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Conserved domains on  [gi|1907157804|ref|XP_036020439|]
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snRNA-activating protein complex subunit 3 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 18-225 2.25e-108

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: 335.47  E-value: 2.25e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   18 IVNQKQYRIP-GGIAEITATIKDLKDAGVVVPTTSPFNSPIWPVQKTDG-SWRMTVDYRKLNQVVTPIAAAVPDVVSLLE 95
Cdd:cd03715      1 PVNQKQYPLPrEAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   96 QINTsPGTWYAAIDLANAFFSVPVHKDHQKQFAFSWQGQQYTFTVLPQGYINSPALCHNLVRRDLDRLDLP-QNITLVHY 174
Cdd:cd03715     81 LLPP-KHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEhEGTILLQY 159

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1907157804  175 IDDIMLIGPSEQEVATTLDSLVTHMRIRGWEINPTKIQGPSTSVKFLGVQW 225
Cdd:cd03715    160 VDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 693-788 3.59e-19

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: 83.52  E-value: 3.59e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  693 PATWWQVDYI-GPLPSWKGQRFVLTGVDTYSGYGFAFP-ARNASAKTTIHGLTECLIYRHGIPHSIASDQGTHFTAREVR 770
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1907157804  771 QWAHDHGIHWSYHIPHHP 788
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 880-967 1.27e-16

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


:

Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 75.99  E-value: 1.27e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  880 AGLEVLAPE---RGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKKGITVL-GGVIDPDYHGEIGLPLHNGGKQDYV 955
Cdd:cd07557      1 AGYDLRLGEdfeGIVLPPGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEPVV 80

                           90
                   ....*....|..
gi 1907157804  956 WSVGDPLGRLLV 967
Cdd:cd07557     81 IKKGDRIAQLVF 92
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 480-617 3.04e-11

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 pfam00075:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 141  Bit Score: 62.39  E-value: 3.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  480 WFTDGSARyaGTTQKWTAAALQPLSGTTLKDTGEG-KSSQWAELRAVHMVLQfvCKKKWPDVRLFTDSWAVANGLAGWSG 558
Cdd:pfam00075    6 VYTDGSCL--GNPGPGGAGAVLYRGHENISAPLPGrTTNNRAELQAVIEALK--ALKSPSKVNIYTDSQYVIGGITQWVH 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907157804  559 TWKDHNWKI--GEKDIWGRSMWIDLSKWAKDVKIFVSHVNAHQKVTSaeeefNNQVDKMTR 617
Cdd:pfam00075   82 GWKKNGWPTtsEGKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRLAK 137
RT_RNaseH_2 super family cl39038
RNase H-like domain found in reverse transcriptase;
309-387 1.04e-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: 50.96  E-value: 1.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  309 LGPYDPADPMVLEVsvadrDAvwS-------LWQaPVGESQKRPLGFWSKALPSSADNYSPFEKQLLACYWALVETERLT 381
Cdd:pfam17919   22 LAHPDPDKPFILET-----DA--SdygigavLSQ-EDDDGGERPIAYASRKLSPAERNYSTTEKELLAIVFALKKFRHYL 93


                   ....*.
gi 1907157804  382 IGHQVT 387
Cdd:pfam17919   94 LGRKFT 99
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 18-225 2.25e-108

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: 335.47  E-value: 2.25e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   18 IVNQKQYRIP-GGIAEITATIKDLKDAGVVVPTTSPFNSPIWPVQKTDG-SWRMTVDYRKLNQVVTPIAAAVPDVVSLLE 95
Cdd:cd03715      1 PVNQKQYPLPrEAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   96 QINTsPGTWYAAIDLANAFFSVPVHKDHQKQFAFSWQGQQYTFTVLPQGYINSPALCHNLVRRDLDRLDLP-QNITLVHY 174
Cdd:cd03715     81 LLPP-KHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEhEGTILLQY 159

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1907157804  175 IDDIMLIGPSEQEVATTLDSLVTHMRIRGWEINPTKIQGPSTSVKFLGVQW 225
Cdd:cd03715    160 VDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 62-224 2.14e-28

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: 113.17  E-value: 2.14e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   62 KTDGSWRM----TVDYRKLNQVV-------TPIAAAVPDVVSLLEQINTSpgTWYAAIDLANAFFSVPVHKDHQKQFAFS 130
Cdd:pfam00078    4 KGKGKYRPisllSIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKA--KWFLKLDLKKAFDQVPLDELDRKLTAFT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  131 -------WQGQ----QYTFTVLPQGYINSPALCHNLVRRDLDRLDLPQNITLVHYIDDIMLIGPSEQEVATTLDSLVTHM 199
Cdd:pfam00078   82 tppininWNGElsggRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161

