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Conserved domains on  [gi|300825689|gb|ADK35878|]
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pol protein [Porcine endogenous retrovirus C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 127-340 2.58e-112

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: 348.18  E-value: 2.58e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  127 PISVRQYPLSREAREEIWPHVQRLIQQGILVPVRSPWNTPLLPVRKPGTNDYRPVQDLREVNKRVQDIHPMVPNPYNLLS 206
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  207 ALPPKRNWYTVLDLKNAFFCLRLHPTSQPLFAFEWRDpgtgrtGQLTWTRLPQGFKNSPTIFDEALHRDLANFRIQHPQV 286
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 300825689  287 TLLQYVDDLLLAGATKQDCLEGTNALLLELSDLGYRASAKKAQICRREVTYLGY 340
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 589-729 1.26e-49

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: 171.75  E-value: 1.26e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  589 TWFTDGSSYVvegkrmARAAVVDGTRTIWASSLSEGTSAQKAELVALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYK 668
Cdd:cd09273     1 TVFTDGSSFK------AGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 300825689  669 QRGLLTSagreVKNKEKILSLLEALHLPKRLAIIHCPGHQKAKDLISRGNQMADRVAKQAA 729
Cdd:cd09273    75 ERGFLKS----IKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
MLVIN_C super family cl40013
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1059-1134 3.38e-30

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


The actual alignment was detected with superfamily member pfam18697:

Pssm-ID: 436671  Cd Length: 83  Bit Score: 114.54  E-value: 3.38e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  1059 HHYQVGDSVYVRRHRAGNLETRWKGPYLVLLTTPTAVKVEGISTWIHASHVKLAPPPDSG------WRAEKT-ENPLKLR 1131
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLedfipsWQVQKDrDNPLKLR 80


                   ...
gi 300825689  1132 LHR 1134
Cdd:pfam18697   81 LRR 83
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 853-948 1.16e-24

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: 99.31  E-value: 1.16e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   853 PGAHWEVDFTEVKPAKYGNK-YLLVFVDTFSGWVEAYPTKKKTSTVVAKKILEEIF-PRFGIPKVIGSDNGPAFVAQVSQ 930
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGGGKlYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 300825689   931 GLAKILGIDWKLHCAYRP 948
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 1-45 7.70e-15

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member cd06095:

Pssm-ID: 472175  Cd Length: 86  Bit Score: 70.82  E-value: 7.70e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 300825689    1 MGATGQRQYPWTTRRT-VDLGVGRVTHLFLVIPECPIPLLGRDLLT 45
Cdd:cd06095    41 RGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLLGRDLLS 86
RT_RNaseH super family cl39037
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 430-534 2.44e-14

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


The actual alignment was detected with superfamily member pfam17917:

Pssm-ID: 465565  Cd Length: 104  Bit Score: 69.85  E-value: 2.44e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   430 DVTKPFTLYVDE-HKGVArGVLTQSL-GPWRRPVAYLSKKLDPVASGWPVCLKAIAAVAILVKDADKSTLGQNITVIAPH 507
Cdd:pfam17917    1 DPSKPFILETDAsDYGIG-AVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 300825689   508 -ALENIVRQppdrWMTNARMTHYQSLLL 534
Cdd:pfam17917   80 kPLKYLFTP----KELNGRLARWALFLQ 103
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 794-833 1.98e-08

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: 51.17  E-value: 1.98e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 300825689   794 HHLTHLGTKHLQQLVRTSpYHVLRLPGVADSVVKHCVPCQ 833
Cdd:pfam09337    1 HALTHLGINKLTALLARK-YHWLGIKETVSEVISSCVACQ 39
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 127-340 2.58e-112

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: 348.18  E-value: 2.58e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  127 PISVRQYPLSREAREEIWPHVQRLIQQGILVPVRSPWNTPLLPVRKPGTNDYRPVQDLREVNKRVQDIHPMVPNPYNLLS 206
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  207 ALPPKRNWYTVLDLKNAFFCLRLHPTSQPLFAFEWRDpgtgrtGQLTWTRLPQGFKNSPTIFDEALHRDLANFRIQHPQV 286
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 300825689  287 TLLQYVDDLLLAGATKQDCLEGTNALLLELSDLGYRASAKKAQICRREVTYLGY 340
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 589-729 1.26e-49

