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Conserved domains on  [gi|514843|gb|AAA19978|]
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pol, partial [Western chimpanzee simian foamy virus]

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 3.45e-83

Spumavirus aspartic protease (A9);


The actual alignment was detected with superfamily member pfam03539:

Pssm-ID: 112362  Cd Length: 163  Bit Score: 267.49  E-value: 3.45e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843       14 VKGTKLLAHWDSGATITCIPESFLEDEQPIKQTLIKTIHGEKQQNVYYLTFKVKGRKVEAEVIASPYEYILLSPTDVPWL 93
Cdd:pfam03539    1 IKGNKLKGYWDSGAEITCVPAIFLIEEEPIGTMLITTIHGEKEQDVYYLTFKIQGRKVEAEVIATPLDYVLIAPSDVPWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843       94 TQQPLQLTILVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPK 173
Cdd:pfam03539   81 KKKPLELTIKIDLEEQQETLLQQSALSKEGKELLKKLFLKYDALWQHWENQVGHRRIKPHKIATGTLKPRPQKQYHINPK 160


                   ...
gi 514843      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 5.00e-50

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: 176.00  E-value: 5.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    165 QKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTPVYPVPKPDGR-WRMVLDYREVNK-TIPLTAAQNQHSAGILATI 242
Cdd:cd03715    4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNdYRMVQDLRLVNQaVLPIHPAVPNPYTLLSLLP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    243 VRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALF----TADAVDLLKEVPNVQV--YVDDI 316
Cdd:cd03715   84 PKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILlqYVDDL 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 514843    317 YLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGF 361
Cdd:cd03715  164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 1064-1126 8.59e-37

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: 132.64  E-value: 8.59e-37
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514843     1064 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 1126
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 ...
 598-747 7.23e-20

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: 87.24  E-value: 7.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPdpTKSNNAGMGIvhaiYNPEYKILNqWSIPL--GHHTAQMAEIAAVEFACKKALKVPGPVLVI-TDSFYVA 674
Cdd:cd09280    4 TDGSCLNNG--KPGARAGIGV----YFGPGDPRN-VSEPLpgRKQTNNRAELLAVIHALEQAPEEGIRKLEIrTDSKYAI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514843    675 ESANKELPYWKSNGFVNNKKEPLKHISKWKSIAECLSIKP-DITIQHEKGHQPIntsihtEGNALADKLATQGS 747
Cdd:cd09280   77 NCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHSGD------PGNEEADRLAREGA 144
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 872-965 7.60e-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: 73.89  E-value: 7.60e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      872 PFDKFFIDYI-GPLPPSQGYLYVLVIVDGMTGFTWLYP-TKAPSTSATVKSLNVLTSIA--IPKVIHSDQGAAFTSSTFA 947
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 514843      948 EWAKERGIHLEFSTPYHP 965
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
428-524 2.52e-14

RNase H-like domain found in reverse transcriptase;


:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 69.84  E-value: 2.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      428 WTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSA-GYVRYYN--ESGKKPIMYLNYVFSKAELKFSMLEKLLT 504
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGiGAVLSQEddDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 514843      505 TMHKALIKAMDLAMGQEILV 524
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 800-856 1.53e-13

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: 66.12  E-value: 1.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 514843      800 PPQSDRQKIVLQAHNLA-HTGREATLLKIANLYWWPNMRKDVVKQLGRCKQCLITNAS 856
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
 
Name Accession Description Interval E-value
Spuma_A9PTase pfam03539
Spumavirus aspartic protease (A9);
14-176 3.45e-83

Spumavirus aspartic protease (A9);


Pssm-ID: 112362  Cd Length: 163  Bit Score: 267.49  E-value: 3.45e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843       14 VKGTKLLAHWDSGATITCIPESFLEDEQPIKQTLIKTIHGEKQQNVYYLTFKVKGRKVEAEVIASPYEYILLSPTDVPWL 93
Cdd:pfam03539    1 IKGNKLKGYWDSGAEITCVPAIFLIEEEPIGTMLITTIHGEKEQDVYYLTFKIQGRKVEAEVIATPLDYVLIAPSDVPWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843       94 TQQPLQLTILVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPK 173
Cdd:pfam03539   81 KKKPLELTIKIDLEEQQETLLQQSALSKEGKELLKKLFLKYDALWQHWENQVGHRRIKPHKIATGTLKPRPQKQYHINPK 160


