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Conserved domains on  [gi|1278944220|gb|ATW64776|]
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Pol [Simian foamy virus 3]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Spuma_A9PTase super family cl08397
Spumavirus aspartic protease (A9);
14-176 1.99e-88

Spumavirus aspartic protease (A9);


The actual alignment was detected with superfamily member pfam03539:

Pssm-ID: 112362  Cd Length: 163  Bit Score: 281.74  E-value: 1.99e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220   14 IKGTKLKAHWDSGATVTCVPQAFLEDETPIKNIWIKTIHGEKEQPVYYLTFKVQGRKVEAEVISSPYDYILVSPSDIPWL 93
Cdd:pfam03539    1 IKGNKLKGYWDSGAEITCVPAIFLIEEEPIGTMLITTIHGEKEQDVYYLTFKIQGRKVEAEVIATPLDYVLIAPSDVPWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220   94 MKKPLQLTTLVPLQEYQERLLKQTALPEREKKILHSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPK 173
Cdd:pfam03539   81 KKKPLELTIKIDLEEQQETLLQQSALSKEGKELLKKLFLKYDALWQHWENQVGHRRIKPHKIATGTLKPRPQKQYHINPK 160


                   ...
gi 1278944220  174 AKP 176
Cdd:pfam03539  161 AKP 163
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 165-361 8.55e-49

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd03715:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 210  Bit Score: 172.53  E-value: 8.55e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  165 QKQYPINPKAKPSIQIVINDLLKQGVLIQQNSVMNTPVYPVPKPDG-KWRMVLDYREVNKTIPLIAAQNQHSAGILSSIV 243
Cdd:cd03715      4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLP 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  244 RE-KYKTTLDLSNGFWAHSITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALF----TADVVDLLKEVPNVQ--AYVDDI 316
Cdd:cd03715     84 PKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTIllQYVDDL 163

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1278944220  317 YISHNDPKEHLEQLEKVFSLLLNAGYVVSLKKSEIAQYEVEFLGF 361
Cdd:cd03715    164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
SH3_11 super family cl39492
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 1063-1125 1.21e-30

Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.


The actual alignment was detected with superfamily member pfam18103:

Pssm-ID: 375552  Cd Length: 63  Bit Score: 114.92  E-value: 1.21e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278944220 1063 RAWSPSVGQLVQERVARPASLRPRWHKPTKVLEVLNPRTVVILDHLGNRRTVSVDNLKLTVYQ 1125
Cdd:pfam18103    1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 597-747 7.79e-18

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 cd09280:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 145  Bit Score: 81.46  E-value: 7.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSAIKhpniNKSHSAGMGIAqVQFKPEFTvLNTwSIPL--GDHTAQLAEVAAVEFACKKALKING-PVLIVTDSFYV 673
Cdd:cd09280      3 YTDGSCLN----NGKPGARAGIG-VYFGPGDP-RNV-SEPLpgRKQTNNRAELLAVIHALEQAPEEGIrKLEIRTDSKYA 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278944220  674 AESANKELPYWQSNGFLNNKKKPLRHISKWKSIAECIQLKP-DISIIHEKGHQptattfHTEGNTLADKLATQGS 747
Cdd:cd09280     76 INCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHS------GDPGNEEADRLAREGA 144
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 871-964 3.04e-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: 75.04  E-value: 3.04e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  871 PFDKFFIDYI-GPLPPSNGYLHVLVVVDGMTGFVWLYP-TKAPSTSATVKALNMLTSIA--VPKVIHSDQGAAFTSATFA 946
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1278944220  947 EWAKDKGIHLEFSTPYHP 964
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 799-854 6.45e-15

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: 69.97  E-value: 6.45e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278944220  799 PPKSDRPQLILQAHNIA-HTGRDSTFLKVSSKYWWPNLRKDVVKVIRQCKQCLVTNA 854
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RT_RNaseH_2 super family cl39038
RNase H-like domain found in reverse transcriptase;
428-524 5.96e-09