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: 171.75  E-value: 1.26e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  589 TWFTDGSSYVvegkrmARAAVVDGTRTIWASSLSEGTSAQKAELVALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYK 668
Cdd:cd09273     1 TVFTDGSSFK------AGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 300825689  669 QRGLLTSagreVKNKEKILSLLEALHLPKRLAIIHCPGHQKAKDLISRGNQMADRVAKQAA 729
Cdd:cd09273    75 ERGFLKS----IKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 586-730 1.28e-32

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: 123.64  E-value: 1.28e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   586 EVLTWFTDGSSYVVEGKRMArAAVVDGTRTIWASSLSEGTSAQKAELVALTQALR-LAEGKSINIYTDSRYAFATAH--V 662
Cdd:pfam00075    2 KAVTVYTDGSCLGNPGPGGA-GAVLYRGHENISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 300825689   663 HGAIYKQRGlLTSAGREVKNKEkILSLLEALHLPKRLAIIHCPGHqkAKDlisRGNQMADRVAKQAAQ 730
Cdd:pfam00075   81 HGWKKNGWP-TTSEGKPVKNKD-LWQLLKALCKKHQVYWQWVKGH--AGN---PGNEMADRLAKQGAE 141
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 170-342 2.87e-30

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: 118.56  E-value: 2.87e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   170 VRKPGTNDYRPV----QDLREVNKRVQD-IHPMVPNPYNL-----LSALPPKRNWYTVLDLKNAFFCLRLHPTSQPLFAF 239
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQpgfrpGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   240 ----EWRDPGTGRTGQL-TWTRLPQGFKNSPTIFDEALHRDLANFRiQHPQVTLLQYVDDLLLAGATKQDCLEGTNALLL 314
Cdd:pfam00078   81 ttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 300825689   315 ELSDLGYRASAKKAQICR--REVTYLGYSL 342
Cdd:pfam00078  160 WLKESGLKINPEKTQFFLksKEVKYLGVTL 189
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1059-1134 3.38e-30

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


Pssm-ID: 436671  Cd Length: 83  Bit Score: 114.54  E-value: 3.38e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  1059 HHYQVGDSVYVRRHRAGNLETRWKGPYLVLLTTPTAVKVEGISTWIHASHVKLAPPPDSG------WRAEKT-ENPLKLR 1131
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLedfipsWQVQKDrDNPLKLR 80


                   ...
gi 300825689  1132 LHR 1134
Cdd:pfam18697   81 LRR 83
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 853-948 1.16e-24

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: 99.31  E-value: 1.16e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   853 PGAHWEVDFTEVKPAKYGNK-YLLVFVDTFSGWVEAYPTKKKTSTVVAKKILEEIF-PRFGIPKVIGSDNGPAFVAQVSQ 930
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGGGKlYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 300825689   931 GLAKILGIDWKLHCAYRP 948
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 843-961 1.76e-15

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 78.02  E-value: 1.76e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  843 PPGKRLR--GSHPGAHWEVDFTEVKPAKYGNK-YLLVFVDTFS--GWVEAYPTKKKTSTVvakKILEEIFPRFGIP-KVI 916
Cdd:NF033577  115 KTGKVKRyeRAHPGELWHIDIKKLGRIPDVGRlYLHTAIDDHSrfAYAELYPDETAETAA---DFLRRAFAEHGIPiRRV 191

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 300825689  917 GSDNGPAFVA---QVSQGLAKiLGIDWKLHCAYRPQSSGQVERMNRTI 961
Cdd:NF033577  192 LTDNGSEFRSrahGFELALAE-LGIEHRRTRPYHPQTNGKVERFHRTL 238
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 1-45 7.70e-15

