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Conserved domains on  [gi|2082373869|ref|XP_042958006|]
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uncharacterized protein LOC122293492 [Carya illinoinensis]

Protein Classification

RNA-directed DNA polymerase; RNA-directed DNA polymerase; reverse transcriptase family protein; reverse transcriptase family protein; RNA-directed DNA polymerase; reverse transcriptase family protein; reverse transcriptase family protein( domain architecture ID 10342468)

RNA-directed DNA polymerase catalyzes DNA replication from an RNA template; contains an exonuclease-endonuclease phosphatase (EEP) domain and may be a fragment of a retrovirus-related Pol polyprotein; RNA-directed DNA polymerase catalyzes DNA replication from an RNA template; contains an exonuclease-endonuclease phosphatase (EEP) domain and may be a fragment of a retrovirus-related Pol polyprotein; reverse transcriptase (RT) family protein similar to non-LTR (long terminal repeat) retrotransposons and non-LTR retrovirus RTs; catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes; reverse transcriptase (RT) family protein containing an exonuclease-endonuclease phosphatase (EEP) domain; RT catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes; may be a fragment of a retrovirus-related Pol polyprotein; reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons; RNA-directed DNA polymerase catalyzes DNA replication from an RNA template; contains an exonuclease-endonuclease phosphatase (EEP) domain and may be a fragment of a retrovirus-related Pol polyprotein; reverse transcriptase (RT) family protein similar to non-LTR (long terminal repeat) retrotransposons and non-LTR retrovirus RTs; catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes; reverse transcriptase (RT) family protein containing an exonuclease-endonuclease phosphatase (EEP) domain; RT catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes; may be a fragment of a retrovirus-related Pol polyprotein; reverse transcriptase (RT) family protein similar to non-LTR (long terminal repeat) retrotransposons and non-LTR retrovirus RTs; catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes; reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 839-1067 2.36e-38

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


:

Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 143.20  E-value: 2.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  839 KGALAEIISPKQSAFLPGRLINDNIMVAYELLHSMRNRKKEkvgSMAMKLDMSKAYDRVEWQFLEAVLfklgfctqwvdl 918
Cdd:cd01650     41 RPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKKS---LVLVFLDFEKAFDSVDHEFLLKAL------------ 105

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  919 vmkcvktasysvlingtpgkkfwpsrGLRQGDPLSPYLFIVCAEGLSSLLDyyekrqmiKRVQVARGGTSINHLLFADDC 998
Cdd:cd01650    106 --------------------------GVRQGDPLSPLLFNLALDDLLRLLN--------KEEEIKLGGPGITHLAYADDI 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2082373869  999 ILFGRTKIEEWRRIQRALQVYEKASGQFLNKEKTAVFFSKNSHPVDKQaIKEAGQNLVCGIYEKYLGLP 1067
Cdd:cd01650    152 VLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKD-ITLNGTPIEAVETFKYLGVT 219
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 1285-1379 2.50e-16

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


:

Pssm-ID: 433612  Cd Length: 84  Bit Score: 75.39  E-value: 2.50e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869 1285 FSIRSAYFLLLELRERNqgecsveerndDRWNKIWELKVPGVTKLFIWRAANNLLPTKENLYKRKVIEEKSCLMCEVEEE 1364
Cdd:pfam13966    1 FSVKSAYNLLRQKRPKV-----------DWAKLIWKKKAPPKVKFFLWLALRNRLPTADRLKKRGIPIDSRCPLCGQEEE 69

                           90
                   ....*....|....*
gi 2082373869 1365 TIMHVLWECPAANNL 1379
Cdd:pfam13966   70 TIDHLFFSCPFARQL 84
DUF4283 super family cl16623
Domain of unknown function (DUF4283); This domain family is found in plants, and is ...
 36-172 4.01e-16

Domain of unknown function (DUF4283); This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues.


The actual alignment was detected with superfamily member pfam14111:

Pssm-ID: 464086  Cd Length: 145  Bit Score: 76.92  E-value: 4.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869   36 QRTLLEKFCSnRLISKEVVENTLAKVWRISKQAQFTEVSPNIFAIVLDNIANKQKVWSGRPWLFDNQLLVLKEFDGFTPL 115
Cdd:pfam14111   10 KLCLVGRFTG-KVPSLGAIRRVLARQWGLGGGVKIKELGDGYFLFRFPSEEDLERVLSKGPWLIGNVPMLLQRWSPDFKP 88

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2082373869  116 KQVNFNSESFWVRFHNLPLSCMMEVRGEQIGSTVGRVERVDVQEDGSGWGKFLRVQI 172
Cdd:pfam14111   89 TPEELTTIPIWVQLPGLPLHLWSREVLSKIASAVGKPLETDENTENKTRLSFARVKV 145
zf-CCHC_4 super family cl18687
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 174-219 3.09e-06

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins.


