21  E-value: 8.24e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907094792  52 PGTHWEIDFTEVR-PGLYGHKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFVSQ 126
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSK 77
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 1-39 5.99e-13

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 60.90  E-value: 5.99e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907094792   1 MRALLDRKESPYYMLNKDKILHEVAESCQACVQVNASKA 39
Cdd:pfam16721  58 MKALLERSHSPYYMLNRDRTLKNITETCKACAQVNASKS 96
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 52-126 8.24e-21

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 81.21  E-value: 8.24e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907094792  52 PGTHWEIDFTEVR-PGLYGHKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFVSQ 126
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSK 77
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 1-39 5.99e-13

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 60.90  E-value: 5.99e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907094792   1 MRALLDRKESPYYMLNKDKILHEVAESCQACVQVNASKA 39
Cdd:pfam16721  58 MKALLERSHSPYYMLNRDRTLKNITETCKACAQVNASKS 96
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1-31 4.77e-06

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 41.16  E-value: 4.77e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1907094792   1 MRALLDRKespYYMLNKDKILHEVAESCQAC 31
Cdd:pfam09337  11 LTALLARK---YHWLGIKETVSEVISSCVAC 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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