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


Pssm-ID: 133159  Cd Length: 86  Bit Score: 70.82  E-value: 7.70e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 300825689    1 MGATGQRQYPWTTRRT-VDLGVGRVTHLFLVIPECPIPLLGRDLLT 45
Cdd:cd06095    41 RGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLLGRDLLS 86
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 430-534 2.44e-14

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


Pssm-ID: 465565  Cd Length: 104  Bit Score: 69.85  E-value: 2.44e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   430 DVTKPFTLYVDE-HKGVArGVLTQSL-GPWRRPVAYLSKKLDPVASGWPVCLKAIAAVAILVKDADKSTLGQNITVIAPH 507
Cdd:pfam17917    1 DPSKPFILETDAsDYGIG-AVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 300825689   508 -ALENIVRQppdrWMTNARMTHYQSLLL 534
Cdd:pfam17917   80 kPLKYLFTP----KELNGRLARWALFLQ 103
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
591-729 3.19e-10

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 59.09  E-value: 3.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  591 FTDGSSyvvEG--KRMARAAVV-DGTRTIWASSLSEGTSAQKAELVALTQALRLAE---GKSINIYTDSRYAFATAHVHG 664
Cdd:COG0328     6 YTDGAC---RGnpGPGGWGAVIrYGGEEKELSGGLGDTTNNRAELTALIAALEALKelgPCEVEIYTDSQYVVNQITGWI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 300825689  665 AIYKQRGLltsagREVKNKEKILSLLEALHLPKrLAIIHCPGHQKakdliSRGNQMADRVAKQAA 729
Cdd:COG0328    83 HGWKKNGW-----KPVKNPDLWQRLDELLARHK-VTFEWVKGHAG-----HPGNERADALANKAL 136
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 794-833 1.98e-08

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: 51.17  E-value: 1.98e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 300825689   794 HHLTHLGTKHLQQLVRTSpYHVLRLPGVADSVVKHCVPCQ 833
Cdd:pfam09337    1 HALTHLGINKLTALLARK-YHWLGIKETVSEVISSCVACQ 39
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
851-961 4.79e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 49.88  E-value: 4.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  851 SHPGaHWEVDFteVKPAKyGNKYLLVFVDTFSGWVEAYPTKKKTSTVVAKKI--LEEIFPRFgIPKVIGSDNGPAFVAqv 928
Cdd:COG2826   170 AEPG-HWEGDL--IIGKR-GKSALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEFAD-- 242

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 300825689  929 SQGLAKILGIDwklhcAY--RPQSS---GQVERMNRTI 961
Cdd:COG2826   243 HKEIEAALGIK-----VYfaDPYSPwqrGTNENTNGLL 275
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 2-51 8.02e-06

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 45.82  E-value: 8.02e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 300825689     2 GATGQRQYPWTTRRTVDLGVGRVTHL--FLVIPECPIPLLGRDLLTKMGAQI 51
Cdd:pfam00077   49 GIGGGINVRQSDQILILIGEDKFRGTvsPLILPTCPVNIIGRDLLQQLGGRL 100
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 873-960 3.79e-04

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 44.01  E-value: 3.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  873 YLLVFVD--TfSGWVEAYPTKKKTsTVVAKKILEEIFPRFGIPKVIGSDNGPAFVAQVSQGLAKI------------LGI 938
Cdd:NF033594  148 TLLVAIDdaT-GRLMGLRFVESES-TFGYFEVTRQYLEKHGKPVAFYSDKHSVFRVNEEELAGKGdgltqfgralkeLGI 225

                          90       100
                  ....*....|....*....|..
gi 300825689  939 DWKlhCAYRPQSSGQVERMNRT 960
Cdd:NF033594  226 EII--CANSPQAKGRVERANQT 245
rnhA PRK00203
ribonuclease H; Reviewed
 631-730 7.34e-04

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 41.35  E-value: 7.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  631 ELVALTQALR-LAEGKSINIYTDSRY---AFaTAHVHGaiYKQRGLLTSAGREVKNKEKILSLLEALhlpKRLAII---- 702
Cdd:PRK00203   47 ELMAAIEALEaLKEPCEVTLYTDSQYvrqGI-TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAAL---KRHQIKwhwv 120

