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Conserved domains on  [gi|1527518114|ref|XP_027108696|]
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uncharacterized protein LOC113728496 [Coffea arabica]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 793-970 3.01e-69

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


:

Pssm-ID: 238825  Cd Length: 177  Bit Score: 230.17  E-value: 3.01e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  793 KMIHEIQYPTWlSNPVMVKKDTGGWRMCVDFTDLNKACPKDCYPLPRIDALVDTAMGYEVLCFLDAFKGYHQIGMSEEDQ 872
Cdd:cd01647      1 GIIEPSSSPYA-SPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  873 EKTAFYTDRGTYCYTTMPFGLKNAGATYQRLINRLFKNQIGRNVEAYVDGILVKSLATSSFLSDVREVFGVLRDSRMKLN 952
Cdd:cd01647     80 PKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLN 159

                          170
                   ....*....|....*...
gi 1527518114  953 PKKCVSGVISGKFLGYLV 970
Cdd:cd01647    160 PEKCEFGVPEVEFLGHIV 177
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1202-1326 1.20e-56

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: 192.30  E-value: 1.20e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1202 WTLYVDGSSNGN--GSGAGLLLEGAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLG 1279
Cdd:cd09279      1 WTLYFDGASRGNpgPAGAGVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1527518114 1280 EYETKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLAS 1326
Cdd:cd09279     81 EYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1033-1130 9.77e-25

RNase H-like domain found in reverse transcriptase;


:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 99.88  E-value: 9.77e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1033 WTEECQAAFDKLKQYLHHLPTLASPRPEEKLYLYLSTADEAVSAVL--IRDEGTQVPVYYVSRALRGPETRYTQVEKLVL 1110
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLsqEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1527518114 1111 GLVHAARRLKPYFLAHPISV 1130
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1486-1582 7.49e-16

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: 74.66  E-value: 7.49e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1486 PFEQWGTDIiGPFPRAV-GGHTFVVTAVDYFTKWVEAEPLRT-ITGLAIQKFFWKCIVCRFGIPQVIISDNGRQFAENPF 1563
Cdd:pfam00665    1 PNQLWQGDF-TYIRIPGgGGKLYLLVIVDDFSREILAWALSSeMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 1527518114 1564 KTWCTNLGIKQHFTSVGHP 1582
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 153-243 6.09e-12

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


:

Pssm-ID: 367628  Cd Length: 97  Bit Score: 63.51  E-value: 6.09e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  153 RAFPIFLHGTARKWFWSLEPGSI---SSLDELIDRFIHRFVSSRPITKTSAYLLNLQQGqGESLRSYAQRFNEENVQIPD 229
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIdafDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQG-TESVREYVERFKRLARQLPH 79

                           90
                   ....*....|....*.
gi 1527518114  230 Q--NEQVTIAAFTNGL 243
Cdd:pfam03732   80 HgrDEEALISAFLRGL 95
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 522-619 3.36e-08

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


:

Pssm-ID: 133136  Cd Length: 92  Bit Score: 52.72  E-value: 3.36e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  522 IEVLTNNYVVKkVYVDPESSVDVLYYRTFESLKLtREQLTPVRTPIVGFGGHVVHPEGMlTLMVTIGRHprCRTVPVSFA 601
Cdd:cd00303      1 LKGKINGVPVR-ALVDSGASVNFISESLAKKLGL-PPRLLPTPLKVKGANGSSVKTLGV-ILPVTIGIG--GKTFTVDFY 75

                           90
                   ....*....|....*...
gi 1527518114  602 VVKaDSPYNMLIGRPTLN 619
Cdd:cd00303     76 VLD-LLSYDVILGRPWLE 92
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1416-1469 1.29e-04

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: 41.46  E-value: 1.29e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1527518114 1416 RHVLHEIHEGlcGAHVG-HRMLAKkaLLLGYFWLSVRQDAQDLVLGCPSCQVHAP 1469
Cdd:pfam17921    7 KEILKEAHDS--GGHLGiEKTLAR--LRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 793-970 3.01e-69