                          170       180
                   ....*....|....*....|....*..
gi 1907157804  200 RIRGWEINPTKIQG--PSTSVKFLGVQ 224
Cdd:pfam00078  162 KESGLKINPEKTQFflKSKEVKYLGVT 188
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 693-788 3.59e-19

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: 83.52  E-value: 3.59e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  693 PATWWQVDYI-GPLPSWKGQRFVLTGVDTYSGYGFAFP-ARNASAKTTIHGLTECLIYRHGIPHSIASDQGTHFTAREVR 770
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1907157804  771 QWAHDHGIHWSYHIPHHP 788
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 880-967 1.27e-16

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 75.99  E-value: 1.27e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  880 AGLEVLAPE---RGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKKGITVL-GGVIDPDYHGEIGLPLHNGGKQDYV 955
Cdd:cd07557      1 AGYDLRLGEdfeGIVLPPGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEPVV 80

                           90
                   ....*....|..
gi 1907157804  956 WSVGDPLGRLLV 967
Cdd:cd07557     81 IKKGDRIAQLVF 92
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 871-976 1.37e-15

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 74.67  E-value: 1.37e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLA--PERGVLLPGATTNISLNWKLRLPPGHFGLLMP---LnqQAKKGITVLG--GVIDPDYHGEIG 943
Cdd:COG0756     13 LPAYATPGSAGLDLRAalDEPVTLKPGERALVPTGLAIALPPGYEAQVRPrsgL--ALKHGITLLNspGTIDSDYRGEIK 90

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907157804  944 LPLHNGGKQDYVWSVGDplgRL--LVLpCPVIKVN 976
Cdd:COG0756     91 VILINLGDEPFTIERGD---RIaqLVI-APVVQAE 121
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 871-970 3.24e-13

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 67.31  E-value: 3.24e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKKGITVLGGVIDPDYHGEIGLPLHNGG 950
Cdd:pfam00692    5 IPTPGSPGDAGYDLYAPYDLTVKPGGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                           90       100
                   ....*....|....*....|
gi 1907157804  951 KQDYVWSVGDPLGRLLVLPC 970
Cdd:pfam00692   85 KSDFTIKKGDRIAQLIFEPI 104
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 868-969 8.69e-13

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 66.49  E-value: 8.69e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  868 KFLLPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKK-GITVL--GGVIDPDYHGEIGL 944
Cdd:TIGR00576   10 NAPLPTYATEGAAGYDLRAAEDVTIPPGERALVPTGIAIELPDGYYGRVAPRSGLALKhGVTIDnsPGVIDADYRGEIKV 89

                           90       100
                   ....*....|....*....|....*
gi 1907157804  945 PLHNGGKQDYVWSVGDPLGRLLVLP 969
Cdd:TIGR00576   90 ILINLGKEDFTVKKGDRIAQLVVEK 114
transpos_IS481 NF033577
IS481 family transposase; null
 697-803 1.66e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 66.08  E-value: 1.66e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  697 WQVD--YIGPLPSwKGQRFVLTGVDTYSGYGFAFPARNASAKTTIHGLtECLIYRHGIP-HSIASDQGTHFTAR--EVRQ 771
Cdd:NF033577   131 WHIDikKLGRIPD-VGRLYLHTAIDDHSRFAYAELYPDETAETAADFL-RRAFAEHGIPiRRVLTDNGSEFRSRahGFEL 208

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907157804  772 WAHDHGIHwsyHI---PHHPEAAGLIERWNGLLKT 803
Cdd:NF033577   209 ALAELGIE---HRrtrPYHPQTNGKVERFHRTLKD 240
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 480-617 3.04e-11

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: 62.39  E-value: 3.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  480 WFTDGSARyaGTTQKWTAAALQPLSGTTLKDTGEG-KSSQWAELRAVHMVLQfvCKKKWPDVRLFTDSWAVANGLAGWSG 558
Cdd:pfam00075    6 VYTDGSCL--GNPGPGGAGAVLYRGHENISAPLPGrTTNNRAELQAVIEALK--ALKSPSKVNIYTDSQYVIGGITQWVH 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907157804  559 TWKDHNWKI--GEKDIWGRSMWIDLSKWAKDVKIFVSHVNAHQKVTSaeeefNNQVDKMTR 617
Cdd:pfam00075   82 GWKKNGWPTtsEGKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRLAK 137
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
691-805 6.30e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.79  E-value: 6.30e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  691 DQPATWWQVD--YIgplPSWKGQRFVLTGVDTYSGY--GFAFpARNASAKTTIHGLTEcLIYRHGIPHSIA--SDQGTHF 764
Cdd:COG2801    146 TAPNQVWVTDitYI---PTAEGWLYLAAVIDLFSREivGWSV-SDSMDAELVVDALEM-AIERRGPPKPLIlhSDNGSQY 220