                   ...
gi 514843      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 5.00e-50

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: 176.00  E-value: 5.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    165 QKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTPVYPVPKPDGR-WRMVLDYREVNK-TIPLTAAQNQHSAGILATI 242
Cdd:cd03715    4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNdYRMVQDLRLVNQaVLPIHPAVPNPYTLLSLLP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    243 VRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALF----TADAVDLLKEVPNVQV--YVDDI 316
Cdd:cd03715   84 PKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILlqYVDDL 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 514843    317 YLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGF 361
Cdd:cd03715  164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 1064-1126 8.59e-37

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: 132.64  E-value: 8.59e-37
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514843     1064 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 1126
Cdd:pfam18103    1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 205-363 3.01e-25

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: 103.92  E-value: 3.01e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      205 VPKPD-GRWRMV----LDYREVNKTIPLTAAQNQHSAGILATIVRQKYK-------TTLDLANGFWAHPITPDSYWLTAF 272
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKRLKPENLDSPPQPGFRPGLAKlkkakwfLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      273 T-------WQGK----QYCWTRLPQGFLNSPALFT---ADAVDLLKEVPNVQV--YVDDIYLSHDNPHEHIQQLEKVFQI 336
Cdd:pfam00078   81 TtppininWNGElsggRYEWKGLPQGLVLSPALFQlfmNELLRPLRKRAGLTLvrYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 514843      337 LLQAGYVVSLKKSEI--GQRTVEFLGFNI 363
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 598-747 7.23e-20

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: 87.24  E-value: 7.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPdpTKSNNAGMGIvhaiYNPEYKILNqWSIPL--GHHTAQMAEIAAVEFACKKALKVPGPVLVI-TDSFYVA 674
Cdd:cd09280    4 TDGSCLNNG--KPGARAGIGV----YFGPGDPRN-VSEPLpgRKQTNNRAELLAVIHALEQAPEEGIRKLEIrTDSKYAI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514843    675 ESANKELPYWKSNGFVNNKKEPLKHISKWKSIAECLSIKP-DITIQHEKGHQPIntsihtEGNALADKLATQGS 747
Cdd:cd09280   77 NCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHSGD------PGNEEADRLAREGA 144
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
598-746 2.47e-17

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 79.50  E-value: 2.47e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPDPtksnnAGMGIVhAIYNPEYKILNQwsiPLGHHTAQMAEIAAVEFACKKALKV-PGPVLVITDSFYVAES 676
Cdd:COG0328    7 TDGACRGNPGP-----GGWGAV-IRYGGEEKELSG---GLGDTTNNRAELTALIAALEALKELgPCEVEIYTDSQYVVNQ 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    677 ANKELPYWKSNGFVnnkkePLKHISKWKSIAEcLSIKPDITIQHEKGHQPIntsihtEGNALADKLATQG 746
Cdd:COG0328   78 ITGWIHGWKKNGWK-----PVKNPDLWQRLDE-LLARHKVTFEWVKGHAGH------PGNERADALANKA 135
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 872-965 7.60e-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: 73.89  E-value: 7.60e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      872 PFDKFFIDYI-GPLPPSQGYLYVLVIVDGMTGFTWLYP-TKAPSTSATVKSLNVLTSIA--IPKVIHSDQGAAFTSSTFA 947
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 514843      948 EWAKERGIHLEFSTPYHP 965
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 ...
 598-748 9.66e-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: 72.41  E-value: 9.66e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      598 TDGSAIKSPDPtksnnAGMGIVHaiynpeYKILNQWSIPL-GHHTAQMAEIAAVEFACKkALKVPGPVLVITDSFYVAES 676
Cdd:pfam00075    8 TDGSCLGNPGP-----GGAGAVL------YRGHENISAPLpGRTTNNRAELQAVIEALK-ALKSPSKVNIYTDSQYVIGG 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514843      677 ANKELPYWKSNGF-VNNKKEPLKHISKWKSIAECLSiKPDITIQHEKGHQPIntsihtEGNALADKLATQGSY 748
Cdd:pfam00075   76 ITQWVHGWKKNGWpTTSEGKPVKNKDLWQLLKALCK-KHQVYWQWVKGHAGN------PGNEMADRLAKQGAE 141
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
428-524 2.52e-14