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: 54.43  E-value: 5.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  428 WTEENSQQLQYIISVLNSAENLEERNPEVKLIMKVNTSPSA-GYIRFYNESAK--RPIMYLNYVYTKAEIKFTNTEKLLT 504
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGiGAVLSQEDDDGgeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1278944220  505 TIHKGLIKALDLAMGQGILV 524
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
 
Name Accession Description Interval E-value
Spuma_A9PTase pfam03539
Spumavirus aspartic protease (A9);
14-176 1.99e-88

Spumavirus aspartic protease (A9);


Pssm-ID: 112362  Cd Length: 163  Bit Score: 281.74  E-value: 1.99e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220   14 IKGTKLKAHWDSGATVTCVPQAFLEDETPIKNIWIKTIHGEKEQPVYYLTFKVQGRKVEAEVISSPYDYILVSPSDIPWL 93
Cdd:pfam03539    1 IKGNKLKGYWDSGAEITCVPAIFLIEEEPIGTMLITTIHGEKEQDVYYLTFKIQGRKVEAEVIATPLDYVLIAPSDVPWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220   94 MKKPLQLTTLVPLQEYQERLLKQTALPEREKKILHSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPK 173
Cdd:pfam03539   81 KKKPLELTIKIDLEEQQETLLQQSALSKEGKELLKKLFLKYDALWQHWENQVGHRRIKPHKIATGTLKPRPQKQYHINPK 160


                   ...
gi 1278944220  174 AKP 176
Cdd:pfam03539  161 AKP 163
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 165-361 8.55e-49

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: 172.53  E-value: 8.55e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  165 QKQYPINPKAKPSIQIVINDLLKQGVLIQQNSVMNTPVYPVPKPDG-KWRMVLDYREVNKTIPLIAAQNQHSAGILSSIV 243
Cdd:cd03715      4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLP 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  244 RE-KYKTTLDLSNGFWAHSITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALF----TADVVDLLKEVPNVQ--AYVDDI 316
Cdd:cd03715     84 PKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTIllQYVDDL 163

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1278944220  317 YISHNDPKEHLEQLEKVFSLLLNAGYVVSLKKSEIAQYEVEFLGF 361
Cdd:cd03715    164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 1063-1125 1.21e-30

Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.


Pssm-ID: 375552  Cd Length: 63  Bit Score: 114.92  E-value: 1.21e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278944220 1063 RAWSPSVGQLVQERVARPASLRPRWHKPTKVLEVLNPRTVVILDHLGNRRTVSVDNLKLTVYQ 1125
Cdd:pfam18103    1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 205-363 4.54e-27

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: 109.31  E-value: 4.54e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  205 VPKPD-GKWRMV----LDYREVNKTIPLIAAQNQH----SAGI---LSSIVREKYKTTLDLSNGFwaHSIT--PESYWLT 270
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKRLKPENLdsppQPGFrpgLAKLKKAKWFLKLDLKKAF--DQVPldELDRKLT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  271 AFT-------WQGK----QYCWTRLPQGFLNSPALFT---ADVVDLLKEVPNVQ--AYVDDIYISHNDPKEHLEQLEKVF 334
Cdd:pfam00078   79 AFTtppininWNGElsggRYEWKGLPQGLVLSPALFQlfmNELLRPLRKRAGLTlvRYADDILIFSKSEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1278944220  335 SLLLNAGYVVSLKKSEIA--QYEVEFLGFNI 363
Cdd:pfam00078  159 EWLKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 597-747 7.79e-18