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 230.17  E-value: 3.01e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  793 KMIHEIQYPTWlSNPVMVKKDTGGWRMCVDFTDLNKACPKDCYPLPRIDALVDTAMGYEVLCFLDAFKGYHQIGMSEEDQ 872
Cdd:cd01647      1 GIIEPSSSPYA-SPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  873 EKTAFYTDRGTYCYTTMPFGLKNAGATYQRLINRLFKNQIGRNVEAYVDGILVKSLATSSFLSDVREVFGVLRDSRMKLN 952
Cdd:cd01647     80 PKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLN 159

                          170
                   ....*....|....*...
gi 1527518114  953 PKKCVSGVISGKFLGYLV 970
Cdd:cd01647    160 PEKCEFGVPEVEFLGHIV 177
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1202-1326 1.20e-56

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: 192.30  E-value: 1.20e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1202 WTLYVDGSSNGN--GSGAGLLLEGAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLG 1279
Cdd:cd09279      1 WTLYFDGASRGNpgPAGAGVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1527518114 1280 EYETKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLAS 1326
Cdd:cd09279     81 EYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 811-968 2.14e-29

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: 116.63  E-value: 2.14e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  811 KKDTGGWRMC----VDFTDLNKAC-------PKDCYPLPRIDALVDTAMGYEVLCFLDAFKGYHQIGMSEEDQEKTAF-- 877
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFtt 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  878 ---------YTDRGTYCYTTMPFGLKNAGATYQRLINRLFK---NQIGRNVEAYVDGILVKSLATSSFLSDVREVFGVLR 945
Cdd:pfam00078   83 ppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRplrKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLK 162

                          170       180
                   ....*....|....*....|....*
gi 1527518114  946 DSRMKLNPKKC--VSGVISGKFLGY 968
Cdd:pfam00078  163 ESGLKINPEKTqfFLKSKEVKYLGV 187
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1033-1130 9.77e-25

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 99.88  E-value: 9.77e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1033 WTEECQAAFDKLKQYLHHLPTLASPRPEEKLYLYLSTADEAVSAVL--IRDEGTQVPVYYVSRALRGPETRYTQVEKLVL 1110
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLsqEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1527518114 1111 GLVHAARRLKPYFLAHPISV 1130
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
RNAseHI_Thmprot NF041175
ribonuclease HI;
1239-1325 1.10e-23

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 98.50  E-value: 1.10e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1239 ATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEYETKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRA 1318
Cdd:NF041175    47 STNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEA 126


                   ....*..
gi 1527518114 1319 DALSRLA 1325
Cdd:NF041175   127 DRLSRIA 133
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1202-1325 1.94e-22

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 94.53  E-value: 1.94e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1202 WTLYVDGSSNGN--GSGAGLLLEgAQGEVCSYALRFGfPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLG 1279
Cdd:COG0328      3 IEIYTDGACRGNpgPGGWGAVIR-YGGEEKELSGGLG-DTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1527518114 1280 EYETKDETM------QRYLSKVRQLTAYfESFEIQRIPRSQ----NKRADALSRLA 1325
Cdd:COG0328     81 WIHGWKKNGwkpvknPDLWQRLDELLAR-HKVTFEWVKGHAghpgNERADALANKA 135
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 1207-1325 6.52e-22

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 99.67  E-value: 6.52e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1207 DGSSNGN----GSGAgLLLEGAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEYE 1282
Cdd:PRK07238     8 DGGSRGNpgpaGYGA-VVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWK 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1527518114 1283 TKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLA 1325
Cdd:PRK07238    87 VKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1064-1166 1.42e-20

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 88.70  E-value: 1.42e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1064 YLYLSTADEAVSAVL--IRDEGTQVPVYYVSRALRGPETRYTQVEKLVLGLVHAARRLKPYFLAHPISVRTD-QPFRQIL 1140
Cdd:cd09274      1 ILETDASDYGIGAVLsqEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDhKALKYLL 80