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 69.84  E-value: 2.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      428 WTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSA-GYVRYYN--ESGKKPIMYLNYVFSKAELKFSMLEKLLT 504
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGiGAVLSQEddDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 514843      505 TMHKALIKAMDLAMGQEILV 524
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 800-856 1.53e-13

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: 66.12  E-value: 1.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 514843      800 PPQSDRQKIVLQAHNLA-HTGREATLLKIANLYWWPNMRKDVVKQLGRCKQCLITNAS 856
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
869-980 8.47e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.40  E-value: 8.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    869 PQKPFDKFFID--YIgPLPpsQGYLYVLVIVDGmtgFT-----WlyptkapSTSATVKSLNVLTSI--AI-------PKV 932
Cdd:COG2801  145 ATAPNQVWVTDitYI-PTA--EGWLYLAAVIDL---FSreivgW-------SVSDSMDAELVVDALemAIerrgppkPLI 211

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 514843    933 IHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 980
Cdd:COG2801  212 LHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
rnhA PRK00203
ribonuclease H; Reviewed
 644-746 2.12e-09

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 57.14  E-value: 2.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     644 MAEIAAVEfackkALKVPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKEPLKHISKWKSIAEcLSIKPDITIQHEKG 723
Cdd:PRK00203   49 MAAIEALE-----ALKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDA-ALKRHQIKWHWVKG 122

                          90       100
                  ....*....|....*....|...
gi 514843     724 HqpintSIHtEGNALADKLATQG 746
Cdd:PRK00203  123 H-----AGH-PENERCDELARAG 139
transpos_IS481 NF033577
IS481 family transposase; null
 854-980 1.80e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 57.22  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     854 NASNKTSGPILRPDRPQkPFDKFFID--YIGPLPpSQGYLYVLVIVDGMT--GFTWLYPTKAPSTSATVksL-NVLTSIA 928
Cdd:NF033577  110 RALDRKTGKVKRYERAH-PGELWHIDikKLGRIP-DVGRLYLHTAIDDHSrfAYAELYPDETAETAADF--LrRAFAEHG 185

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 514843     929 IP-KVIHSDQGAAFTSST--FAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 980
Cdd:NF033577  186 IPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
888-980 1.86e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.96  E-value: 1.86e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     888 QGYLYVLVIVDGmtgFT-----WlYPTKAPSTSATVKSLNvltsIAI-------PKVIHSDQGAAFTSSTFAEWAKERGI 955
Cdd:NF033516  230 EGWLYLAVVLDL---FSreivgW-SVSTSMSAELVLDALE----MAIewrgkpeGLILHSDNGSQYTSKAYREWLKEHGI 301

                          90       100
                  ....*....|....*....|....*
gi 514843     956 HLEFSTPYHPQSSGKVERKNSDIKR 980
Cdd:NF033516  302 TQSMSRPGNCWDNAVAESFFGTLKR 326
 
Name Accession Description Interval E-value
Spuma_A9PTase pfam03539
Spumavirus aspartic protease (A9);
14-176 3.45e-83

Spumavirus aspartic protease (A9);