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: 81.46  E-value: 7.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSAIKhpniNKSHSAGMGIAqVQFKPEFTvLNTwSIPL--GDHTAQLAEVAAVEFACKKALKING-PVLIVTDSFYV 673
Cdd:cd09280      3 YTDGSCLN----NGKPGARAGIG-VYFGPGDP-RNV-SEPLpgRKQTNNRAELLAVIHALEQAPEEGIrKLEIRTDSKYA 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278944220  674 AESANKELPYWQSNGFLNNKKKPLRHISKWKSIAECIQLKP-DISIIHEKGHQptattfHTEGNTLADKLATQGS 747
Cdd:cd09280     76 INCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHS------GDPGNEEADRLAREGA 144
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 871-964 3.04e-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: 75.04  E-value: 3.04e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  871 PFDKFFIDYI-GPLPPSNGYLHVLVVVDGMTGFVWLYP-TKAPSTSATVKALNMLTSIA--VPKVIHSDQGAAFTSATFA 946
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1278944220  947 EWAKDKGIHLEFSTPYHP 964
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 593-748 1.76e-15

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: 74.34  E-value: 1.76e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  593 SMVFYTDGSAIKHPNinkshsAGmGIAQVQFKPEftvlNTWSIPL-GDHTAQLAEVAAVEFACKkALKINGPVLIVTDSF 671
Cdd:pfam00075    3 AVTVYTDGSCLGNPG------PG-GAGAVLYRGH----ENISAPLpGRTTNNRAELQAVIEALK-ALKSPSKVNIYTDSQ 70

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278944220  672 YVAESANKELPYWQSNGFLN-NKKKPLRHISKWKSIAECIQlKPDISIIHEKGHqptaTTFhtEGNTLADKLATQGSY 748
Cdd:pfam00075   71 YVIGGITQWVHGWKKNGWPTtSEGKPVKNKDLWQLLKALCK-KHQVYWQWVKGH----AGN--PGNEMADRLAKQGAE 141
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 799-854 6.45e-15

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: 69.97  E-value: 6.45e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278944220  799 PPKSDRPQLILQAHNIA-HTGRDSTFLKVSSKYWWPNLRKDVVKVIRQCKQCLVTNA 854
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
597-746 1.16e-13

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 69.10  E-value: 1.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSAIKHPNInkshsAGMGIAqVQFKPEFTVLntwSIPLGDHTAQLAEVAAVEFACKKALKING-PVLIVTDSFYVAE 675
Cdd:COG0328      6 YTDGACRGNPGP-----GGWGAV-IRYGGEEKEL---SGGLGDTTNNRAELTALIAALEALKELGPcEVEIYTDSQYVVN 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278944220  676 SANKELPYWQSNGFlnnkkKPLRHISKWKSIAECIQlKPDISIIHEKGHQPtattfhTEGNTLADKLATQG 746
Cdd:COG0328     77 QITGWIHGWKKNGW-----KPVKNPDLWQRLDELLA-RHKVTFEWVKGHAG------HPGNERADALANKA 135
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
887-979 5.38e-13

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 71.34  E-value: 5.38e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  887 NGYLHVLVVVDGMTGFV--W-LYPTkaPSTSATVKALNMLT---SIAVPKVIHSDQGAAFTSATFAEWAKDKGIHLEFST 960
Cdd:COG2801    163 EGWLYLAAVIDLFSREIvgWsVSDS--MDAELVVDALEMAIerrGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSR 240

                           90
                   ....*....|....*....
gi 1278944220  961 PYHPQSSGKVERKNSDIKR 979
Cdd:COG2801    241 PGNPQDNAFIESFFGTLKY 259
transpos_IS3 NF033516
IS3 family transposase;
887-979 3.67e-10

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 62.97  E-value: 3.67e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  887 NGYLHVLVVVDGMTGFV--WlYPTKAPSTSATVKALNMLTSIA---VPKVIHSDQGAAFTSATFAEWAKDKGIHLEFSTP 961
Cdd:NF033516   230 EGWLYLAVVLDLFSREIvgW-SVSTSMSAELVLDALEMAIEWRgkpEGLILHSDNGSQYTSKAYREWLKEHGITQSMSRP 308

