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Conserved domains on  [gi|723754139|ref|XP_010314926|]
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uncharacterized protein LOC104645271 [Solanum lycopersicum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 125-218 5.55e-09

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: 51.93  E-value: 5.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723754139  125 WGMDFiGPIEPTASNGHRFILVTLDYFIKWVEAASY-KSVTKKFVANFVRNNLICRFGVPESIITNNGANLNSHLMREIC 203
Cdd:pfam00665   5 WQGDF-TYIRIPGGGGKLYLLVIVDDFSREILAWALsSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFL 83

                          90
                  ....*....|....*
gi 723754139  204 EKFNITHRNSTSYRP 218
Cdd:pfam00665  84 KDLGIKPSFSRPGNP 98
RT_RNaseH_2 super family cl39038
RNase H-like domain found in reverse transcriptase;
18-59 1.52e-07

RNase H-like domain found in reverse transcriptase;


The actual alignment was detected with superfamily member pfam17919:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 48.26  E-value: 1.52e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 723754139   18 WIEECQTAFEAIKNYLSNLPVLVPPRERSPLLLYLSVSDSAF 59
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGI 42
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 62-91 1.91e-04

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member cd09279:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 128  Bit Score: 40.15  E-value: 1.91e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 723754139  62 KLRKRFRKIEFRHTPRIKNELVDALATIAL 91
Cdd:cd09279   98 ELLAKFELVELKWIPREQNKEADALANQAL 127
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 125-218 5.55e-09

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: 51.93  E-value: 5.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723754139  125 WGMDFiGPIEPTASNGHRFILVTLDYFIKWVEAASY-KSVTKKFVANFVRNNLICRFGVPESIITNNGANLNSHLMREIC 203
Cdd:pfam00665   5 WQGDF-TYIRIPGGGGKLYLLVIVDDFSREILAWALsSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFL 83

                          90
                  ....*....|....*
gi 723754139  204 EKFNITHRNSTSYRP 218
Cdd:pfam00665  84 KDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 122-233 1.33e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 54.13  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723754139 122 PDAWGMDF--IGPIEPTasnGHRFILVTLDYFIKWVEAASYKSVTKKFVANFVRNnLICRFGVP-ESIITNNGANLNSHL 198
Cdd:NF033577 128 GELWHIDIkkLGRIPDV---GRLYLHTAIDDHSRFAYAELYPDETAETAADFLRR-AFAEHGIPiRRVLTDNGSEFRSRA 203

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 723754139 199 M--REICEKFNITHRNSTSYRPQMNGAVEATNKNIKN 233
Cdd:NF033577 204 HgfELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
18-59 1.52e-07

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 48.26  E-value: 1.52e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 723754139   18 WIEECQTAFEAIKNYLSNLPVLVPPRERSPLLLYLSVSDSAF 59
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGI 42
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 62-91 1.91e-04

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 40.15  E-value: 1.91e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 723754139  62 KLRKRFRKIEFRHTPRIKNELVDALATIAL 91
Cdd:cd09279   98 ELLAKFELVELKWIPREQNKEADALANQAL 127
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 125-218 5.55e-09

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: 51.93  E-value: 5.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723754139  125 WGMDFiGPIEPTASNGHRFILVTLDYFIKWVEAASY-KSVTKKFVANFVRNNLICRFGVPESIITNNGANLNSHLMREIC 203
Cdd:pfam00665   5 WQGDF-TYIRIPGGGGKLYLLVIVDDFSREILAWALsSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFL 83

                          90
                  ....*....|....*
gi 723754139  204 EKFNITHRNSTSYRP 218
Cdd:pfam00665  84 KDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 122-233 1.33e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 54.13  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723754139 122 PDAWGMDF--IGPIEPTasnGHRFILVTLDYFIKWVEAASYKSVTKKFVANFVRNnLICRFGVP-ESIITNNGANLNSHL 198
Cdd:NF033577 128 GELWHIDIkkLGRIPDV---GRLYLHTAIDDHSRFAYAELYPDETAETAADFLRR-AFAEHGIPiRRVLTDNGSEFRSRA 203

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 723754139 199 M--REICEKFNITHRNSTSYRPQMNGAVEATNKNIKN 233
Cdd:NF033577 204 HgfELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
18-59 1.52e-07

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 48.26  E-value: 1.52e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 723754139   18 WIEECQTAFEAIKNYLSNLPVLVPPRERSPLLLYLSVSDSAF 59
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGI 42
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 62-91 1.91e-04

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 40.15  E-value: 1.91e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 723754139  62 KLRKRFRKIEFRHTPRIKNELVDALATIAL 91
Cdd:cd09279   98 ELLAKFELVELKWIPREQNKEADALANQAL 127
 
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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