Pssm-ID: 112362  Cd Length: 163  Bit Score: 267.49  E-value: 3.45e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843       14 VKGTKLLAHWDSGATITCIPESFLEDEQPIKQTLIKTIHGEKQQNVYYLTFKVKGRKVEAEVIASPYEYILLSPTDVPWL 93
Cdd:pfam03539    1 IKGNKLKGYWDSGAEITCVPAIFLIEEEPIGTMLITTIHGEKEQDVYYLTFKIQGRKVEAEVIATPLDYVLIAPSDVPWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843       94 TQQPLQLTILVPLQEYQDRILNKTALPEEQKQQLKALFTKYDNLWQHWENQVGHRKIRPHNIATGDYPPRPQKQYPINPK 173
Cdd:pfam03539   81 KKKPLELTIKIDLEEQQETLLQQSALSKEGKELLKKLFLKYDALWQHWENQVGHRRIKPHKIATGTLKPRPQKQYHINPK 160


                   ...
gi 514843      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 5.00e-50

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: 176.00  E-value: 5.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    165 QKQYPINPKAKPSIQIVIDDLLKQGVLTPQNSTMNTPVYPVPKPDGR-WRMVLDYREVNK-TIPLTAAQNQHSAGILATI 242
Cdd:cd03715    4 QKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNdYRMVQDLRLVNQaVLPIHPAVPNPYTLLSLLP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    243 VRQKYKTTLDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALF----TADAVDLLKEVPNVQV--YVDDI 316
Cdd:cd03715   84 PKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILlqYVDDL 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 514843    317 YLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIGQRTVEFLGF 361
Cdd:cd03715  164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 189-363 4.96e-42

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: 151.98  E-value: 4.96e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    189 GVLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTIPLTAAQNQHSAGILATIVRQKYKTTLDLANGFWAHPITPDSYW 268
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    269 LTAFTWQGKQYCWTRLPQGFLNSPALFTADAVDLLKEV--PNVQVYVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSL 346
Cdd:cd01647   81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlgDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                        170
                 ....*....|....*..
gi 514843    347 KKSEIGQRTVEFLGFNI 363
Cdd:cd01647  161 EKCEFGVPEVEFLGHIV 177
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 1064-1126 8.59e-37

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: 132.64  E-value: 8.59e-37
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514843     1064 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 1126
Cdd:pfam18103    1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 166-363 4.98e-30

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: 118.54  E-value: 4.98e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    166 KQYPIN-PKAKPSIQIViDDLLKQGVLTPQNSTMNTPVYPVPKPDGRWRMVLDYREVNKTI-PLTAAQnqhsAGI--LAT 241
Cdd:cd01645    5 KQWPLTeEKLEALTELV-TEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTqDMGALQ----PGLphPAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    242 IVRQKYKTTLDLANGFWAHPITPDSYWLTAFTW-------QGKQYCWTRLPQGFLNSPALFTADAVDLLKEV----PNVQ 310
Cdd:cd01645   80 LPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVpsinnkgPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFrkqyPDIV 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 514843    311 V--YVDDIYLSHDNPHEHIQQLEKVFQILLQAGYVVSLKKSEIgQRTVEFLGFNI 363
Cdd:cd01645  160 IyhYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQYLGYEL 213
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 205-363 3.01e-25

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: 103.92  E-value: 3.01e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      205 VPKPD-GRWRMV----LDYREVNKTIPLTAAQNQHSAGILATIVRQKYK-------TTLDLANGFWAHPITPDSYWLTAF 272
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKRLKPENLDSPPQPGFRPGLAKlkkakwfLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      273 T-------WQGK----QYCWTRLPQGFLNSPALFT---ADAVDLLKEVPNVQV--YVDDIYLSHDNPHEHIQQLEKVFQI 336
Cdd:pfam00078   81 TtppininWNGElsggRYEWKGLPQGLVLSPALFQlfmNELLRPLRKRAGLTLvrYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 514843      337 LLQAGYVVSLKKSEI--GQRTVEFLGFNI 363
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 598-747 7.23e-20

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: 87.24  E-value: 7.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPdpTKSNNAGMGIvhaiYNPEYKILNqWSIPL--GHHTAQMAEIAAVEFACKKALKVPGPVLVI-TDSFYVA 674
Cdd:cd09280    4 TDGSCLNNG--KPGARAGIGV----YFGPGDPRN-VSEPLpgRKQTNNRAELLAVIHALEQAPEEGIRKLEIrTDSKYAI 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514843    675 ESANKELPYWKSNGFVNNKKEPLKHISKWKSIAECLSIKP-DITIQHEKGHQPIntsihtEGNALADKLATQGS 747
Cdd:cd09280   77 NCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHSGD------PGNEEADRLAREGA 144
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
598-746 2.47e-17