                           90       100
                   ....*....|....*....|....*.
gi 1527518114 1141 MRPEASGRLTKWAVELGEYDLSYEPR 1166
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYR 106
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 1206-1325 1.87e-20

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 88.48  E-value: 1.87e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1206 VDGSSNGNG--SGAGLLLEGAQGEVC-SYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEyE 1282
Cdd:pfam13456    2 FDGAFKCDSglAGAGVVIRDPNGNVLlAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1527518114 1283 TKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLA 1325
Cdd:pfam13456   81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1486-1582 7.49e-16

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: 74.66  E-value: 7.49e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1486 PFEQWGTDIiGPFPRAV-GGHTFVVTAVDYFTKWVEAEPLRT-ITGLAIQKFFWKCIVCRFGIPQVIISDNGRQFAENPF 1563
Cdd:pfam00665    1 PNQLWQGDF-TYIRIPGgGGKLYLLVIVDDFSREILAWALSSeMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 1527518114 1564 KTWCTNLGIKQHFTSVGHP 1582
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1479-1596 1.60e-14

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 75.71  E-value: 1.60e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1479 VPITSPWPFEQWGTDIIGPFPRAVGGHTFVVTAVDYFTKWVEAEPL---RTITglAIQkfFWKCIVCRFGIP-QVIISDN 1554
Cdd:NF033577   120 KRYERAHPGELWHIDIKKLGRIPDVGRLYLHTAIDDHSRFAYAELYpdeTAET--AAD--FLRRAFAEHGIPiRRVLTDN 195

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1527518114 1555 GRQF--AENPFKTWCTNLGIKQHFTSVGHPQANGQAENFNRTLL 1596
Cdd:NF033577   196 GSEFrsRAHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 153-243 6.09e-12

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 63.51  E-value: 6.09e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  153 RAFPIFLHGTARKWFWSLEPGSI---SSLDELIDRFIHRFVSSRPITKTSAYLLNLQQGqGESLRSYAQRFNEENVQIPD 229
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIdafDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQG-TESVREYVERFKRLARQLPH 79

                           90
                   ....*....|....*.
gi 1527518114  230 Q--NEQVTIAAFTNGL 243
Cdd:pfam03732   80 HgrDEEALISAFLRGL 95
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1486-1595 3.72e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.17  E-value: 3.72e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1486 PFEQWGTDI--IgpfpRAVGGHTFVVTAVDYFTK----WVEAEPLRT-ITGLAIQKFFWKCivcRFGIPQVIISDNGRQF 1558
Cdd:COG2801    148 PNQVWVTDItyI----PTAEGWLYLAAVIDLFSReivgWSVSDSMDAeLVVDALEMAIERR---GPPKPLILHSDNGSQY 220

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1527518114 1559 AENPFKTWCTNLGIKQHFTSVGHPQANGQAENFNRTL 1595
Cdd:COG2801    221 TSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 522-619 3.36e-08

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 52.72  E-value: 3.36e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  522 IEVLTNNYVVKkVYVDPESSVDVLYYRTFESLKLtREQLTPVRTPIVGFGGHVVHPEGMlTLMVTIGRHprCRTVPVSFA 601
Cdd:cd00303      1 LKGKINGVPVR-ALVDSGASVNFISESLAKKLGL-PPRLLPTPLKVKGANGSSVKTLGV-ILPVTIGIG--GKTFTVDFY 75

                           90
                   ....*....|....*...
gi 1527518114  602 VVKaDSPYNMLIGRPTLN 619
Cdd:cd00303     76 VLD-LLSYDVILGRPWLE 92
transpos_IS3 NF033516
IS3 family transposase;
1538-1595 4.46e-07

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 54.11  E-value: 4.46e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1527518114 1538 KCIVCRFGIPQVII-SDNGRQFAENPFKTWCTNLGIKQHFTSVGHPQANGQAENFNRTL 1595
Cdd:NF033516   266 MAIEWRGKPEGLILhSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTL 324
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1416-1469 1.29e-04