                          90       100       110
                  ....*....|....*....|....*....|
gi 300825689  703 --HCpGHqkakdlisRGNQMADRVAKQAAQ 730
Cdd:PRK00203  121 kgHA-GH--------PENERCDELARAGAE 141
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 127-340 2.58e-112

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: 348.18  E-value: 2.58e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  127 PISVRQYPLSREAREEIWPHVQRLIQQGILVPVRSPWNTPLLPVRKPGTNDYRPVQDLREVNKRVQDIHPMVPNPYNLLS 206
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  207 ALPPKRNWYTVLDLKNAFFCLRLHPTSQPLFAFEWRDpgtgrtGQLTWTRLPQGFKNSPTIFDEALHRDLANFRIQHPQV 286
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 300825689  287 TLLQYVDDLLLAGATKQDCLEGTNALLLELSDLGYRASAKKAQICRREVTYLGY 340
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGV 208
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 589-729 1.26e-49

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: 171.75  E-value: 1.26e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  589 TWFTDGSSYVvegkrmARAAVVDGTRTIWASSLSEGTSAQKAELVALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYK 668
Cdd:cd09273     1 TVFTDGSSFK------AGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 300825689  669 QRGLLTSagreVKNKEKILSLLEALHLPKRLAIIHCPGHQKAKDLISRGNQMADRVAKQAA 729
Cdd:cd09273    75 ERGFLKS----IKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 127-342 2.36e-40

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: 148.20  E-value: 2.36e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  127 PISVRQYPLSREAREEIWPHVQRLIQQGILVPVRSPWNTPLLPVRKPgTNDYRPVQDLREVNKRVQD---IHPMVPNPyn 203
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK-SGKWRLLHDLRAVNAQTQDmgaLQPGLPHP-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  204 llSALPpkRNWY-TVLDLKNAFFCLRLHPTSQPLFAFEWRDPGTGRTGQ-LTWTRLPQGFKNSPTIFDEALHRDLANFRI 281
Cdd:cd01645    78 --AALP--KGWPlIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKrYQWKVLPQGMKNSPTICQSFVAQALEPFRK 153

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 300825689  282 QHPQVTLLQYVDDLLLAGATKQDCLEGTNALLLELSDLGYRASAKKAQIcRREVTYLGYSL 342
Cdd:cd01645   154 QYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQYLGYEL 213
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 154-340 1.26e-38

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: 141.96  E-value: 1.26e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  154 GILVPVRSPWNTPLLPVRKPGtNDYRPVQDLREVNKR-VQDIHPMvPNPYNLLSALPPKRnWYTVLDLKNAFFCLRLHPT 232
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKD-GKLRLCVDYRKLNKVtIKDRYPL-PTIDELLEELAGAK-VFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  233 SQPLFAFewrdpgTGRTGQLTWTRLPQGFKNSPTIF----DEALHRDLANFriqhpqvtLLQYVDDLLLAGATKQDCLEG 308
Cdd:cd01647    78 SRPKTAF------RTPFGLYEYTRMPFGLKNAPATFqrlmNKILGDLLGDF--------VEVYLDDILVYSKTEEEHLEH 143

                         170       180       190
                  ....*....|....*....|....*....|..
gi 300825689  309 TNALLLELSDLGYRASAKKAQICRREVTYLGY 340
Cdd:cd01647   144 LREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 586-730 1.28e-32

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: 123.64  E-value: 1.28e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   586 EVLTWFTDGSSYVVEGKRMArAAVVDGTRTIWASSLSEGTSAQKAELVALTQALR-LAEGKSINIYTDSRYAFATAH--V 662
Cdd:pfam00075    2 KAVTVYTDGSCLGNPGPGGA-GAVLYRGHENISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 300825689   663 HGAIYKQRGlLTSAGREVKNKEkILSLLEALHLPKRLAIIHCPGHqkAKDlisRGNQMADRVAKQAAQ 730
Cdd:pfam00075   81 HGWKKNGWP-TTSEGKPVKNKD-LWQLLKALCKKHQVYWQWVKGH--AGN---PGNEMADRLAKQGAE 141
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 170-342 2.87e-30