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 79.50  E-value: 2.47e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPDPtksnnAGMGIVhAIYNPEYKILNQwsiPLGHHTAQMAEIAAVEFACKKALKV-PGPVLVITDSFYVAES 676
Cdd:COG0328    7 TDGACRGNPGP-----GGWGAV-IRYGGEEKELSG---GLGDTTNNRAELTALIAALEALKELgPCEVEIYTDSQYVVNQ 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    677 ANKELPYWKSNGFVnnkkePLKHISKWKSIAEcLSIKPDITIQHEKGHQPIntsihtEGNALADKLATQG 746
Cdd:COG0328   78 ITGWIHGWKKNGWK-----PVKNPDLWQRLDE-LLARHKVTFEWVKGHAGH------PGNERADALANKA 135
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 598-746 3.76e-17

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: 79.06  E-value: 3.76e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPDPtksnnAGMGIVhAIYNPEYKILNQWSIplgHHTAQMAEIAAVEFACKkALKVPGPVLVITDSFYVAESA 677
Cdd:cd09278    6 TDGACLGNPGP-----GGWAAV-IRYGDHEKELSGGEP---GTTNNRMELTAAIEALE-ALKEPCPVTIYTDSQYVINGI 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514843    678 NKELPYWKSNGFVNNKKEPLKHISKWKSIAEcLSIKPDITIQHEKGHQPIntsihtEGNALADKLATQG 746
Cdd:cd09278   76 TKWIKGWKKNGWKTADGKPVKNRDLWQELDA-LLAGHKVTWEWVKGHAGH------PGNERADRLANKA 137
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 872-965 7.60e-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: 73.89  E-value: 7.60e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      872 PFDKFFIDYI-GPLPPSQGYLYVLVIVDGMTGFTWLYP-TKAPSTSATVKSLNVLTSIA--IPKVIHSDQGAAFTSSTFA 947
Cdd:pfam00665    1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 514843      948 EWAKERGIHLEFSTPYHP 965
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 ...
 598-748 9.66e-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: 72.41  E-value: 9.66e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      598 TDGSAIKSPDPtksnnAGMGIVHaiynpeYKILNQWSIPL-GHHTAQMAEIAAVEFACKkALKVPGPVLVITDSFYVAES 676
Cdd:pfam00075    8 TDGSCLGNPGP-----GGAGAVL------YRGHENISAPLpGRTTNNRAELQAVIEALK-ALKSPSKVNIYTDSQYVIGG 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514843      677 ANKELPYWKSNGF-VNNKKEPLKHISKWKSIAECLSiKPDITIQHEKGHQPIntsihtEGNALADKLATQGSY 748
Cdd:pfam00075   76 ITQWVHGWKKNGWpTTSEGKPVKNKDLWQLLKALCK-KHQVYWQWVKGHAGN------PGNEMADRLAKQGAE 141
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
428-524 2.52e-14

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 69.84  E-value: 2.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843      428 WTEDNTKQLNKVIEALNTASNLEERLPDQRLVIKVNTSPSA-GYVRYYN--ESGKKPIMYLNYVFSKAELKFSMLEKLLT 504
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGiGAVLSQEddDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 514843      505 TMHKALIKAMDLAMGQEILV 524
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 800-856 1.53e-13

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: 66.12  E-value: 1.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 514843      800 PPQSDRQKIVLQAHNLA-HTGREATLLKIANLYWWPNMRKDVVKQLGRCKQCLITNAS 856
Cdd:pfam17921    1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
869-980 8.47e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.40  E-value: 8.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    869 PQKPFDKFFID--YIgPLPpsQGYLYVLVIVDGmtgFT-----WlyptkapSTSATVKSLNVLTSI--AI-------PKV 932
Cdd:COG2801  145 ATAPNQVWVTDitYI-PTA--EGWLYLAAVIDL---FSreivgW-------SVSDSMDAELVVDALemAIerrgppkPLI 211