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: 41.46  E-value: 1.29e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1527518114 1416 RHVLHEIHEGlcGAHVG-HRMLAKkaLLLGYFWLSVRQDAQDLVLGCPSCQVHAP 1469
Cdd:pfam17921    7 KEILKEAHDS--GGHLGiEKTLAR--LRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 793-970 3.01e-69

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 230.17  E-value: 3.01e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  793 KMIHEIQYPTWlSNPVMVKKDTGGWRMCVDFTDLNKACPKDCYPLPRIDALVDTAMGYEVLCFLDAFKGYHQIGMSEEDQ 872
Cdd:cd01647      1 GIIEPSSSPYA-SPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  873 EKTAFYTDRGTYCYTTMPFGLKNAGATYQRLINRLFKNQIGRNVEAYVDGILVKSLATSSFLSDVREVFGVLRDSRMKLN 952
Cdd:cd01647     80 PKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLN 159

                          170
                   ....*....|....*...
gi 1527518114  953 PKKCVSGVISGKFLGYLV 970
Cdd:cd01647    160 PEKCEFGVPEVEFLGHIV 177
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1202-1326 1.20e-56

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: 192.30  E-value: 1.20e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1202 WTLYVDGSSNGN--GSGAGLLLEGAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLG 1279
Cdd:cd09279      1 WTLYFDGASRGNpgPAGAGVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1527518114 1280 EYETKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLAS 1326
Cdd:cd09279     81 EYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 811-968 2.14e-29

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: 116.63  E-value: 2.14e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  811 KKDTGGWRMC----VDFTDLNKAC-------PKDCYPLPRIDALVDTAMGYEVLCFLDAFKGYHQIGMSEEDQEKTAF-- 877
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFtt 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  878 ---------YTDRGTYCYTTMPFGLKNAGATYQRLINRLFK---NQIGRNVEAYVDGILVKSLATSSFLSDVREVFGVLR 945
Cdd:pfam00078   83 ppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRplrKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLK 162

                          170       180
                   ....*....|....*....|....*
gi 1527518114  946 DSRMKLNPKKC--VSGVISGKFLGY 968
Cdd:pfam00078  163 ESGLKINPEKTqfFLKSKEVKYLGV 187
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1033-1130 9.77e-25

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 99.88  E-value: 9.77e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1033 WTEECQAAFDKLKQYLHHLPTLASPRPEEKLYLYLSTADEAVSAVL--IRDEGTQVPVYYVSRALRGPETRYTQVEKLVL 1110
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLsqEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1527518114 1111 GLVHAARRLKPYFLAHPISV 1130
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
RNAseHI_Thmprot NF041175
ribonuclease HI;
1239-1325 1.10e-23

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 98.50  E-value: 1.10e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1239 ATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEYETKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRA 1318
Cdd:NF041175    47 STNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEA 126


                   ....*..
gi 1527518114 1319 DALSRLA 1325
Cdd:NF041175   127 DRLSRIA 133
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1202-1325 1.94e-22

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 94.53  E-value: 1.94e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1202 WTLYVDGSSNGN--GSGAGLLLEgAQGEVCSYALRFGfPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLG 1279
Cdd:COG0328      3 IEIYTDGACRGNpgPGGWGAVIR-YGGEEKELSGGLG-DTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1527518114 1280 EYETKDETM------QRYLSKVRQLTAYfESFEIQRIPRSQ----NKRADALSRLA 1325
Cdd:COG0328     81 WIHGWKKNGwkpvknPDLWQRLDELLAR-HKVTFEWVKGHAghpgNERADALANKA 135
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 1207-1325 6.52e-22

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 99.67  E-value: 6.52e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1207 DGSSNGN----GSGAgLLLEGAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEYE 1282
Cdd:PRK07238     8 DGGSRGNpgpaGYGA-VVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWK 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1527518114 1283 TKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLA 1325
Cdd:PRK07238    87 VKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1059-1158 7.79e-22

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 91.80  E-value: 7.79e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1059 PEEKLYLYLSTADEAVSAVL--IRDEGTQVPVYYVSRALRGPETRYTQVEKLVLGLVHAARRLKPYFLAHPISVRTD-QP 1135
Cdd:pfam17917    2 PSKPFILETDASDYGIGAVLsqKDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDhKP 81

