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Conserved domains on  [gi|12324507|gb|AAG52212|]
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putative gag-pol polyprotein; 76173-77576 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Retrotran_gag_2 super family cl26047
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 66-195 2.83e-10

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


The actual alignment was detected with superfamily member pfam14223:

Pssm-ID: 464108  Cd Length: 130  Bit Score: 58.02  E-value: 2.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12324507    66 LLFQAIPESMVLQIGELDTAKKVWEAIKEKNvgaERVKEARLQTLMNEFDRLKMKDSENIEAFSGRLAEIASKSAALGEN 145
Cdd:pfam14223   3 LIVLSLSDSLLRLVRNADTAKEAWDKLESTY---ERKSPANKLTLRRQLHSLKMKEGESVLEHINKFEELVNKLSALGVE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 12324507   146 IETEKLVKKFLKSLPrKKYIQIVASLEQVLDLKNtsFEDIVGRIKVYEER 195
Cdd:pfam14223  80 ISDEDLVVKLLRSLP-ESYENFVTAIESSSDKIT--LEELISKLLDEEER 126
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 422-460 5.16e-05

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


:

Pssm-ID: 372857  Cd Length: 67  Bit Score: 41.20  E-value: 5.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 12324507   422 RLYKVQMG-LRNRECLYLTSVSEASLWHARMGHMNSATLK 460
Cdd:pfam13976   1 GLYLLDLSsVANSSIAVASKDDETWLWHRRLGHPSFKGLK 40
DUF4219 super family cl47255
Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal ...
 25-51 1.40e-04

Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.


The actual alignment was detected with superfamily member pfam13961:

Pssm-ID: 433608  Cd Length: 27  Bit Score: 38.64  E-value: 1.40e-04
                          10        20
                  ....*....|....*....|....*..
gi 12324507    25 LNTTNYTVWAMKMKVALKVHKTWDVIE 51
Cdd:pfam13961   1 LDGDNYETWKLRMKLYLQAQDLWEVVE 27
ZnF_C2HC smart00343
zinc finger;
251-265 1.24e-03

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 1.24e-03
                           10
                   ....*....|....*
gi 12324507    251 CFRCDKMGHYASQCP 265
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
 
Name Accession Description Interval E-value
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 66-195 2.83e-10

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 58.02  E-value: 2.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12324507    66 LLFQAIPESMVLQIGELDTAKKVWEAIKEKNvgaERVKEARLQTLMNEFDRLKMKDSENIEAFSGRLAEIASKSAALGEN 145
Cdd:pfam14223   3 LIVLSLSDSLLRLVRNADTAKEAWDKLESTY---ERKSPANKLTLRRQLHSLKMKEGESVLEHINKFEELVNKLSALGVE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 12324507   146 IETEKLVKKFLKSLPrKKYIQIVASLEQVLDLKNtsFEDIVGRIKVYEER 195
Cdd:pfam14223  80 ISDEDLVVKLLRSLP-ESYENFVTAIESSSDKIT--LEELISKLLDEEER 126
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 422-460 5.16e-05

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


Pssm-ID: 372857  Cd Length: 67  Bit Score: 41.20  E-value: 5.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 12324507   422 RLYKVQMG-LRNRECLYLTSVSEASLWHARMGHMNSATLK 460
Cdd:pfam13976   1 GLYLLDLSsVANSSIAVASKDDETWLWHRRLGHPSFKGLK 40
DUF4219 pfam13961
Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal ...
 25-51 1.40e-04

Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.


Pssm-ID: 433608  Cd Length: 27  Bit Score: 38.64  E-value: 1.40e-04
                          10        20
                  ....*....|....*....|....*..
gi 12324507    25 LNTTNYTVWAMKMKVALKVHKTWDVIE 51
Cdd:pfam13961   1 LDGDNYETWKLRMKLYLQAQDLWEVVE 27
ZnF_C2HC smart00343
zinc finger;
251-265 1.24e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 1.24e-03
                           10
                   ....*....|....*
gi 12324507    251 CFRCDKMGHYASQCP 265
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
 
Name Accession Description Interval E-value
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 66-195 2.83e-10

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 58.02  E-value: 2.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12324507    66 LLFQAIPESMVLQIGELDTAKKVWEAIKEKNvgaERVKEARLQTLMNEFDRLKMKDSENIEAFSGRLAEIASKSAALGEN 145
Cdd:pfam14223   3 LIVLSLSDSLLRLVRNADTAKEAWDKLESTY---ERKSPANKLTLRRQLHSLKMKEGESVLEHINKFEELVNKLSALGVE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 12324507   146 IETEKLVKKFLKSLPrKKYIQIVASLEQVLDLKNtsFEDIVGRIKVYEER 195
Cdd:pfam14223  80 ISDEDLVVKLLRSLP-ESYENFVTAIESSSDKIT--LEELISKLLDEEER 126
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 422-460 5.16e-05

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


Pssm-ID: 372857  Cd Length: 67  Bit Score: 41.20  E-value: 5.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 12324507   422 RLYKVQMG-LRNRECLYLTSVSEASLWHARMGHMNSATLK 460
Cdd:pfam13976   1 GLYLLDLSsVANSSIAVASKDDETWLWHRRLGHPSFKGLK 40
DUF4219 pfam13961
Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal ...
 25-51 1.40e-04

Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.


Pssm-ID: 433608  Cd Length: 27  Bit Score: 38.64  E-value: 1.40e-04
                          10        20
                  ....*....|....*....|....*..
gi 12324507    25 LNTTNYTVWAMKMKVALKVHKTWDVIE 51
Cdd:pfam13961   1 LDGDNYETWKLRMKLYLQAQDLWEVVE 27
ZnF_C2HC smart00343
zinc finger;
251-265 1.24e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 1.24e-03
                           10
                   ....*....|....*
gi 12324507    251 CFRCDKMGHYASQCP 265
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
 
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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