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1907157804  765 TAREVRQWAHDHGIHWSYHIPHHPEAAGLIERWNGLLKTQL 805
Cdd:COG2801    221 TSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
dut PRK00601
dUTP diphosphatase;
869-976 1.02e-09

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 57.87  E-value: 1.02e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  869 FLLPVPITLGSAGLEVLA--PERGVLLPGATTNISLNWKLRLPPGHFGLLMP---LNqqAKKGITVLG--GVIDPDYHGE 941
Cdd:PRK00601    17 FPLPAYATEGSAGLDLRAclDEPVTLAPGERALVPTGLAIHIPDGYEAQILPrsgLA--HKHGIVLGNlpGTIDSDYRGE 94

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907157804  942 IGLPLHNGGKQDYVWSVGDPLGRLLVLpcPVIKVN 976
Cdd:PRK00601    95 LKVSLWNRGQEPFTIEPGERIAQLVIV--PVVQAE 127
transpos_IS3 NF033516
IS3 family transposase;
705-808 1.48e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.96  E-value: 1.48e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  705 LPSWKGQRFVLTGVDTYSGYGFAF-PARNASAKTTIHGLTEcLIYRHGIPHS--IASDQGTHFTAREVRQWAHDHGIHWS 781
Cdd:NF033516   226 IRTAEGWLYLAVVLDLFSREIVGWsVSTSMSAELVLDALEM-AIEWRGKPEGliLHSDNGSQYTSKAYREWLKEHGITQS 304

                           90       100
                   ....*....|....*....|....*..
gi 1907157804  782 YHIPHHPEAAGLIERWNGLLKTQLQRQ 808
Cdd:NF033516   305 MSRPGNCWDNAVAESFFGTLKRECLYR 331
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 480-619 2.54e-08

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 53.50  E-value: 2.54e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  480 WFTDGSARYAGttqkwtAAALQPLSGTTLKDTGEGKSSQWAELRAVHMVLQFVCKKKwpdVRLFTDSWAVANGL----AG 555
Cdd:cd09273      2 VFTDGSSFKAG------YAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKP---VNIYTDSAYAVHALhlleTI 72

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907157804  556 W--SGTWKDHNWKigekdiwgrSMWIDLSK--WAKDvKIFVSHVNAHQKVTSAEEEFNNQVDKMTRSV 619
Cdd:cd09273     73 GieRGFLKSIKNL---------SLFLQLLEavQRPK-PVAIIHIRAHSKLPGPLAEGNAQADAAAKQA 130
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
481-617 8.25e-08

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 52.15  E-value: 8.25e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  481 FTDGSAR------------YAGTTQKWtaaalqpLSGttlkdtGEGKSS-QWAELRAVHMVLQFvCKKKWPD-VRLFTDS 546
Cdd:COG0328      6 YTDGACRgnpgpggwgaviRYGGEEKE-------LSG------GLGDTTnNRAELTALIAALEA-LKELGPCeVEIYTDS 71

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907157804  547 WAVANGLAGWSGTWKDHNWK-IGEKDIWGRsmwidLSKWAKDVKIFVSHVNAHQKVtsaeeEFNNQVDKMTR 617
Cdd:COG0328     72 QYVVNQITGWIHGWKKNGWKpVKNPDLWQR-----LDELLARHKVTFEWVKGHAGH-----PGNERADALAN 133
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
309-387 1.04e-07

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 50.96  E-value: 1.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  309 LGPYDPADPMVLEVsvadrDAvwS-------LWQaPVGESQKRPLGFWSKALPSSADNYSPFEKQLLACYWALVETERLT 381
Cdd:pfam17919   22 LAHPDPDKPFILET-----DA--SdygigavLSQ-EDDDGGERPIAYASRKLSPAERNYSTTEKELLAIVFALKKFRHYL 93


                   ....*.
gi 1907157804  382 IGHQVT 387
Cdd:pfam17919   94 LGRKFT 99
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 333-374 1.11e-04

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: 42.86  E-value: 1.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1907157804  333 LWQaPVGESQKRPLGFWSKALPSSADNYSPFEKQLLACYWAL 374
Cdd:cd09274     15 LSQ-EDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWAL 55
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 18-225 2.25e-108