                           90
                   ....*....|....*...
gi 1278944220  962 YHPQSSGKVERKNSDIKR 979
Cdd:NF033516   309 GNCWDNAVAESFFGTLKR 326
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
428-524 5.96e-09

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 54.43  E-value: 5.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  428 WTEENSQQLQYIISVLNSAENLEERNPEVKLIMKVNTSPSA-GYIRFYNESAK--RPIMYLNYVYTKAEIKFTNTEKLLT 504
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGiGAVLSQEDDDGgeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1278944220  505 TIHKGLIKALDLAMGQGILV 524
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
transpos_IS481 NF033577
IS481 family transposase; null
 864-979 2.27e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 56.83  E-value: 2.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  864 RPDRPIKPF------DKFFID--YIGPLPPSnGYLHVLVVVDGMTGFVW--LYPTKAPSTSATV--KALNmltsiAVPKV 931
Cdd:NF033577   114 RKTGKVKRYerahpgELWHIDikKLGRIPDV-GRLYLHTAIDDHSRFAYaeLYPDETAETAADFlrRAFA-----EHGIP 187

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1278944220  932 IH---SDQGAAFTSAT--FAEWAKDKGIHLEFSTPYHPQSSGKVERKNSDIKR 979
Cdd:NF033577   188 IRrvlTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
PRK08719 PRK08719
ribonuclease H; Reviewed
 590-747 1.89e-06

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 48.70  E-value: 1.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  590 SEFSMVFYTDGSAikhPNiNKSHSAGMGIAQVQFKPEFTVLNTWSIPLGDHTAQ-----LAEVAAVEFACkkalkiNGPV 664
Cdd:PRK08719     1 MRASYSIYIDGAA---PN-NQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNaelelLALIEALEYAR------DGDV 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  665 lIVTDSFYVAESANKELPYWQSNGFLNNKKKPLRHISKWKSIAEcIQLKPDISIIHEKGHQptattfHTEGNTLADKLAT 744
Cdd:PRK08719    71 -IYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDE-LRARKYVEVEKVTAHS------GIEGNEAADMLAQ 142


                   ...
gi 1278944220  745 QGS 747
Cdd:PRK08719   143 AAA 145
 
Name Accession Description Interval E-value
Spuma_A9PTase pfam03539
Spumavirus aspartic protease (A9);
14-176 1.99e-88

Spumavirus aspartic protease (A9);


Pssm-ID: 112362  Cd Length: 163  Bit Score: 281.74  E-value: 1.99e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220   14 IKGTKLKAHWDSGATVTCVPQAFLEDETPIKNIWIKTIHGEKEQPVYYLTFKVQGRKVEAEVISSPYDYILVSPSDIPWL 93
Cdd:pfam03539    1 IKGNKLKGYWDSGAEITCVPAIFLIEEEPIGTMLITTIHGEKEQDVYYLTFKIQGRKVEAEVIATPLDYVLIAPSDVPWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220   94 MKKPLQLTTLVPLQEYQERLLKQTALPEREKKILHSLFLKYDALWQHWENQVGHRRIKPHHIATGTVNPRPQKQYPINPK 173
Cdd:pfam03539   81 KKKPLELTIKIDLEEQQETLLQQSALSKEGKELLKKLFLKYDALWQHWENQVGHRRIKPHKIATGTLKPRPQKQYHINPK 160


                   ...
gi 1278944220  174 AKP 176
Cdd:pfam03539  161 AKP 163
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 165-361 8.55e-49

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: 172.53  E-value: 8.55e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  165 QKQYPINPKAKPSIQIVINDLLKQGVLIQQNSVMNTPVYPVPKPDG-KWRMVLDYREVNKTIPLIAAQNQHSAGILSSIV 243
Cdd:cd03715      4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLP 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  244 RE-KYKTTLDLSNGFWAHSITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALF----TADVVDLLKEVPNVQ--AYVDDI 316
Cdd:cd03715     84 PKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTIllQYVDDL 163