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 514843    933 IHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 980
Cdd:COG2801  212 LHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 614-746 1.25e-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: 57.98  E-value: 1.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    614 AGMGIVhaiYNPEYkiLNQWSIPL-----GHHTAQMAE----IAAVEFACKKALKVPGP---VLVITDSFYVAESANKEL 681
Cdd:cd13934   18 AGYGVY---FGPDS--SYNVSGRLedtggHPQTSQRAElraaIAALRFRSWIIDPDGEGlktVVIATDSEYVVKGATEWI 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514843    682 PYWKSNGFVNNKKEPLKHISKWKSIAECLSIKPD--ITIQ--HekghqpintsIHTEGNALADKLATQG 746
Cdd:cd13934   93 PKWKRNGWRTSKGKPVKNRDLFELLLDEIEDLEEggVEVQfwH----------VPRELNKEADRLAKAA 151
rnhA PRK00203
ribonuclease H; Reviewed
 644-746 2.12e-09

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 57.14  E-value: 2.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     644 MAEIAAVEfackkALKVPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKEPLKHISKWKSIAEcLSIKPDITIQHEKG 723
Cdd:PRK00203   49 MAAIEALE-----ALKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDA-ALKRHQIKWHWVKG 122

                          90       100
                  ....*....|....*....|...
gi 514843     724 HqpintSIHtEGNALADKLATQG 746
Cdd:PRK00203  123 H-----AGH-PENERCDELARAG 139
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 634-743 4.14e-09

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: 55.78  E-value: 4.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    634 SIPLGHHTAQMAEIAAVEFACKKALKVPG-PVLVITDSFYVAESANKELPYWKSNGFVnnkkepLKHISKWksiaecLSI 712
Cdd:cd06222   32 ALKIGAPTALEAELLALLLALELALDLGYlKVIIESDSKYVVDLINSGSFKWSPNILL------IEDILLL------LSR 99

                         90       100       110
                 ....*....|....*....|....*....|.
gi 514843    713 KPDITIQHekghqpintsIHTEGNALADKLA 743
Cdd:cd06222  100 FWSVKISH----------VPREGNQVADALA 120
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 251-363 6.98e-09

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: 55.04  E-value: 6.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    251 LDLANGFWAHPITPDSYWLTAFTWQGKQYCWTRLPQGFLNSPALFT--ADAV--DLLKEVPNVQVYVDD-IYLSHDnphe 325
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTkvVEALlaPLRLLGVRIFSYLDDlLIIASS---- 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 514843    326 hIQQLEKVFQILL-----QAGYVVSLKKSEIG-QRTVEFLGFNI 363
Cdd:cd03714   77 -IKTSEAVLRHLRatllaNLGFTLNLEKSKLGpTQRITFLGLEL 119
transpos_IS481 NF033577
IS481 family transposase; null
 854-980 1.80e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 57.22  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     854 NASNKTSGPILRPDRPQkPFDKFFID--YIGPLPpSQGYLYVLVIVDGMT--GFTWLYPTKAPSTSATVksL-NVLTSIA 928
Cdd:NF033577  110 RALDRKTGKVKRYERAH-PGELWHIDikKLGRIP-DVGRLYLHTAIDDHSrfAYAELYPDETAETAADF--LrRAFAEHG 185

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 514843     929 IP-KVIHSDQGAAFTSST--FAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 980
Cdd:NF033577  186 IPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
888-980 1.86e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.96  E-value: 1.86e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     888 QGYLYVLVIVDGmtgFT-----WlYPTKAPSTSATVKSLNvltsIAI-------PKVIHSDQGAAFTSSTFAEWAKERGI 955
Cdd:NF033516  230 EGWLYLAVVLDL---FSreivgW-SVSTSMSAELVLDALE----MAIewrgkpeGLILHSDNGSQYTSKAYREWLKEHGI 301