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: 335.47  E-value: 2.25e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   18 IVNQKQYRIP-GGIAEITATIKDLKDAGVVVPTTSPFNSPIWPVQKTDG-SWRMTVDYRKLNQVVTPIAAAVPDVVSLLE 95
Cdd:cd03715      1 PVNQKQYPLPrEAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   96 QINTsPGTWYAAIDLANAFFSVPVHKDHQKQFAFSWQGQQYTFTVLPQGYINSPALCHNLVRRDLDRLDLP-QNITLVHY 174
Cdd:cd03715     81 LLPP-KHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEhEGTILLQY 159

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1907157804  175 IDDIMLIGPSEQEVATTLDSLVTHMRIRGWEINPTKIQGPSTSVKFLGVQW 225
Cdd:cd03715    160 VDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 37-224 2.20e-35

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: 133.95  E-value: 2.20e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   37 IKDLKDAGVVVPTTSPFNSPIWPVQKTDGSWRMTVDYRKLNQVVTPIAAAVPDVVSLleqiNTSPGTWY-AAIDLANAFF 115
Cdd:cd01645     21 VTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHP----AALPKGWPlIVLDLKDCFF 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  116 SVPVHKDHQKQFAFSW-------QGQQYTFTVLPQGYINSPALCHNLVRRDLD--RLDLPqNITLVHYIDDIMLIGPSEQ 186
Cdd:cd01645     97 SIPLHPDDRERFAFTVpsinnkgPAKRYQWKVLPQGMKNSPTICQSFVAQALEpfRKQYP-DIVIYHYMDDILIASDLEG 175

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1907157804  187 EVATTLDSLVTHMRIRGWEINPTKIQgPSTSVKFLGVQ 224
Cdd:cd01645    176 QLREIYEELRQTLLRWGLTIPPEKVQ-KEPPFQYLGYE 212
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 44-222 3.16e-31

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: 120.78  E-value: 3.16e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   44 GVVVPTTSPFNSPIWPVQKTDGSWRMTVDYRKLNQVVTPIAAAVPDVVSLLEQIntSPGTWYAAIDLANAFFSVPVHKDH 123
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEEL--AGAKVFSKLDLRSGYHQIPLAEES 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  124 QKQFAFSWQGQQYTFTVLPQGYINSPALCHNLVRRDLDrlDLPQNITLVhYIDDIMLIGPSEQEVATTLDSLVTHMRIRG 203
Cdd:cd01647     79 RPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILG--DLLGDFVEV-YLDDILVYSKTEEEHLEHLREVLERLREAG 155

                          170
                   ....*....|....*....
gi 1907157804  204 WEINPTKIQGPSTSVKFLG 222
Cdd:cd01647    156 LKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 62-224 2.14e-28

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: 113.17  E-value: 2.14e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   62 KTDGSWRM----TVDYRKLNQVV-------TPIAAAVPDVVSLLEQINTSpgTWYAAIDLANAFFSVPVHKDHQKQFAFS 130
Cdd:pfam00078    4 KGKGKYRPisllSIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKA--KWFLKLDLKKAFDQVPLDELDRKLTAFT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  131 -------WQGQ----QYTFTVLPQGYINSPALCHNLVRRDLDRLDLPQNITLVHYIDDIMLIGPSEQEVATTLDSLVTHM 199
Cdd:pfam00078   82 tppininWNGElsggRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161

                          170       180
                   ....*....|....*....|....*..
gi 1907157804  200 RIRGWEINPTKIQG--PSTSVKFLGVQ 224
Cdd:pfam00078  162 KESGLKINPEKTQFflKSKEVKYLGVT 188
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 693-788 3.59e-19

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: 83.52  E-value: 3.59e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  693 PATWWQVDYI-GPLPSWKGQRFVLTGVDTYSGYGFAFP-ARNASAKTTIHGLTECLIYRHGIPHSIASDQGTHFTAREVR 770
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1907157804  771 QWAHDHGIHWSYHIPHHP 788
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 880-967 1.27e-16

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 75.99  E-value: 1.27e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  880 AGLEVLAPE---RGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKKGITVL-GGVIDPDYHGEIGLPLHNGGKQDYV 955
Cdd:cd07557      1 AGYDLRLGEdfeGIVLPPGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEPVV 80

                           90
                   ....*....|..
gi 1907157804  956 WSVGDPLGRLLV 967
Cdd:cd07557     81 IKKGDRIAQLVF 92
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 871-976 1.37e-15