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1278944220  317 YISHNDPKEHLEQLEKVFSLLLNAGYVVSLKKSEIAQYEVEFLGF 361
Cdd:cd03715    164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 189-363 4.71e-41

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: 148.90  E-value: 4.71e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  189 GVLIQQNSVMNTPVYPVPKPDGKWRMVLDYREVNKT-------IPLIAaqnqhsaGILSSIVREKYKTTLDLSNGFWAHS 261
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVtikdrypLPTID-------ELLEELAGAKVFSKLDLRSGYHQIP 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  262 ITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFTADVVDLLKEV--PNVQAYVDDIYISHNDPKEHLEQLEKVFSLLLN 339
Cdd:cd01647     74 LAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLRE 153

                          170       180
                   ....*....|....*....|....
gi 1278944220  340 AGYVVSLKKSEIAQYEVEFLGFNI 363
Cdd:cd01647    154 AGLKLNPEKCEFGVPEVEFLGHIV 177
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 1063-1125 1.21e-30

Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.


Pssm-ID: 375552  Cd Length: 63  Bit Score: 114.92  E-value: 1.21e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278944220 1063 RAWSPSVGQLVQERVARPASLRPRWHKPTKVLEVLNPRTVVILDHLGNRRTVSVDNLKLTVYQ 1125
Cdd:pfam18103    1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 166-363 1.34e-29

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: 117.38  E-value: 1.34e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  166 KQYPIN-PKAKPSIQIViNDLLKQGVLIQQNSVMNTPVYPVPKPDGKWRMVLDYREVNKTI-PLIAAQnqhsAGI--LSS 241
Cdd:cd01645      5 KQWPLTeEKLEALTELV-TEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTqDMGALQ----PGLphPAA 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  242 IVREKYKTTLDLSNGFWAHSITPESYWLTAFTW-------QGKQYCWTRLPQGFLNSPALFTADVVDLLKEV----PNVQ 310
Cdd:cd01645     80 LPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVpsinnkgPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFrkqyPDIV 159

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1278944220  311 A--YVDDIYISHNDPKEHLEQLEKVFSLLLNAGYVVSLKKSEIaQYEVEFLGFNI 363
Cdd:cd01645    160 IyhYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 205-363 4.54e-27

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: 109.31  E-value: 4.54e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  205 VPKPD-GKWRMV----LDYREVNKTIPLIAAQNQH----SAGI---LSSIVREKYKTTLDLSNGFwaHSIT--PESYWLT 270
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKRLKPENLdsppQPGFrpgLAKLKKAKWFLKLDLKKAF--DQVPldELDRKLT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  271 AFT-------WQGK----QYCWTRLPQGFLNSPALFT---ADVVDLLKEVPNVQ--AYVDDIYISHNDPKEHLEQLEKVF 334
Cdd:pfam00078   79 AFTtppininWNGElsggRYEWKGLPQGLVLSPALFQlfmNELLRPLRKRAGLTlvRYADDILIFSKSEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1278944220  335 SLLLNAGYVVSLKKSEIA--QYEVEFLGFNI 363
Cdd:pfam00078  159 EWLKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 597-747 7.79e-18

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: 81.46  E-value: 7.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSAIKhpniNKSHSAGMGIAqVQFKPEFTvLNTwSIPL--GDHTAQLAEVAAVEFACKKALKING-PVLIVTDSFYV 673
Cdd:cd09280      3 YTDGSCLN----NGKPGARAGIG-VYFGPGDP-RNV-SEPLpgRKQTNNRAELLAVIHALEQAPEEGIrKLEIRTDSKYA 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278944220  674 AESANKELPYWQSNGFLNNKKKPLRHISKWKSIAECIQLKP-DISIIHEKGHQptattfHTEGNTLADKLATQGS 747
Cdd:cd09280     76 INCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHS------GDPGNEEADRLAREGA 144
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 871-964 3.04e-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: 75.04  E-value: 3.04e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  871 PFDKFFIDYI-GPLPPSNGYLHVLVVVDGMTGFVWLYP-TKAPSTSATVKALNMLTSIA--VPKVIHSDQGAAFTSATFA 946
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1278944220  947 EWAKDKGIHLEFSTPYHP 964
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 593-748 1.76e-15