                          90       100
                  ....*....|....*....|....*
gi 514843     956 HLEFSTPYHPQSSGKVERKNSDIKR 980
Cdd:NF033516  302 TQSMSRPGNCWDNAVAESFFGTLKR 326
PRK08719 PRK08719
ribonuclease H; Reviewed
 615-747 5.90e-07

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 50.24  E-value: 5.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843     615 GMGIVhaIYNPEYKILNQWSIPLGHHT--AQMAEIAAVEfackkALKVPGPVLVI-TDSFYVAESANKELPYWKSNGFVN 691
Cdd:PRK08719   24 GIGLV--VYDEAGEIVDEQSITVNRYTdnAELELLALIE-----ALEYARDGDVIySDSDYCVRGFNEWLDTWKQKGWRK 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 514843     692 NKKEPLKHISKWKSIAEcLSIKPDITIQHEKGHQpintsiHTEGNALADKLATQGS 747
Cdd:PRK08719   97 SDKKPVANRDLWQQVDE-LRARKYVEVEKVTAHS------GIEGNEAADMLAQAAA 145
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 598-747 6.74e-07

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


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 49.39  E-value: 6.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSAIKSPDPtksnnAGMGIVhaIYNPEYKILnQWSIPLGHH-TAQMAEIAAVEFACKKALKVP-GPVLVITDSFYVAE 675
Cdd:cd09279    5 FDGASRGNPGP-----AGAGVV--IYSPGGEVL-ELSERLGFPaTNNEAEYEALIAGLELALELGaEKLEIYGDSQLVVN 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514843    676 SANKElpyWKsngfVNNKKepLKHIskWKSIAECLSIKPDITIQHekghqpintsIHTEGNALADKLATQGS 747
Cdd:cd09279   77 QLNGE---YK----VKNER--LKPL--LEKVLELLAKFELVELKW----------IPREQNKEADALANQAL 127
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 598-745 1.34e-05

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: 45.79  E-value: 1.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    598 TDGSaikspdptkSNNAGMGIVHAIYNPEYKILNQWSiplghhTAQMAEIAAVEFACKkaLKVPGPVLVITDSFYVAESA 677
Cdd:cd09273    4 TDGS---------SFKAGYAIVSGTEIVEAQPLPPGT------SAQRAELIALIQALE--LAKGKPVNIYTDSAYAVHAL 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514843    678 NKELPYWKSNGFVNnkkePLKHISKWKSIAECLSIKPDITIQHEKGHQPINTSIhTEGNALADKLATQ 745
Cdd:cd09273   67 HLLETIGIERGFLK----SIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPL-AEGNAQADAAAKQ 129
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 283-363 2.12e-05

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: 44.26  E-value: 2.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    283 RLPQGFLNSPALFT-------ADAVDLLKEVPNVQvYVDDIYLSHDNPHeHIQQLEKVFQILLQAGYVVSLKKS--EIGQ 353
Cdd:cd00304   11 PLPQGSPLSPALANlymekleAPILKQLLDITLIR-YVDDLVVIAKSEQ-QAVKKRELEEFLARLGLNLSDEKTqfTEKE 88

                         90
                 ....*....|
gi 514843    354 RTVEFLGFNI 363
Cdd:cd00304   89 KKFKFLGILV 98
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
886-1021 3.34e-03

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 41.02  E-value: 3.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514843    886 PSQGYLYVLVIVDGMTGFTWLypTKAPS-TSATV-KSLNVLTSIAIPKVIHS---DQGAAFTSstFAEWAKERGIHLEFS 960
Cdd:COG2826  182 GKRGKSALLTLVERKSRFVIL--LKLPDkTAESVaDALIRLLRKLPAFLRKSittDNGKEFAD--HKEIEAALGIKVYFA 257

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514843    961 TPYHPQSSGKVER----------KNSDIKRLLTKllvgrptkwyDLLPVVQLaLNNTysP--VLKY-TPHQLLF 1021
Cdd:COG2826  258 DPYSPWQRGTNENtngllrqyfpKGTDFSTVTQE----------ELDAIADR-LNNR--PrkCLGYkTPAEVFA 318
 
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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