                           90       100
                   ....*....|....*....|...
gi 1527518114 1136 FRQILMRPEASGRLTKWAVELGE 1158
Cdd:pfam17917   82 LKYLFTPKELNGRLARWALFLQE 104
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1064-1166 1.42e-20

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 88.70  E-value: 1.42e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1064 YLYLSTADEAVSAVL--IRDEGTQVPVYYVSRALRGPETRYTQVEKLVLGLVHAARRLKPYFLAHPISVRTD-QPFRQIL 1140
Cdd:cd09274      1 ILETDASDYGIGAVLsqEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDhKALKYLL 80

                           90       100
                   ....*....|....*....|....*.
gi 1527518114 1141 MRPEASGRLTKWAVELGEYDLSYEPR 1166
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYR 106
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 1206-1325 1.87e-20

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 88.48  E-value: 1.87e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1206 VDGSSNGNG--SGAGLLLEGAQGEVC-SYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEyE 1282
Cdd:pfam13456    2 FDGAFKCDSglAGAGVVIRDPNGNVLlAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1527518114 1283 TKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLA 1325
Cdd:pfam13456   81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
rnhA PRK13907
ribonuclease H; Provisional
 1204-1325 4.13e-18

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 82.02  E-value: 4.13e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1204 LYVDGSSNGNG--SGAGLLLEGAQGEVcsyalRFGFP---ATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVL 1278
Cdd:PRK13907     4 VYIDGASKGNPgpSGAGVFIKGVQPAV-----QLSLPlgtMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1527518114 1279 GEYeTKDETMQRYLSKVRQLTAYFESFEIQRIPRSQNKRADALSRLA 1325
Cdd:PRK13907    79 KEY-AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKA 124
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1204-1323 6.16e-17

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.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 78.51  E-value: 6.16e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1204 LYVDGSSNGNG--SGAGLLLEGAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVVRQVLGEY 1281
Cdd:cd06222      1 INVDGSCRGNPgpAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1527518114 1282 ETKDETMQRYLSKVRQLTaYFESFEIQRIPRSQNKRADALSR 1323
Cdd:cd06222     81 FKWSPNILLIEDILLLLS-RFWSVKISHVPREGNQVADALAK 121
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1486-1582 7.49e-16

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: 74.66  E-value: 7.49e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1486 PFEQWGTDIiGPFPRAV-GGHTFVVTAVDYFTKWVEAEPLRT-ITGLAIQKFFWKCIVCRFGIPQVIISDNGRQFAENPF 1563
Cdd:pfam00665    1 PNQLWQGDF-TYIRIPGgGGKLYLLVIVDDFSREILAWALSSeMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAF 79

                           90
                   ....*....|....*....
gi 1527518114 1564 KTWCTNLGIKQHFTSVGHP 1582
Cdd:pfam00665   80 REFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 1479-1596 1.60e-14

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 75.71  E-value: 1.60e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1479 VPITSPWPFEQWGTDIIGPFPRAVGGHTFVVTAVDYFTKWVEAEPL---RTITglAIQkfFWKCIVCRFGIP-QVIISDN 1554
Cdd:NF033577   120 KRYERAHPGELWHIDIKKLGRIPDVGRLYLHTAIDDHSRFAYAELYpdeTAET--AAD--FLRRAFAEHGIPiRRVLTDN 195

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1527518114 1555 GRQF--AENPFKTWCTNLGIKQHFTSVGHPQANGQAENFNRTLL 1596
Cdd:NF033577   196 GSEFrsRAHGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
PRK07708 PRK07708
hypothetical protein; Validated
 1193-1325 4.65e-14

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 73.14  E-value: 4.65e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1193 SAEVST-PSLWTLYVDGSSNGNGSGAGLllegaqGEVCSYAL-----------RFGFPATNNEAEYEALIAGLQLARRLG 1260
Cdd:PRK07708    64 SKEVEEePHEILVYFDGGFDKETKLAGL------GIVIYYKQgnkryrirrnaYIEGIYDNNEAEYAALYYAMQELEELG 137