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: 118.56  E-value: 2.87e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   170 VRKPGTNDYRPV----QDLREVNKRVQD-IHPMVPNPYNL-----LSALPPKRNWYTVLDLKNAFFCLRLHPTSQPLFAF 239
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQpgfrpGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   240 ----EWRDPGTGRTGQL-TWTRLPQGFKNSPTIFDEALHRDLANFRiQHPQVTLLQYVDDLLLAGATKQDCLEGTNALLL 314
Cdd:pfam00078   81 ttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 300825689   315 ELSDLGYRASAKKAQICR--REVTYLGYSL 342
Cdd:pfam00078  160 WLKESGLKINPEKTQFFLksKEVKYLGVTL 189
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1059-1134 3.38e-30

Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail.


Pssm-ID: 436671  Cd Length: 83  Bit Score: 114.54  E-value: 3.38e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  1059 HHYQVGDSVYVRRHRAGNLETRWKGPYLVLLTTPTAVKVEGISTWIHASHVKLAPPPDSG------WRAEKT-ENPLKLR 1131
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLedfipsWQVQKDrDNPLKLR 80


                   ...
gi 300825689  1132 LHR 1134
Cdd:pfam18697   81 LRR 83
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 853-948 1.16e-24

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: 99.31  E-value: 1.16e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   853 PGAHWEVDFTEVKPAKYGNK-YLLVFVDTFSGWVEAYPTKKKTSTVVAKKILEEIF-PRFGIPKVIGSDNGPAFVAQVSQ 930
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGGGKlYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 300825689   931 GLAKILGIDWKLHCAYRP 948
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 628-730 2.83e-17

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: 79.92  E-value: 2.83e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  628 QKAELVALTQALRLA---EGKSINIYTDSRYAFATAHVHGAIYKQRGLLTSAGREVKNKEKILSLLEALH-LPKRLAIIH 703
Cdd:cd09280    44 NRAELLAVIHALEQApeeGIRKLEIRTDSKYAINCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRkRGIKVKFEH 123

                          90       100
                  ....*....|....*....|....*..
gi 300825689  704 CPGHQKakdliSRGNQMADRVAKQAAQ 730
Cdd:cd09280   124 VKGHSG-----DPGNEEADRLAREGAD 145
transpos_IS481 NF033577
IS481 family transposase; null
 843-961 1.76e-15

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 78.02  E-value: 1.76e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  843 PPGKRLR--GSHPGAHWEVDFTEVKPAKYGNK-YLLVFVDTFS--GWVEAYPTKKKTSTVvakKILEEIFPRFGIP-KVI 916
Cdd:NF033577  115 KTGKVKRyeRAHPGELWHIDIKKLGRIPDVGRlYLHTAIDDHSrfAYAELYPDETAETAA---DFLRRAFAEHGIPiRRV 191

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 300825689  917 GSDNGPAFVA---QVSQGLAKiLGIDWKLHCAYRPQSSGQVERMNRTI 961
Cdd:NF033577  192 LTDNGSEFRSrahGFELALAE-LGIEHRRTRPYHPQTNGKVERFHRTL 238
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 1-45 7.70e-15

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


Pssm-ID: 133159  Cd Length: 86  Bit Score: 70.82  E-value: 7.70e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 300825689    1 MGATGQRQYPWTTRRT-VDLGVGRVTHLFLVIPECPIPLLGRDLLT 45
Cdd:cd06095    41 RGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLLGRDLLS 86
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 430-534 2.44e-14

