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Conserved domains on  [gi|13236413|gb|AAK16155|]
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pol polyprotein, partial [Mus cervicolor popaeus endogenous virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MLVIN_C super family cl40013
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 109-191 5.49e-37

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


The actual alignment was detected with superfamily member pfam18697:

Pssm-ID: 436671  Cd Length: 83  Bit Score: 123.40  E-value: 5.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13236413   109 HPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKSADPRPrRRTSPEPTWQIHRS-QNPLKI 187
Cdd:pfam18697   1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHA-VLEDFIPSWQVQKDrDNPLKL 79


                  ....
gi 13236413   188 RLTR 191
Cdd:pfam18697  80 RLRR 83
 
Name Accession Description Interval E-value
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 109-191 5.49e-37

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


Pssm-ID: 436671  Cd Length: 83  Bit Score: 123.40  E-value: 5.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13236413   109 HPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKSADPRPrRRTSPEPTWQIHRS-QNPLKI 187
Cdd:pfam18697   1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHA-VLEDFIPSWQVQKDrDNPLKL 79


                  ....
gi 13236413   188 RLTR 191
Cdd:pfam18697  80 RLRR 83
 
Name Accession Description Interval E-value
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 109-191 5.49e-37

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


Pssm-ID: 436671  Cd Length: 83  Bit Score: 123.40  E-value: 5.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13236413   109 HPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKSADPRPrRRTSPEPTWQIHRS-QNPLKI 187
Cdd:pfam18697   1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHA-VLEDFIPSWQVQKDrDNPLKL 79


                  ....
gi 13236413   188 RLTR 191
Cdd:pfam18697  80 RLRR 83
 
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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