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: 74.34  E-value: 1.76e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  593 SMVFYTDGSAIKHPNinkshsAGmGIAQVQFKPEftvlNTWSIPL-GDHTAQLAEVAAVEFACKkALKINGPVLIVTDSF 671
Cdd:pfam00075    3 AVTVYTDGSCLGNPG------PG-GAGAVLYRGH----ENISAPLpGRTTNNRAELQAVIEALK-ALKSPSKVNIYTDSQ 70

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278944220  672 YVAESANKELPYWQSNGFLN-NKKKPLRHISKWKSIAECIQlKPDISIIHEKGHqptaTTFhtEGNTLADKLATQGSY 748
Cdd:pfam00075   71 YVIGGITQWVHGWKKNGWPTtSEGKPVKNKDLWQLLKALCK-KHQVYWQWVKGH----AGN--PGNEMADRLAKQGAE 141
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 799-854 6.45e-15

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: 69.97  E-value: 6.45e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278944220  799 PPKSDRPQLILQAHNIA-HTGRDSTFLKVSSKYWWPNLRKDVVKVIRQCKQCLVTNA 854
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
597-746 1.16e-13

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 69.10  E-value: 1.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSAIKHPNInkshsAGMGIAqVQFKPEFTVLntwSIPLGDHTAQLAEVAAVEFACKKALKING-PVLIVTDSFYVAE 675
Cdd:COG0328      6 YTDGACRGNPGP-----GGWGAV-IRYGGEEKEL---SGGLGDTTNNRAELTALIAALEALKELGPcEVEIYTDSQYVVN 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278944220  676 SANKELPYWQSNGFlnnkkKPLRHISKWKSIAECIQlKPDISIIHEKGHQPtattfhTEGNTLADKLATQG 746
Cdd:COG0328     77 QITGWIHGWKKNGW-----KPVKNPDLWQRLDELLA-RHKVTFEWVKGHAG------HPGNERADALANKA 135
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 656-746 5.02e-13

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: 67.51  E-value: 5.02e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  656 KALKINGPVLIVTDSFYVAESANKELPYWQSNGFLNNKKKPLRHISKWKSIAECIQlKPDISIIHEKGHQptattfHTEG 735
Cdd:cd09278     54 EALKEPCPVTIYTDSQYVINGITKWIKGWKKNGWKTADGKPVKNRDLWQELDALLA-GHKVTWEWVKGHA------GHPG 126

                           90
                   ....*....|.
gi 1278944220  736 NTLADKLATQG 746
Cdd:cd09278    127 NERADRLANKA 137
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
887-979 5.38e-13

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 71.34  E-value: 5.38e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  887 NGYLHVLVVVDGMTGFV--W-LYPTkaPSTSATVKALNMLT---SIAVPKVIHSDQGAAFTSATFAEWAKDKGIHLEFST 960
Cdd:COG2801    163 EGWLYLAAVIDLFSREIvgWsVSDS--MDAELVVDALEMAIerrGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSR 240

                           90
                   ....*....|....*....
gi 1278944220  961 PYHPQSSGKVERKNSDIKR 979
Cdd:COG2801    241 PGNPQDNAFIESFFGTLKY 259
transpos_IS3 NF033516
IS3 family transposase;
887-979 3.67e-10

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 62.97  E-value: 3.67e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  887 NGYLHVLVVVDGMTGFV--WlYPTKAPSTSATVKALNMLTSIA---VPKVIHSDQGAAFTSATFAEWAKDKGIHLEFSTP 961
Cdd:NF033516   230 EGWLYLAVVLDLFSREIvgW-SVSTSMSAELVLDALEMAIEWRgkpEGLILHSDNGSQYTSKAYREWLKEHGITQSMSRP 308