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


Pssm-ID: 465565  Cd Length: 104  Bit Score: 69.85  E-value: 2.44e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   430 DVTKPFTLYVDE-HKGVArGVLTQSL-GPWRRPVAYLSKKLDPVASGWPVCLKAIAAVAILVKDADKSTLGQNITVIAPH 507
Cdd:pfam17917    1 DPSKPFILETDAsDYGIG-AVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 300825689   508 -ALENIVRQppdrWMTNARMTHYQSLLL 534
Cdd:pfam17917   80 kPLKYLFTP----KELNGRLARWALFLQ 103
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 591-730 1.40e-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: 69.05  E-value: 1.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  591 FTDGSSYVVEGKrMARAAVV-DGTRTIWASSLSEGTSAQKAELVALTQALR-LAEGKSINIYTDSRYAF--ATAHVHGai 666
Cdd:cd09278     5 YTDGACLGNPGP-GGWAAVIrYGDHEKELSGGEPGTTNNRMELTAAIEALEaLKEPCPVTIYTDSQYVIngITKWIKG-- 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 300825689  667 YKQRGLLTSAGREVKNKEKILSLLEALhLPKRLAIIHCPGHQKakdliSRGNQMADRVAKQAAQ 730
Cdd:cd09278    82 WKKNGWKTADGKPVKNRDLWQELDALL-AGHKVTWEWVKGHAG-----HPGNERADRLANKAAD 139
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 256-340 1.38e-12

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: 64.68  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  256 RLPQGFKNSPTIFDEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQdCLEGTNALLLELSDLGYRASAKKAQICR--R 333
Cdd:cd00304    11 PLPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQ-QAVKKRELEEFLARLGLNLSDEKTQFTEkeK 89


                  ....*..
gi 300825689  334 EVTYLGY 340
Cdd:cd00304    90 KFKFLGI 96
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 591-729 3.50e-11

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 61.85  E-value: 3.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  591 FTDGSSYvvEGKrmARAAVV---DGTRTIWASSLSEGTSAQKAELVALTQALRLA-----EGKSINIYTDSRyafatahv 662
Cdd:cd09276     3 YTDGSKL--EGS--VGAGFViyrGGEVISRSYRLGTHASVFDAELEAILEALELAlatarRARKVTIFTDSQ-------- 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 300825689  663 hGAIykqRGLLTSA--GREVKNKEKILSLLEALHLPKRLAIIHCPGHQKakdliSRGNQMADRVAKQAA 729
Cdd:cd09276    71 -SAL---QALRNPRrsSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVG-----IEGNEAADRLAKEAA 130
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 218-339 2.27e-10

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: 59.28  E-value: 2.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  218 LDLKNAFFCLRLHPTSQPLFAFEWRdpgtGRTGQltWTRLPQGFKNSPTIFDEALHRDLANFRIQhpQVTLLQYVDDLLL 297
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQ----GETYQ--FKALPFGLSLAPRVFTKVVEALLAPLRLL--GVRIFSYLDDLLI 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 300825689  298 AGATKQDC-LEGTNALLLELSDLGYRASAKKAQIC-RREVTYLG 339
Cdd:cd03714    73 IASSIKTSeAVLRHLRATLLANLGFTLNLEKSKLGpTQRITFLG 116
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
591-729 3.19e-10

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 59.09  E-value: 3.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  591 FTDGSSyvvEG--KRMARAAVV-DGTRTIWASSLSEGTSAQKAELVALTQALRLAE---GKSINIYTDSRYAFATAHVHG 664
Cdd:COG0328     6 YTDGAC---RGnpGPGGWGAVIrYGGEEKELSGGLGDTTNNRAELTALIAALEALKelgPCEVEIYTDSQYVVNQITGWI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 300825689  665 AIYKQRGLltsagREVKNKEKILSLLEALHLPKrLAIIHCPGHQKakdliSRGNQMADRVAKQAA 729
Cdd:COG0328    83 HGWKKNGW-----KPVKNPDLWQRLDELLARHK-VTFEWVKGHAG-----HPGNERADALANKAL 136
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 590-726 9.57e-10