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1527518114 1261 A--QQIHVRSDSQLVVRQVLGEYETKDETMQRYLSKVRQLtayFESFEIQ----RIPRSQNKRADALSRLA 1325
Cdd:PRK07708   138 VkhEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQK---LKQLKLTpvyePISRKQNKEADQLATQA 205
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 153-243 6.09e-12

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 63.51  E-value: 6.09e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  153 RAFPIFLHGTARKWFWSLEPGSI---SSLDELIDRFIHRFVSSRPITKTSAYLLNLQQGqGESLRSYAQRFNEENVQIPD 229
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIdafDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQG-TESVREYVERFKRLARQLPH 79

                           90
                   ....*....|....*.
gi 1527518114  230 Q--NEQVTIAAFTNGL 243
Cdd:pfam03732   80 HgrDEEALISAFLRGL 95
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1486-1595 3.72e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.17  E-value: 3.72e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1486 PFEQWGTDI--IgpfpRAVGGHTFVVTAVDYFTK----WVEAEPLRT-ITGLAIQKFFWKCivcRFGIPQVIISDNGRQF 1558
Cdd:COG2801    148 PNQVWVTDItyI----PTAEGWLYLAAVIDLFSReivgWSVSDSMDAeLVVDALEMAIERR---GPPKPLILHSDNGSQY 220

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1527518114 1559 AENPFKTWCTNLGIKQHFTSVGHPQANGQAENFNRTL 1595
Cdd:COG2801    221 TSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 522-619 3.36e-08

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 52.72  E-value: 3.36e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  522 IEVLTNNYVVKkVYVDPESSVDVLYYRTFESLKLtREQLTPVRTPIVGFGGHVVHPEGMlTLMVTIGRHprCRTVPVSFA 601
Cdd:cd00303      1 LKGKINGVPVR-ALVDSGASVNFISESLAKKLGL-PPRLLPTPLKVKGANGSSVKTLGV-ILPVTIGIG--GKTFTVDFY 75

                           90
                   ....*....|....*...
gi 1527518114  602 VVKaDSPYNMLIGRPTLN 619
Cdd:cd00303     76 VLD-LLSYDVILGRPWLE 92
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 766-969 3.63e-08

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 55.43  E-value: 3.63e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  766 PVLQKRRHFGSERSKAISDEVDKLLPAKMIHEIQYPtWLSnPVM-VKKDTGG-WRMCVDFTDLNKACPKDCYPLPRIDAL 843
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSP-WNT-PILpVKKPGGNdYRMVQDLRLVNQAVLPIHPAVPNPYTL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  844 VD---TAMGYevLCFLDAFKGYHQIGMSEEDQEKTAFYTDRGTYCYTTMPFGLKNAGAtyqrlinrLFKNQIGRNVEA-- 918
Cdd:cd03715     79 LSllpPKHQW--YTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPT--------LFHEALARDLAPfp 148

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1527518114  919 ----------YVDGILVKSLATSSFLSDVREVFGVLRDSRMKLNPKKCVSGVISGKFLGYL 969
Cdd:cd03715    149 lehegtillqYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVV 209
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1203-1274 5.53e-08

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 53.54  E-value: 5.53e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1527518114 1203 TLYVDGSSNGNG--SGAGLLLEgaqGEVCSYALRFGFPATNNEAEYEALIAGLQLARRlgAQQIHVRSDSQLVV 1274
Cdd:pfam00075    5 TVYTDGSCLGNPgpGGAGAVLY---RGHENISAPLPGRTTNNRAELQAVIEALKALKS--PSKVNIYTDSQYVI 73
transpos_IS3 NF033516
IS3 family transposase;
1538-1595 4.46e-07

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 54.11  E-value: 4.46e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1527518114 1538 KCIVCRFGIPQVII-SDNGRQFAENPFKTWCTNLGIKQHFTSVGHPQANGQAENFNRTL 1595
Cdd:NF033516   266 MAIEWRGKPEGLILhSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTL 324
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1203-1327 8.18e-07