                           90
                   ....*....|....*...
gi 1278944220  962 YHPQSSGKVERKNSDIKR 979
Cdd:NF033516   309 GNCWDNAVAESFFGTLKR 326
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 595-746 5.03e-09

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: 56.44  E-value: 5.03e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  595 VFYTDGSAikhPNINKSHS-AGMGIAqvqFKPEfTVLNtWSIPL-----GDHTAQLAEVAAVEFACKKALKINGP----- 663
Cdd:cd13934      1 LVYIDGAC---RNNGRPDArAGYGVY---FGPD-SSYN-VSGRLedtggHPQTSQRAELRAAIAALRFRSWIIDPdgegl 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  664 --VLIVTDSFYVAESANKELPYWQSNGFLNNKKKPLRHISKWKSIAECIQLkpdisiiHEKGHqpTATTF---HTEGNTL 738
Cdd:cd13934     73 ktVVIATDSEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIED-------LEEGG--VEVQFwhvPRELNKE 143


                   ....*...
gi 1278944220  739 ADKLATQG 746
Cdd:cd13934    144 ADRLAKAA 151
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
428-524 5.96e-09

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 54.43  E-value: 5.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  428 WTEENSQQLQYIISVLNSAENLEERNPEVKLIMKVNTSPSA-GYIRFYNESAK--RPIMYLNYVYTKAEIKFTNTEKLLT 504
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGiGAVLSQEDDDGgeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1278944220  505 TIHKGLIKALDLAMGQGILV 524
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 597-745 1.69e-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: 54.27  E-value: 1.69e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSaikhpninkSHSAGMGIAQvqfKPEFTvlntWSIPLGDHT-AQLAEVAAVEFACK--KALKINgpvlIVTDSFYV 673
Cdd:cd09273      3 FTDGS---------SFKAGYAIVS---GTEIV----EAQPLPPGTsAQRAELIALIQALElaKGKPVN----IYTDSAYA 62

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278944220  674 AESANKELPYWQSNGFLNNKKkplrHISKWKSIAECIQLKPDISIIHEKGHQpTATTFHTEGNTLADKLATQ 745
Cdd:cd09273     63 VHALHLLETIGIERGFLKSIK----NLSLFLQLLEAVQRPKPVAIIHIRAHS-KLPGPLAEGNAQADAAAKQ 129
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 251-363 1.85e-08

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: 53.50  E-value: 1.85e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  251 LDLSNGFWAHSITPESYWLTAFTWQGKQYCWTRLPQGFLNSPALFTADVVDLLKE----VPNVQAYVDDIYI--SHNDPK 324
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPlrllGVRIFSYLDDLLIiaSSIKTS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1278944220  325 EHLEQLEKVfSLLLNAGYVVSLKKSEIA-QYEVEFLGFNI 363
Cdd:cd03714     81 EAVLRHLRA-TLLANLGFTLNLEKSKLGpTQRITFLGLEL 119
transpos_IS481 NF033577
IS481 family transposase; null
 864-979 2.27e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 56.83  E-value: 2.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  864 RPDRPIKPF------DKFFID--YIGPLPPSnGYLHVLVVVDGMTGFVW--LYPTKAPSTSATV--KALNmltsiAVPKV 931
Cdd:NF033577   114 RKTGKVKRYerahpgELWHIDikKLGRIPDV-GRLYLHTAIDDHSRFAYaeLYPDETAETAADFlrRAFA-----EHGIP 187

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1278944220  932 IH---SDQGAAFTSAT--FAEWAKDKGIHLEFSTPYHPQSSGKVERKNSDIKR 979
Cdd:NF033577   188 IRrvlTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
PRK08719 PRK08719
ribonuclease H; Reviewed
 590-747 1.89e-06