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: 57.32  E-value: 9.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  590 WFTDGSsYVVEGKRMARAAVVDGTRTIW---ASSLSEGTSAQKAELVALTQALRLA---EGKSINIYTDSRYAFATahVH 663
Cdd:cd06222     1 INVDGS-CRGNPGPAGIGGVLRDHEGGWlggFALKIGAPTALEAELLALLLALELAldlGYLKVIIESDSKYVVDL--IN 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 300825689  664 GAIYKQRglltsagrevKNKEKILSLLEALHLPKRLAIIHCPGHqkakdlisrGNQMADRVAK 726
Cdd:cd06222    78 SGSFKWS----------PNILLIEDILLLLSRFWSVKISHVPRE---------GNQVADALAK 121
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 794-833 1.98e-08

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: 51.17  E-value: 1.98e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 300825689   794 HHLTHLGTKHLQQLVRTSpYHVLRLPGVADSVVKHCVPCQ 833
Cdd:pfam09337    1 HALTHLGINKLTALLARK-YHWLGIKETVSEVISSCVACQ 39
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
405-485 1.40e-07

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 50.58  E-value: 1.40e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   405 WAPEHQKAFDAIKKALLSAPALALPDVTKPFTLYVD--EHkGVArGVLTQ-SLGPWRRPVAYLSKKLDPVASGWPVCLKA 481
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDasDY-GIG-AVLSQeDDDGGERPIAYASRKLSPAERNYSTTEKE 78


                   ....
gi 300825689   482 IAAV 485
Cdd:pfam17919   79 LLAI 82
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 625-730 1.23e-06

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 49.50  E-value: 1.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  625 TSaQKAELVALTQALRLA--------EG-KSINIYTDSRYAfatahVHGA---IYK--QRGLLTSAGREVKNKEKILSLL 690
Cdd:cd13934    45 TS-QRAELRAAIAALRFRswiidpdgEGlKTVVIATDSEYV-----VKGAtewIPKwkRNGWRTSKGKPVKNRDLFELLL 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 300825689  691 EAL-------------HLPKRLaiihcpghqkakdlisrgNQMADRVAKQAAQ 730
Cdd:cd13934   119 DEIedleeggvevqfwHVPREL------------------NKEADRLAKAAAE 153
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
851-961 4.79e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 49.88  E-value: 4.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  851 SHPGaHWEVDFteVKPAKyGNKYLLVFVDTFSGWVEAYPTKKKTSTVVAKKI--LEEIFPRFgIPKVIGSDNGPAFVAqv 928
Cdd:COG2826   170 AEPG-HWEGDL--IIGKR-GKSALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEFAD-- 242

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 300825689  929 SQGLAKILGIDwklhcAY--RPQSS---GQVERMNRTI 961
Cdd:COG2826   243 HKEIEAALGIK-----VYfaDPYSPwqrGTNENTNGLL 275
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 2-51 8.02e-06

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 45.82  E-value: 8.02e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 300825689     2 GATGQRQYPWTTRRTVDLGVGRVTHL--FLVIPECPIPLLGRDLLTKMGAQI 51
Cdd:pfam00077   49 GIGGGINVRQSDQILILIGEDKFRGTvsPLILPTCPVNIIGRDLLQQLGGRL 100
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
841-961 2.79e-05

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 47.46  E-value: 2.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  841 RIPPGKRLRGSHPGAHWEVDFTEVkPAKYGNKYLLVFVDTFSGWVEAYPTKKKTSTVVAKKILEEIFPRFGI--PKVIGS 918
Cdd:COG2801   136 PIAPNLLFTATAPNQVWVTDITYI-PTAEGWLYLAAVIDLFSREIVGWSVSDSMDAELVVDALEMAIERRGPpkPLILHS 214

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 300825689  919 DNGPAFVAQVSQGLAKILGIDWKLHCAYRPQSSGQVERMNRTI 961
Cdd:COG2801   215 DNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTL 257
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 591-730 1.48e-04