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 74.67  E-value: 1.37e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLA--PERGVLLPGATTNISLNWKLRLPPGHFGLLMP---LnqQAKKGITVLG--GVIDPDYHGEIG 943
Cdd:COG0756     13 LPAYATPGSAGLDLRAalDEPVTLKPGERALVPTGLAIALPPGYEAQVRPrsgL--ALKHGITLLNspGTIDSDYRGEIK 90

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907157804  944 LPLHNGGKQDYVWSVGDplgRL--LVLpCPVIKVN 976
Cdd:COG0756     91 VILINLGDEPFTIERGD---RIaqLVI-APVVQAE 121
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 108-224 5.72e-15

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 71.99  E-value: 5.72e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  108 IDLANAFFSVPVHKDHQKQFAFSWQGQQYTFTVLPQGYINSPALCHNLVRRDLDRLDLpQNITLVHYIDDIMLIGPSEqe 187
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRL-LGVRIFSYLDDLLIIASSI-- 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1907157804  188 vaTTLDSLVTHMRIR-----GWEINPTK-IQGPSTSVKFLGVQ 224
Cdd:cd03714     78 --KTSEAVLRHLRATllanlGFTLNLEKsKLGPTQRITFLGLE 118
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 871-970 3.24e-13

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 67.31  E-value: 3.24e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKKGITVLGGVIDPDYHGEIGLPLHNGG 950
Cdd:pfam00692    5 IPTPGSPGDAGYDLYAPYDLTVKPGGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                           90       100
                   ....*....|....*....|
gi 1907157804  951 KQDYVWSVGDPLGRLLVLPC 970
Cdd:pfam00692   85 KSDFTIKKGDRIAQLIFEPI 104
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 868-969 8.69e-13

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 66.49  E-value: 8.69e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  868 KFLLPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQAKK-GITVL--GGVIDPDYHGEIGL 944
Cdd:TIGR00576   10 NAPLPTYATEGAAGYDLRAAEDVTIPPGERALVPTGIAIELPDGYYGRVAPRSGLALKhGVTIDnsPGVIDADYRGEIKV 89

                           90       100
                   ....*....|....*....|....*
gi 1907157804  945 PLHNGGKQDYVWSVGDPLGRLLVLP 969
Cdd:TIGR00576   90 ILINLGKEDFTVKKGDRIAQLVVEK 114
transpos_IS481 NF033577
IS481 family transposase; null
 697-803 1.66e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 66.08  E-value: 1.66e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  697 WQVD--YIGPLPSwKGQRFVLTGVDTYSGYGFAFPARNASAKTTIHGLtECLIYRHGIP-HSIASDQGTHFTAR--EVRQ 771
Cdd:NF033577   131 WHIDikKLGRIPD-VGRLYLHTAIDDHSRFAYAELYPDETAETAADFL-RRAFAEHGIPiRRVLTDNGSEFRSRahGFEL 208

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907157804  772 WAHDHGIHwsyHI---PHHPEAAGLIERWNGLLKT 803
Cdd:NF033577   209 ALAELGIE---HRrtrPYHPQTNGKVERFHRTLKD 240
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 480-617 3.04e-11

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: 62.39  E-value: 3.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  480 WFTDGSARyaGTTQKWTAAALQPLSGTTLKDTGEG-KSSQWAELRAVHMVLQfvCKKKWPDVRLFTDSWAVANGLAGWSG 558
Cdd:pfam00075    6 VYTDGSCL--GNPGPGGAGAVLYRGHENISAPLPGrTTNNRAELQAVIEALK--ALKSPSKVNIYTDSQYVIGGITQWVH 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907157804  559 TWKDHNWKI--GEKDIWGRSMWIDLSKWAKDVKIFVSHVNAHQKVTSaeeefNNQVDKMTR 617
Cdd:pfam00075   82 GWKKNGWPTtsEGKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRLAK 137
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
691-805 6.30e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.79  E-value: 6.30e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  691 DQPATWWQVD--YIgplPSWKGQRFVLTGVDTYSGY--GFAFpARNASAKTTIHGLTEcLIYRHGIPHSIA--SDQGTHF 764
Cdd:COG2801    146 TAPNQVWVTDitYI---PTAEGWLYLAAVIDLFSREivGWSV-SDSMDAELVVDALEM-AIERRGPPKPLIlhSDNGSQY 220

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1907157804  765 TAREVRQWAHDHGIHWSYHIPHHPEAAGLIERWNGLLKTQL 805
Cdd:COG2801    221 TSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
dut PRK00601
dUTP diphosphatase;
869-976 1.02e-09