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two 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). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 49.91  E-value: 8.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1203 TLYVDGSSNGNGSGAGLLLEgAQGEVCSYALRFGFPATNNEAEYEALIAGLQLARRLG--AQQIHVRSDSQLVVRQVLGE 1280
Cdd:cd09276      1 VIYTDGSKLEGSVGAGFVIY-RGGEVISRSYRLGTHASVFDAELEAILEALELALATArrARKVTIFTDSQSALQALRNP 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1527518114 1281 YETKDETM-QRYLSKVRQLTAYFESFEIQRIPRSQ----NKRADALSRLAST 1327
Cdd:cd09276     80 RRSSGQVIlIRILRLLRLLKAKGVKVRLRWVPGHVgiegNEAADRLAKEAAS 131
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 1204-1325 3.94e-06

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. 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.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 48.35  E-value: 3.94e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1204 LYVDGSSNGNGSGagllleGAQGevcSYALRFG----------------FPATNNEAEYEALIAGLQLARRL------GA 1261
Cdd:cd13934      2 VYIDGACRNNGRP------DARA---GYGVYFGpdssynvsgrledtggHPQTSQRAELRAAIAALRFRSWIidpdgeGL 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1262 QQIHVRSDSQLVVRQV---LGEYETKD------------ETMQRYLSKVRQLTAyfESFEIQ--RIPRSQNKRADALSRL 1324
Cdd:cd13934     73 KTVVIATDSEYVVKGAtewIPKWKRNGwrtskgkpvknrDLFELLLDEIEDLEE--GGVEVQfwHVPRELNKEADRLAKA 150


                   .
gi 1527518114 1325 A 1325
Cdd:cd13934    151 A 151
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1203-1275 6.50e-06

RNase HI family found mainly in prokaryotes; 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. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 47.48  E-value: 6.50e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1527518114 1203 TLYVDGSSNGN-GSG--AGLLLEGAQGEVcsyalRFGF--PATNNEAEYEALIAGLQLARRlgAQQIHVRSDSQLVVR 1275
Cdd:cd09278      3 VIYTDGACLGNpGPGgwAAVIRYGDHEKE-----LSGGepGTTNNRMELTAAIEALEALKE--PCPVTIYTDSQYVIN 73
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1205-1275 1.58e-05

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote 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. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 46.40  E-value: 1.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1205 YVDGSSNGNGSgaglllEGAQ---------GEVCSYALR-FGFPATNNEAEYEALIAGLQLARRLGAQQIHVRSDSQLVV 1274
Cdd:cd09280      3 YTDGSCLNNGK------PGARagigvyfgpGDPRNVSEPlPGRKQTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAI 76


                   .
gi 1527518114 1275 R 1275
Cdd:cd09280     77 N 77
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 777-970 8.15e-05

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 45.74  E-value: 8.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  777 ERSKAISDEVDKLLPAKMIHEIQYPtWlSNPVMV-KKDTGGWRMCVDFTDLNKACpKDCYPL-PRIDALVDTAMGYEVLc 854
Cdd:cd01645     12 EKLEALTELVTEQLKEGHIEPSTSP-W-NTPVFViKKKSGKWRLLHDLRAVNAQT-QDMGALqPGLPHPAALPKGWPLI- 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  855 FLDAFKGYHQIGMSEEDQEKTAFY---------TDRgtYCYTTMPFGLKNAGATYQRLINRLFKNQIGRNVEA----YVD 921
Cdd:cd01645     88 VLDLKDCFFSIPLHPDDRERFAFTvpsinnkgpAKR--YQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIviyhYMD 165

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1527518114  922 GILVKSLATSSFLSDVREVFGVLRDSRMKLNPKKcVSGVISGKFLGYLV 970
Cdd:cd01645    166 DILIASDLEGQLREIYEELRQTLLRWGLTIPPEK-VQKEPPFQYLGYEL 213
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1416-1469 1.29e-04