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


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 42.84  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  591 FTDGSSYVVEGKrmARAAVV----DGTRTIWASSLSEGTSAQKAELVALTQALRLAEG---KSINIYTDSRyaFATAHVH 663
Cdd:cd09279     4 YFDGASRGNPGP--AGAGVViyspGGEVLELSERLGFPATNNEAEYEALIAGLELALElgaEKLEIYGDSQ--LVVNQLN 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 300825689  664 GaIYKqrglltsagreVKNK------EKILSLLEALhlpKRLAIIHCPGHQkakdlisrgNQMADRVAKQAAQ 730
Cdd:cd09279    80 G-EYK-----------VKNErlkpllEKVLELLAKF---ELVELKWIPREQ---------NKEADALANQALD 128
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 873-960 3.79e-04

ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1.


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 44.01  E-value: 3.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  873 YLLVFVD--TfSGWVEAYPTKKKTsTVVAKKILEEIFPRFGIPKVIGSDNGPAFVAQVSQGLAKI------------LGI 938
Cdd:NF033594  148 TLLVAIDdaT-GRLMGLRFVESES-TFGYFEVTRQYLEKHGKPVAFYSDKHSVFRVNEEELAGKGdgltqfgralkeLGI 225

                          90       100
                  ....*....|....*....|..
gi 300825689  939 DWKlhCAYRPQSSGQVERMNRT 960
Cdd:NF033594  226 EII--CANSPQAKGRVERANQT 245
rnhA PRK00203
ribonuclease H; Reviewed
 631-730 7.34e-04

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 41.35  E-value: 7.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  631 ELVALTQALR-LAEGKSINIYTDSRY---AFaTAHVHGaiYKQRGLLTSAGREVKNKEKILSLLEALhlpKRLAII---- 702
Cdd:PRK00203   47 ELMAAIEALEaLKEPCEVTLYTDSQYvrqGI-TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAAL---KRHQIKwhwv 120

                          90       100       110
                  ....*....|....*....|....*....|
gi 300825689  703 --HCpGHqkakdlisRGNQMADRVAKQAAQ 730
Cdd:PRK00203  121 kgHA-GH--------PENERCDELARAGAE 141
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 749-840 1.27e-03

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 39.33  E-value: 1.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689   749 QYTLEDWQEIKKIDQFSETPEgTCYTSDGKEILPHKEGLEYVQQIHHLTHLGTKHLQQLVRT--SPYHVLRLPGVADSVV 826
Cdd:pfam16721    4 HYTVTDIKDLTKLGAIYDKTK-KYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERshSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|....
gi 300825689   827 KHCVPCQLVNDNPS 840
Cdd:pfam16721   83 ETCKACAQVNASKS 96
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
853-961 7.39e-03

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 40.21  E-value: 7.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  853 PGAHWEVDFTEVKPAKYGNK----YLLVFVDTFSG--WVEAYPTKKKTSTVVAkkiLEEIFPRF-GIPKVIGSDNGPAFV 925
Cdd:COG4584   120 PGEQAQVDWGEATVPPITGErrkvYVFVAVLGYSRykYVEAYPSQTQEDLLEA---HVRAFEFFgGVPREIVYDNLKTAV 196

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 300825689  926 AQVSQG----------LAKILGIDWKLHCAYRPQSSGQVERMNRTI 961
Cdd:COG4584   197 TKADRGepvlnerflaFAAHYGFEPRPCRPRRPKEKGKVENAVGYV 242
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 219-320 8.41e-03

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 39.21  E-value: 8.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825689  219 DLKNAFFCLRLHPTSQPLFAFEWRDPGTGRTGQ-LTWTRLPQGFKNSPTIFDEAL--------HRDLANFRIQHpqvtll 289
Cdd:cd01644    65 DIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIeYRMTVVPFGAASAPFLANRALkqhaedhpHEAAAKIIKRN------ 138

                          90       100       110
                  ....*....|....*....|....*....|.
gi 300825689  290 QYVDDLLLAGATKQDCLEGTNALLLELSDLG 320
Cdd:cd01644   139 FYVDDILVSTDTLNEAVNVAKRLIALLKKGG 169
 
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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