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 57.87  E-value: 1.02e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  869 FLLPVPITLGSAGLEVLA--PERGVLLPGATTNISLNWKLRLPPGHFGLLMP---LNqqAKKGITVLG--GVIDPDYHGE 941
Cdd:PRK00601    17 FPLPAYATEGSAGLDLRAclDEPVTLAPGERALVPTGLAIHIPDGYEAQILPrsgLA--HKHGIVLGNlpGTIDSDYRGE 94

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907157804  942 IGLPLHNGGKQDYVWSVGDPLGRLLVLpcPVIKVN 976
Cdd:PRK00601    95 LKVSLWNRGQEPFTIEPGERIAQLVIV--PVVQAE 127
transpos_IS3 NF033516
IS3 family transposase;
705-808 1.48e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.96  E-value: 1.48e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  705 LPSWKGQRFVLTGVDTYSGYGFAF-PARNASAKTTIHGLTEcLIYRHGIPHS--IASDQGTHFTAREVRQWAHDHGIHWS 781
Cdd:NF033516   226 IRTAEGWLYLAVVLDLFSREIVGWsVSTSMSAELVLDALEM-AIEWRGKPEGliLHSDNGSQYTSKAYREWLKEHGITQS 304

                           90       100
                   ....*....|....*....|....*..
gi 1907157804  782 YHIPHHPEAAGLIERWNGLLKTQLQRQ 808
Cdd:NF033516   305 MSRPGNCWDNAVAESFFGTLKRECLYR 331
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 480-619 2.54e-08

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 53.50  E-value: 2.54e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  480 WFTDGSARYAGttqkwtAAALQPLSGTTLKDTGEGKSSQWAELRAVHMVLQFVCKKKwpdVRLFTDSWAVANGL----AG 555
Cdd:cd09273      2 VFTDGSSFKAG------YAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKP---VNIYTDSAYAVHALhlleTI 72

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907157804  556 W--SGTWKDHNWKigekdiwgrSMWIDLSK--WAKDvKIFVSHVNAHQKVTSAEEEFNNQVDKMTRSV 619
Cdd:cd09273     73 GieRGFLKSIKNL---------SLFLQLLEavQRPK-PVAIIHIRAHSKLPGPLAEGNAQADAAAKQA 130
TERT cd01648
TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that ...
 108-227 3.90e-08

TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at the chromosome ends protects against the erosion of gene-encoding DNA. Telomerase is not normally expressed in somatic cells. It has been suggested that exogenous TERT may extend the lifespan of, or even immortalize, the cell. However, recent studies have shown that telomerase activity can be induced by a number of oncogenes. Conversely, the oncogene c-myc can be activated in human TERT immortalized cells. Sequence comparisons place the telomerase proteins in the RT family but reveal hallmarks that distinguish them from retroviral and retrotransposon relatives.


Pssm-ID: 238826  Cd Length: 119  Bit Score: 52.65  E-value: 3.90e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  108 IDLANAFFSVPvhkdhqkqfafswqgQQYTFTV-LPQGYINSPALCH----NLVRRDLDRLDLPQNITLVH-YIDDIMLI 181
Cdd:cd01648      1 TDIKKCYDSIP---------------QYYRQKVgIPQGSPLSSLLCSlyyaDLENKYLSFLDVIDKDSLLLrLVDDFLLI 65

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1907157804  182 GPSEQEVATTLDSLVTHM-RIRGWEINPTKIQGPSTSVKFLG---VQWCG 227
Cdd:cd01648     66 TTSLDKAIKFLNLLLRGFiNQYKTFVNFDKTQINFSFAQLDSsdlIPWCG 115
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
481-617 8.25e-08

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 52.15  E-value: 8.25e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  481 FTDGSAR------------YAGTTQKWtaaalqpLSGttlkdtGEGKSS-QWAELRAVHMVLQFvCKKKWPD-VRLFTDS 546
Cdd:COG0328      6 YTDGACRgnpgpggwgaviRYGGEEKE-------LSG------GLGDTTnNRAELTALIAALEA-LKELGPCeVEIYTDS 71

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907157804  547 WAVANGLAGWSGTWKDHNWK-IGEKDIWGRsmwidLSKWAKDVKIFVSHVNAHQKVtsaeeEFNNQVDKMTR 617
Cdd:COG0328     72 QYVVNQITGWIHGWKKNGWKpVKNPDLWQR-----LDELLARHKVTFEWVKGHAGH-----PGNERADALAN 133
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
309-387 1.04e-07