The actual alignment was detected with superfamily member pfam14392:

Pssm-ID: 433930  Cd Length: 49  Bit Score: 45.40  E-value: 3.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2082373869  174 IDLNQPL-TRGRTLMVKGKDIWIPFSYEKMPRICFLCGCIKHGQDEC 219
Cdd:pfam14392    1 IDITKPLrFFRRIRFPSGEWALIRFKYERLRRFCFICGRLGHSDKFC 47
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 839-1067 2.36e-38

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 143.20  E-value: 2.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  839 KGALAEIISPKQSAFLPGRLINDNIMVAYELLHSMRNRKKEkvgSMAMKLDMSKAYDRVEWQFLEAVLfklgfctqwvdl 918
Cdd:cd01650     41 RPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKKS---LVLVFLDFEKAFDSVDHEFLLKAL------------ 105

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  919 vmkcvktasysvlingtpgkkfwpsrGLRQGDPLSPYLFIVCAEGLSSLLDyyekrqmiKRVQVARGGTSINHLLFADDC 998
Cdd:cd01650    106 --------------------------GVRQGDPLSPLLFNLALDDLLRLLN--------KEEEIKLGGPGITHLAYADDI 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2082373869  999 ILFGRTKIEEWRRIQRALQVYEKASGQFLNKEKTAVFFSKNSHPVDKQaIKEAGQNLVCGIYEKYLGLP 1067
Cdd:cd01650    152 VLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKD-ITLNGTPIEAVETFKYLGVT 219
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 859-1040 2.03e-18

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 84.66  E-value: 2.03e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  859 INDNIMVAYELLHSMRNRKKEKVGSMAMKLDMSKAYDRVEWQFLEAVLFKLGFCTQWVDlvmkcvktasysvlINGTPGK 938
Cdd:pfam00078   30 LKPENLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPPININ--------------WNGELSG 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  939 KFWPSRGLRQGDPLSPYLFIVCAEGLSSLLdyyekrqmikrvqvaRGGTSINHLLFADDCILFGRTKiEEWRRIQRALQV 1018
Cdd:pfam00078   96 GRYEWKGLPQGLVLSPALFQLFMNELLRPL---------------RKRAGLTLVRYADDILIFSKSE-EEHQEALEEVLE 159

                          170       180
                   ....*....|....*....|..
gi 2082373869 1019 YEKASGQFLNKEKTAVFFSKNS 1040
Cdd:pfam00078  160 WLKESGLKINPEKTQFFLKSKE 181
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 1285-1379 2.50e-16

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


Pssm-ID: 433612  Cd Length: 84  Bit Score: 75.39  E-value: 2.50e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869 1285 FSIRSAYFLLLELRERNqgecsveerndDRWNKIWELKVPGVTKLFIWRAANNLLPTKENLYKRKVIEEKSCLMCEVEEE 1364
Cdd:pfam13966    1 FSVKSAYNLLRQKRPKV-----------DWAKLIWKKKAPPKVKFFLWLALRNRLPTADRLKKRGIPIDSRCPLCGQEEE 69

                           90
                   ....*....|....*
gi 2082373869 1365 TIMHVLWECPAANNL 1379
Cdd:pfam13966   70 TIDHLFFSCPFARQL 84
DUF4283 pfam14111
Domain of unknown function (DUF4283); This domain family is found in plants, and is ...
 36-172 4.01e-16

Domain of unknown function (DUF4283); This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues.


Pssm-ID: 464086  Cd Length: 145  Bit Score: 76.92  E-value: 4.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869   36 QRTLLEKFCSnRLISKEVVENTLAKVWRISKQAQFTEVSPNIFAIVLDNIANKQKVWSGRPWLFDNQLLVLKEFDGFTPL 115
Cdd:pfam14111   10 KLCLVGRFTG-KVPSLGAIRRVLARQWGLGGGVKIKELGDGYFLFRFPSEEDLERVLSKGPWLIGNVPMLLQRWSPDFKP 88

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2082373869  116 KQVNFNSESFWVRFHNLPLSCMMEVRGEQIGSTVGRVERVDVQEDGSGWGKFLRVQI 172
Cdd:pfam14111   89 TPEELTTIPIWVQLPGLPLHLWSREVLSKIASAVGKPLETDENTENKTRLSFARVKV 145
zf-CCHC_4 pfam14392
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 174-219 3.09e-06

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins.


