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Conserved domains on  [gi|189040862|sp|Q8K259|]
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RecName: Full=Gypsy retrotransposon integrase-like protein 1; Short=GIN-1; AltName: Full=Zinc finger H2C2 domain-containing protein

Protein Classification

integrase( domain architecture ID 16053859)

integrase containing a zinc-binding domain, such as Mus musculus Gypsy retrotransposon integrase-like protein 1 (GIN1)

Gene Ontology:  GO:0003676|GO:0015074
PubMed:  11774877

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 65-124 4.88e-12

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 60.72  E-value: 4.88e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 189040862   65 VSEEEKKKVLRECHENGpgVHHGISRTLTLVESGYYWTSVTNDVKQWVYACQHCQVAKNT 124
Cdd:pfam17921   1 VPKSLRKEILKEAHDSG--GHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve super family cl47583
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 155-211 6.62e-04

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.


The actual alignment was detected with superfamily member pfam00665:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 39.22  E-value: 6.62e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 189040862  155 NRSHVYAIIMTDLFTKWVMILPLCDVSASEISKAIINIFFLY--GPPQKIIMDQRDEFI 211
Cdd:pfam00665  17 GGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYT 75
 
Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 65-124 4.88e-12

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 60.72  E-value: 4.88e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 189040862   65 VSEEEKKKVLRECHENGpgVHHGISRTLTLVESGYYWTSVTNDVKQWVYACQHCQVAKNT 124
Cdd:pfam17921   1 VPKSLRKEILKEAHDSG--GHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 155-211 6.62e-04

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: 39.22  E-value: 6.62e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 189040862  155 NRSHVYAIIMTDLFTKWVMILPLCDVSASEISKAIINIFFLY--GPPQKIIMDQRDEFI 211
Cdd:pfam00665  17 GGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYT 75
 
Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 65-124 4.88e-12

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 60.72  E-value: 4.88e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 189040862   65 VSEEEKKKVLRECHENGpgVHHGISRTLTLVESGYYWTSVTNDVKQWVYACQHCQVAKNT 124
Cdd:pfam17921   1 VPKSLRKEILKEAHDSG--GHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 155-211 6.62e-04

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: 39.22  E-value: 6.62e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 189040862  155 NRSHVYAIIMTDLFTKWVMILPLCDVSASEISKAIINIFFLY--GPPQKIIMDQRDEFI 211
Cdd:pfam00665  17 GGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYT 75
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 85-119 9.11e-03

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: 34.22  E-value: 9.11e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 189040862   85 HHGISRTLTLVESGYYWTSVTNDVKQWVYACQHCQ 119
Cdd:pfam09337   5 HLGINKLTALLARKYHWLGIKETVSEVISSCVACQ 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.
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