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 50.96  E-value: 1.04e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  309 LGPYDPADPMVLEVsvadrDAvwS-------LWQaPVGESQKRPLGFWSKALPSSADNYSPFEKQLLACYWALVETERLT 381
Cdd:pfam17919   22 LAHPDPDKPFILET-----DA--SdygigavLSQ-EDDDGGERPIAYASRKLSPAERNYSTTEKELLAIVFALKKFRHYL 93


                   ....*.
gi 1907157804  382 IGHQVT 387
Cdd:pfam17919   94 LGRKFT 99
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 871-966 2.35e-07

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 51.52  E-value: 2.35e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQA-KKGITVLGGVIDPDYHGEIGLPLHNG 949
Cdd:PHA02703    25 IPTRGSPGAAGLDLCSACDCIVPAGCRCVVFTDLLIKLPDGCYGRIAPRSGLAvKHFIDVGAGVIDADYRGNVGVVLFNF 104

                           90
                   ....*....|....*..
gi 1907157804  950 GKQDYVWSVGDPLGRLL 966
Cdd:PHA02703   105 GHNDFEVKKGDRIAQLI 121
PLN02547 PLN02547
dUTP pyrophosphatase
 871-975 4.68e-07

dUTP pyrophosphatase


Pssm-ID: 215302  Cd Length: 157  Bit Score: 50.56  E-value: 4.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQA-KKGITVLGGVIDPDYHGEIGLPLHNG 949
Cdd:PLN02547    28 LPSRGSALAAGYDLSSAYDTVVPARGKALVPTDLSIAIPEGTYARIAPRSGLAwKHSIDVGAGVIDADYRGPVGVILFNH 107

                           90       100       110
                   ....*....|....*....|....*....|
gi 1907157804  950 GKQDYVWSVGDPLGRL----LVLPcPVIKV 975
Cdd:PLN02547   108 SDVDFEVKVGDRIAQLilekIVTP-EVVEV 136
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
697-831 9.27e-07

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 52.19  E-value: 9.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  697 WQVDYIGPlpsWKGQRFVLTGVDTYSGYGFAFPARNASAKTTIHGLTECL-IYRHGIPHSIASDQGTHFTAREvrQWAHD 775
Cdd:COG2826    175 WEGDLIIG---KRGKSALLTLVERKSRFVILLKLPDKTAESVADALIRLLrKLPAFLRKSITTDNGKEFADHK--EIEAA 249

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907157804  776 HGIHwSYHI-PHHPEAAGLIERWNGLLKTQLQRqlgGNSLEGWG-RVLQKAVYALNQR 831
Cdd:COG2826    250 LGIK-VYFAdPYSPWQRGTNENTNGLLRQYFPK---GTDFSTVTqEELDAIADRLNNR 303
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 481-617 1.94e-06

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: 48.33  E-value: 1.94e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  481 FTDGSARYAGTtqKWTAA-------------ALQPLSGttlkdtgEGKSSQWAELRAVHMVLQFVCKKKWPDVRLFTDSW 547
Cdd:cd09280      3 YTDGSCLNNGK--PGARAgigvyfgpgdprnVSEPLPG-------RKQTNNRAELLAVIHALEQAPEEGIRKLEIRTDSK 73

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907157804  548 AVANGLAGWSGTWKDHNWK--IGE----KDIWgrsMWID--LSKWAKDVKIfvSHVNAHQKvtsaeEEFNNQVDKMTR 617
Cdd:cd09280     74 YAINCITKWIPKWKKNGWKtsKGKpvknQDLI---KELDklLRKRGIKVKF--EHVKGHSG-----DPGNEEADRLAR 141
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 108-225 3.02e-06

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. 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.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 46.58  E-value: 3.02e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  108 IDLANAFFSVPvhkdhqkqfafswqgqqytftvLPQGYINSPAL---CHNLVRRDLDRLDLPqnITLVHYIDDIMLIGPS 184
Cdd:cd00304      1 FDVKSFFTSIP----------------------LPQGSPLSPALanlYMEKLEAPILKQLLD--ITLIRYVDDLVVIAKS 56

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1907157804  185 EQEvATTLDSLVTHMRIRGWEINPTKIQ--GPSTSVKFLGVQW 225
Cdd:cd00304     57 EQQ-AVKKRELEEFLARLGLNLSDEKTQftEKEKKFKFLGILV 98
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 109-226 4.44e-05

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 45.76  E-value: 4.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  109 DLANAFFSVPVHKDHQKQFAFSWQG-------QQYTFTVLPQGYINSPAL---CHNLVRRDLDRLDLPQNITLVHYIDDI 178
Cdd:cd01644     65 DIEKMFHQVKVRPEDRDVLRFLWRKdgdepkpIEYRMTVVPFGAASAPFLanrALKQHAEDHPHEAAAKIIKRNFYVDDI 144