Pssm-ID: 433930  Cd Length: 49  Bit Score: 45.40  E-value: 3.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2082373869  174 IDLNQPL-TRGRTLMVKGKDIWIPFSYEKMPRICFLCGCIKHGQDEC 219
Cdd:pfam14392    1 IDITKPLrFFRRIRFPSGEWALIRFKYERLRRFCFICGRLGHSDKFC 47
 
Name Accession Description Interval E-value
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 839-1067 2.36e-38

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 143.20  E-value: 2.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  839 KGALAEIISPKQSAFLPGRLINDNIMVAYELLHSMRNRKKEkvgSMAMKLDMSKAYDRVEWQFLEAVLfklgfctqwvdl 918
Cdd:cd01650     41 RPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKKS---LVLVFLDFEKAFDSVDHEFLLKAL------------ 105

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  919 vmkcvktasysvlingtpgkkfwpsrGLRQGDPLSPYLFIVCAEGLSSLLDyyekrqmiKRVQVARGGTSINHLLFADDC 998
Cdd:cd01650    106 --------------------------GVRQGDPLSPLLFNLALDDLLRLLN--------KEEEIKLGGPGITHLAYADDI 151

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2082373869  999 ILFGRTKIEEWRRIQRALQVYEKASGQFLNKEKTAVFFSKNSHPVDKQaIKEAGQNLVCGIYEKYLGLP 1067
Cdd:cd01650    152 VLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKD-ITLNGTPIEAVETFKYLGVT 219
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 859-1040 2.03e-18

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 84.66  E-value: 2.03e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  859 INDNIMVAYELLHSMRNRKKEKVGSMAMKLDMSKAYDRVEWQFLEAVLFKLGFCTQWVDlvmkcvktasysvlINGTPGK 938
Cdd:pfam00078   30 LKPENLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPPININ--------------WNGELSG 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869  939 KFWPSRGLRQGDPLSPYLFIVCAEGLSSLLdyyekrqmikrvqvaRGGTSINHLLFADDCILFGRTKiEEWRRIQRALQV 1018
Cdd:pfam00078   96 GRYEWKGLPQGLVLSPALFQLFMNELLRPL---------------RKRAGLTLVRYADDILIFSKSE-EEHQEALEEVLE 159

                          170       180
                   ....*....|....*....|..
gi 2082373869 1019 YEKASGQFLNKEKTAVFFSKNS 1040
Cdd:pfam00078  160 WLKESGLKINPEKTQFFLKSKE 181
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 1285-1379 2.50e-16

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


Pssm-ID: 433612  Cd Length: 84  Bit Score: 75.39  E-value: 2.50e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869 1285 FSIRSAYFLLLELRERNqgecsveerndDRWNKIWELKVPGVTKLFIWRAANNLLPTKENLYKRKVIEEKSCLMCEVEEE 1364
Cdd:pfam13966    1 FSVKSAYNLLRQKRPKV-----------DWAKLIWKKKAPPKVKFFLWLALRNRLPTADRLKKRGIPIDSRCPLCGQEEE 69

                           90
                   ....*....|....*
gi 2082373869 1365 TIMHVLWECPAANNL 1379
Cdd:pfam13966   70 TIDHLFFSCPFARQL 84
DUF4283 pfam14111
Domain of unknown function (DUF4283); This domain family is found in plants, and is ...
 36-172 4.01e-16

Domain of unknown function (DUF4283); This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues.


Pssm-ID: 464086  Cd Length: 145  Bit Score: 76.92  E-value: 4.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373869   36 QRTLLEKFCSnRLISKEVVENTLAKVWRISKQAQFTEVSPNIFAIVLDNIANKQKVWSGRPWLFDNQLLVLKEFDGFTPL 115
Cdd:pfam14111   10 KLCLVGRFTG-KVPSLGAIRRVLARQWGLGGGVKIKELGDGYFLFRFPSEEDLERVLSKGPWLIGNVPMLLQRWSPDFKP 88

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2082373869  116 KQVNFNSESFWVRFHNLPLSCMMEVRGEQIGSTVGRVERVDVQEDGSGWGKFLRVQI 172
Cdd:pfam14111   89 TPEELTTIPIWVQLPGLPLHLWSREVLSKIASAVGKPLETDENTENKTRLSFARVKV 145
zf-CCHC_4 pfam14392
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 174-219 3.09e-06

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins.


Pssm-ID: 433930  Cd Length: 49  Bit Score: 45.40  E-value: 3.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2082373869  174 IDLNQPL-TRGRTLMVKGKDIWIPFSYEKMPRICFLCGCIKHGQDEC 219
Cdd:pfam14392    1 IDITKPLrFFRRIRFPSGEWALIRFKYERLRRFCFICGRLGHSDKFC 47
 
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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