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 48.70  E-value: 1.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  590 SEFSMVFYTDGSAikhPNiNKSHSAGMGIAQVQFKPEFTVLNTWSIPLGDHTAQ-----LAEVAAVEFACkkalkiNGPV 664
Cdd:PRK08719     1 MRASYSIYIDGAA---PN-NQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNaelelLALIEALEYAR------DGDV 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  665 lIVTDSFYVAESANKELPYWQSNGFLNNKKKPLRHISKWKSIAEcIQLKPDISIIHEKGHQptattfHTEGNTLADKLAT 744
Cdd:PRK08719    71 -IYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDE-LRARKYVEVEKVTAHS------GIEGNEAADMLAQ 142


                   ...
gi 1278944220  745 QGS 747
Cdd:PRK08719   143 AAA 145
rnhA PRK00203
ribonuclease H; Reviewed
 656-746 4.46e-06

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 47.51  E-value: 4.46e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  656 KALKINGPVLIVTDSFYVAESANKELPYWQSNGFLNNKKKPLRHISKWKSIAECIQlkpdisiIHE------KGHqptat 729
Cdd:PRK00203    56 EALKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-------RHQikwhwvKGH----- 123

                           90
                   ....*....|....*..
gi 1278944220  730 TFHtEGNTLADKLATQG 746
Cdd:PRK00203   124 AGH-PENERCDELARAG 139
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 597-743 5.62e-06

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: 46.54  E-value: 5.62e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  597 YTDGSAIKHPNInkshsAGMGIAqvqFKPEFTVLNTW-SIPLGDHTAQLAEVAAVEFACKKALKING-PVLIVTDSFYVA 674
Cdd:cd06222      2 NVDGSCRGNPGP-----AGIGGV---LRDHEGGWLGGfALKIGAPTALEAELLALLLALELALDLGYlKVIIESDSKYVV 73

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278944220  675 ESANKELPYWQSNGFLnnkkkpLRHISKWKSiaeciqLKPDISIIHEkghqptattfHTEGNTLADKLA 743
Cdd:cd06222     74 DLINSGSFKWSPNILL------IEDILLLLS------RFWSVKISHV----------PREGNQVADALA 120
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 283-363 1.28e-03

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: 39.26  E-value: 1.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  283 RLPQGFLNSPALFT-------ADVVDLLKEVPNVQaYVDDIYISHNDPkEHLEQLEKVFSLLLNAGYVVSLKKS--EIAQ 353
Cdd:cd00304     11 PLPQGSPLSPALANlymekleAPILKQLLDITLIR-YVDDLVVIAKSE-QQAVKKRELEEFLARLGLNLSDEKTqfTEKE 88

                           90
                   ....*....|
gi 1278944220  354 YEVEFLGFNI 363
Cdd:cd00304     89 KKFKFLGILV 98
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 812-849 5.69e-03

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 35.76  E-value: 5.69e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1278944220  812 HNIAHTGRDSTFLKVSSKYWWPNLRKDVVKVIRQCKQC 849
Cdd:pfam09337    1 HALTHLGINKLTALLARKYHWLGIKETVSEVISSCVAC 38
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
885-981 7.71e-03

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 39.86  E-value: 7.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278944220  885 PSNGYLHVLVVVDGMTGFVWLypTKAPS-TSATV-KALNMLTSIAVPKVIHS---DQGAAFtsATFAEWAKDKGIHLEFS 959
Cdd:COG2826    182 GKRGKSALLTLVERKSRFVIL--LKLPDkTAESVaDALIRLLRKLPAFLRKSittDNGKEF--ADHKEIEAALGIKVYFA 257

                           90       100
                   ....*....|....*....|..
gi 1278944220  960 TPYHPQSSGKVERKNsdikRLL 981
Cdd:COG2826    258 DPYSPWQRGTNENTN----GLL 275
 
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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