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907157804  179 MLIGPSEQE---VATTLDSLVTH--MRIRGW------------EINPTKIQGPSTSVKFLGVQWC 226
Cdd:cd01644    145 LVSTDTLNEavnVAKRLIALLKKggFNLRKWasnsqevlddlpEERVLLDRDSDVTEKTLGLRWN 209
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 480-596 5.67e-05

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: 43.46  E-value: 5.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  480 WFTDGSARyaGTTQKWTAAAL------QPLSGTTLKdtGEGKSSQWAELRAVHMVLQFVCKKKWPDVRLFTDSWAVANGL 553
Cdd:cd06222      1 INVDGSCR--GNPGPAGIGGVlrdhegGWLGGFALK--IGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLI 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1907157804  554 AGWSGTWKDHNWKIgekdiwgrsmWIDLSKWAKDVKIFVSHVN 596
Cdd:cd06222     77 NSGSFKWSPNILLI----------EDILLLLSRFWSVKISHVP 109
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 313-389 6.67e-05

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: 42.88  E-value: 6.67e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907157804  313 DPADPMVLEVSVADR--DAVwsLWQaPVGESQKRPLGFWSKALPSSADNYSPFEKQLLACYWALVETERLTIGHQVTMR 389
Cdd:pfam17917    1 DPSKPFILETDASDYgiGAV--LSQ-KDEDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVY 76
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 333-374 1.11e-04

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: 42.86  E-value: 1.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1907157804  333 LWQaPVGESQKRPLGFWSKALPSSADNYSPFEKQLLACYWAL 374
Cdd:cd09274     15 LSQ-EDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWAL 55
PHA03094 PHA03094
dUTPase; Provisional
 871-966 1.54e-04

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 42.83  E-value: 1.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  871 LPVPITLGSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFGLLMPLNQQA-KKGITVLGGVIDPDYHGEIGLPLHNG 949
Cdd:PHA03094    17 IPTRSSPKSAGYDLYSAYDYTVPPKERILVKTDISLSIPKFCYGRIAPRSGLSlNYGIDIGGGVIDEDYRGNIGVIFINN 96

                           90
                   ....*....|....*..
gi 1907157804  950 GKQDYVWSVGDPLGRLL 966
Cdd:PHA03094    97 GKCTFNIKTGDRIAQII 113
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 508-566 7.54e-04

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: 41.03  E-value: 7.54e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907157804  508 LKDTGEGK-SSQWAELRAVHMVLQFVC------KKKWPDVRLFTDSWAVANGLAGWSGTWKDHNWK 566
Cdd:cd13934     36 LEDTGGHPqTSQRAELRAAIAALRFRSwiidpdGEGLKTVVIATDSEYVVKGATEWIPKWKRNGWR 101
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 90-223 1.09e-03

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: 41.51  E-value: 1.09e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804   90 VVSLLEQINTSPGTWYAA-IDLANAFFSVPvhkdhqkqfafswqgQQYTFTVL--PQGYINSPAL---CHNLVRRDLDRL 163
Cdd:cd01650     68 LREVIEKAKEKKKSLVLVfLDFEKAFDSVD---------------HEFLLKALgvRQGDPLSPLLfnlALDDLLRLLNKE 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  164 DLPQ----NITLVHYIDDIMLIGPSEQEVATT-LDSLVTHMRIRGWEINPTK---------------------IQGPSTS 217
Cdd:cd01650    133 EEIKlggpGITHLAYADDIVLFSEGKSRKLQElLQRLQEWSKESGLKINPSKskvmlignkkkrlkditlngtPIEAVET 212


                   ....*.
gi 1907157804  218 VKFLGV 223
Cdd:cd01650    213 FKYLGV 218
PTZ00143 PTZ00143
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
 878-962 4.53e-03

deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional


Pssm-ID: 240288 [Multi-domain]  Cd Length: 155  Bit Score: 38.95  E-value: 4.53e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157804  878 GSAGLEVLAPERGVLLPGATTNISLNWKLRLPPGHFG---------LLMPLNQQAKKGITVLG--GVIDPDYHGEIGLPL 946
Cdd:PTZ00143    25 GDSGLDLFIVKDQTIKPGETAFIKLGIKAAAFQKDEDgsdgknvswLLFPRSSISKTPLRLANsiGLIDAGYRGELIAAV 104

                           90
                   ....*....|....*.
gi 1907157804  947 HNGGKQDYVWSVGDPL 962
Cdd:PTZ00143   105 DNIKDEPYTIKKGDRL 120
 
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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