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: 41.46  E-value: 1.29e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1527518114 1416 RHVLHEIHEGlcGAHVG-HRMLAKkaLLLGYFWLSVRQDAQDLVLGCPSCQVHAP 1469
Cdd:pfam17921    7 KEILKEAHDS--GGHLGiEKTLAR--LRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1203-1324 1.89e-04

DIRS1 family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 42.66  E-value: 1.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1203 TLYVDGSsnGNGSGAGLLLEGAQGevcsyalrfgfPATNNEA-------EYEALIAGLQ-LARRLGAQQIHVRSDSQLVV 1274
Cdd:cd09275      1 VLFTDAS--LSGWGAYLLNSRAHG-----------PWSADERnkhinllELKAVLLALQhFAAELKNRKILIRTDNTTAV 67

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1527518114 1275 RQVLGEYETKdetMQRYLSKVRQLTAYFESFEIQ----RIPRSQNKRADALSRL 1324
Cdd:cd09275     68 AYINKQGGTS---SPPLLALARQILLWCEQRNIWlrasHIPGVLNTEADRLSRL 118
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 114-265 5.86e-04

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 42.84  E-value: 5.86e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  114 PNFKLPNLHTYDGRGDPEdHLRAFISAFRLYCVPDAVICRAFPIF-----LHGTARKWF--WSLEPG-SISSLDELIDRF 185
Cdd:pfam19259    7 PNFMIQVILPFRGRKDVL-KLKSFISEIMLQMSMIFWPNDAERIVfcarhLTGPAAQWFhdFVQEQGiLDATFDTFIKAF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  186 IHRFVSSRPITKTSAYLLNLQQGQGESLRsYAQRFNEENVQIPDQ--NEQVTIAAFTNGLVAGIFNTEIHRQyPRTLREL 263
Cdd:pfam19259   86 KQHFYGKPDINKLFNDIVNLSEAKLGIER-YNSHFNRLWDLLPPDflSEKAAIMFYIRGLKPETYIIVRLAK-PSTLKEA 163


                   ..
gi 1527518114  264 WE 265
Cdd:pfam19259  164 ME 165
rve_3 pfam13683
Integrase core domain;
1570-1595 2.32e-03

Integrase core domain;


Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 37.97  E-value: 2.32e-03
                           10        20
                   ....*....|....*....|....*.
gi 1527518114 1570 LGIKQHFTSVGHPQANGQAENFNRTL 1595
Cdd:pfam13683    1 LGIEISYIAPGKPMQNGLVESFNGTL 26
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1494-1595 2.68e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 41.79  E-value: 2.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114 1494 IIGPfpravGGHTFVVTAVDYFTKWVEAEPLRTITGLAIQKFFwKCIVCRFGIPQV--IISDNGRQFAEnpFKTWCTNLG 1571
Cdd:COG2826    180 IIGK-----RGKSALLTLVERKSRFVILLKLPDKTAESVADAL-IRLLRKLPAFLRksITTDNGKEFAD--HKEIEAALG 251

                           90       100
                   ....*....|....*....|....
gi 1527518114 1572 IKQHFTSVGHPQANGQAENFNRTL 1595
Cdd:COG2826    252 IKVYFADPYSPWQRGTNENTNGLL 275
retropepsin_like_LTR_1 cd05481
Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal ...
 522-617 4.35e-03

Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats; Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133148  Cd Length: 93  Bit Score: 38.01  E-value: 4.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1527518114  522 IEVLTNNYVVKKVYVDPESSVDVLYYRTFESLKLTREQ-LTPVRTPIVGFGGHVVHPEGMLTLMVTIgRHPRCRtvpVSF 600
Cdd:cd05481      1 LDMKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPeLRPSPVRLTAYGGSTIPVEGGVKLKCRY-RNPKYN---LTF 76

                           90
                   ....*....|....*..
gi 1527518114  601 AVVKADSPynMLIGRPT 617
Cdd:cd05481     77 QVVKEEGP--PLLGAKA 91
 
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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