NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|929558014|gb|ALF08211|]
View 

polymerase protein, partial [Macaque simian foamy virus]

Protein Classification

integrase( domain architecture ID 16054273)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 34-89 1.76e-16

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: 69.97  E-value: 1.76e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 929558014   34 PPKADREKIVSTAHNIA-HTGRDATFLKVSSKYWWPNLRKDVVKVIRQCKQCLLTNA 89
Cdd:pfam17921   1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 106-193 4.35e-13

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: 62.33  E-value: 4.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 929558014  106 PFDKFYIDYI-GPLPPSNGYLHVLVVVDGMTGFVWLYP-TKAPSTSATVKALNMLTSIA--IPKVLHSDQGAAFTSSTFA 181
Cdd:pfam00665   1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|..
gi 929558014  182 DWAKEKGIQLEF 193
Cdd:pfam00665  81 EFLKDLGIKPSF 92
 
Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 34-89 1.76e-16

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: 69.97  E-value: 1.76e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 929558014   34 PPKADREKIVSTAHNIA-HTGRDATFLKVSSKYWWPNLRKDVVKVIRQCKQCLLTNA 89
Cdd:pfam17921   1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 106-193 4.35e-13

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: 62.33  E-value: 4.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 929558014  106 PFDKFYIDYI-GPLPPSNGYLHVLVVVDGMTGFVWLYP-TKAPSTSATVKALNMLTSIA--IPKVLHSDQGAAFTSSTFA 181
Cdd:pfam00665   1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|..
gi 929558014  182 DWAKEKGIQLEF 193
Cdd:pfam00665  81 EFLKDLGIKPSF 92
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
122-193 6.01e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 54.39  E-value: 6.01e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 929558014 122 NGYLHVLVVVDGMTGFV--W-LYPTkaPSTSATVKALNMLT---SIAIPKVLHSDQGAAFTSSTFADWAKEKGIQLEF 193
Cdd:COG2801  163 EGWLYLAAVIDLFSREIvgWsVSDS--MDAELVVDALEMAIerrGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSM 238
transpos_IS3 NF033516
IS3 family transposase;
122-193 8.24e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 51.03  E-value: 8.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 929558014 122 NGYLHVLVVVDGMTGFV--WlYPTKAPSTSATVKALNMltsiAI-------PKVLHSDQGAAFTSSTFADWAKEKGIQLE 192
Cdd:NF033516 230 EGWLYLAVVLDLFSREIvgW-SVSTSMSAELVLDALEM----AIewrgkpeGLILHSDNGSQYTSKAYREWLKEHGITQS 304


                 .
gi 929558014 193 F 193
Cdd:NF033516 305 M 305
 
Name Accession Description Interval E-value
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 34-89 1.76e-16

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: 69.97  E-value: 1.76e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 929558014   34 PPKADREKIVSTAHNIA-HTGRDATFLKVSSKYWWPNLRKDVVKVIRQCKQCLLTNA 89
Cdd:pfam17921   1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 106-193 4.35e-13

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: 62.33  E-value: 4.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 929558014  106 PFDKFYIDYI-GPLPPSNGYLHVLVVVDGMTGFVWLYP-TKAPSTSATVKALNMLTSIA--IPKVLHSDQGAAFTSSTFA 181
Cdd:pfam00665   1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|..
gi 929558014  182 DWAKEKGIQLEF 193
Cdd:pfam00665  81 EFLKDLGIKPSF 92
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
122-193 6.01e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 54.39  E-value: 6.01e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 929558014 122 NGYLHVLVVVDGMTGFV--W-LYPTkaPSTSATVKALNMLT---SIAIPKVLHSDQGAAFTSSTFADWAKEKGIQLEF 193
Cdd:COG2801  163 EGWLYLAAVIDLFSREIvgWsVSDS--MDAELVVDALEMAIerrGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSM 238
transpos_IS3 NF033516
IS3 family transposase;
122-193 8.24e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 51.03  E-value: 8.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 929558014 122 NGYLHVLVVVDGMTGFV--WlYPTKAPSTSATVKALNMltsiAI-------PKVLHSDQGAAFTSSTFADWAKEKGIQLE 192
Cdd:NF033516 230 EGWLYLAVVLDLFSREIvgW-SVSTSMSAELVLDALEM----AIewrgkpeGLILHSDNGSQYTSKAYREWLKEHGITQS 304


                 .
gi 929558014 193 F 193
Cdd:NF033516 305 M 305
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 47-84 8.78e-04

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: 35.76  E-value: 8.78e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 929558014   47 HNIAHTGRDATFLKVSSKYWWPNLRKDVVKVIRQCKQC 84
Cdd:pfam09337   1 HALTHLGINKLTALLARKYHWLGIKETVSEVISSCVAC 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH