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Conserved domains on  [gi|1841786952|gb|QJT93250|]
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pol protein, partial [Macroglossus minimus gammaretrovirus]

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 ...
 175-390 4.52e-113

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: 350.49  E-value: 4.52e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  175 PVAVRQYPMSREAQEGIRPHIQRFLDLGVLVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLS 254
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  255 SLPPSHTWYTVLDLKDAFFCLKLHPNSQPLFAFEWRDpekghtGQLTWTRLPQGFKNSPTLFDEALHRDLASFRASNPQV 334
Cdd:cd03715     81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1841786952  335 VLLQYVDDLLVAAPTYEDCKEGTQKLLQELSNLGYRVSAKKAQLCQKEVTYLGYLL 390
Cdd:cd03715    155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 637-776 4.35e-53

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: 181.77  E-value: 4.35e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  637 WYTDGSSFitegkrRAGAAIVDSKRTVWMSSLPEGTSAQKAELIALTQALRLANGRDINIYTDSRYAFATAHIHGAIYRQ 716
Cdd:cd09273      2 VFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIE 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  717 RGLLtsagKEIKNREEILALLEAIHLPRRVAIIHCPGHQKGNDPVAVGNRRADEAAKQAA 776
Cdd:cd09273     76 RGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
MLVIN_C super family cl40013
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1081-1154 1.73e-29

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: 112.62  E-value: 1.73e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1841786952 1081 HSFQVGDRVLVRRHRPSSLEPRWKGPYLVLLTTPTAVKVDGIAAWIHASHLKPAPPLAPDE----SWELEKT-DHPLKL 1154
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEdfipSWQVQKDrDNPLKL 79
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 13-94 2.09e-28

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: 109.34  E-value: 2.09e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEPLGKVG---PRRTVVEGATGSKVYPWTTQR-LLRVGHKQVTHSFLVIPECPAPLL 88
Cdd:cd06095      1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQelsTTSVLIRGVSGQSQQPVTTYRtLVDLGGHTVSHSFLVVPNCPDPLL 80


                   ....*.
gi 1841786952   89 GRDLLT 94
Cdd:cd06095     81 GRDLLS 86
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 876-971 7.03e-23

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: 94.30  E-value: 7.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  876 PGVYWEVDFTEVK-PGRYGNKYLLVFIDTFSGWVEAFPTKTETALTVCKKILEEIL-PRFGIPKVLGSDNGPAFVAQVSQ 953
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1841786952  954 GLATQLGIDWKLHCAYRP 971
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RT_RNaseH super family cl39037
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 478-583 9.94e-16

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: 74.08  E-value: 9.94e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  478 DLTKPFALYVDERD-GVArGVLTQTL-GPWRRPVAYLSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASH 555
Cdd:pfam17917    1 DPSKPFILETDASDyGIG-AVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*....
gi 1841786952  556 -SLESIVRQppdrWMTNARMTHYQSLLLN 583
Cdd:pfam17917   80 kPLKYLFTP----KELNGRLARWALFLQE 104
zf-H2C2 super family cl07828
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 817-856 3.14e-06

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


The actual alignment was detected with superfamily member pfam09337:

Pssm-ID: 447530  Cd Length: 39  Bit Score: 45.01  E-value: 3.14e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1841786952  817 HQLTHLGPEKLLQLAsRTSLRIPSLQSVVREVTGQCQACA 856
Cdd:pfam09337    1 HALTHLGINKLTALL-ARKYHWLGIKETVSEVISSCVACQ 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 ...
 175-390 4.52e-113

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: 350.49  E-value: 4.52e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  175 PVAVRQYPMSREAQEGIRPHIQRFLDLGVLVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLS 254
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  255 SLPPSHTWYTVLDLKDAFFCLKLHPNSQPLFAFEWRDpekghtGQLTWTRLPQGFKNSPTLFDEALHRDLASFRASNPQV 334
Cdd:cd03715     81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1841786952  335 VLLQYVDDLLVAAPTYEDCKEGTQKLLQELSNLGYRVSAKKAQLCQKEVTYLGYLL 390
Cdd:cd03715    155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 637-776 4.35e-53

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: 181.77  E-value: 4.35e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  637 WYTDGSSFitegkrRAGAAIVDSKRTVWMSSLPEGTSAQKAELIALTQALRLANGRDINIYTDSRYAFATAHIHGAIYRQ 716
Cdd:cd09273      2 VFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIE 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  717 RGLLtsagKEIKNREEILALLEAIHLPRRVAIIHCPGHQKGNDPVAVGNRRADEAAKQAA 776
Cdd:cd09273     76 RGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 637-776 9.91e-35

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: 129.42  E-value: 9.91e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  637 WYTDGSSFITEGKRRAGAaIVDSKRTVWMSSLPEGTSAQKAELIALTQALR-LANGRDINIYTDSRYAFATAH--IHGAI 713
Cdd:pfam00075    6 VYTDGSCLGNPGPGGAGA-VLYRGHENISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwVHGWK 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1841786952  714 YRQRGlLTSAGKEIKNReEILALLEAIHLPRRVAIIHCPGHqKGNdpvaVGNRRADEAAKQAA 776
Cdd:pfam00075   85 KNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGN----PGNEMADRLAKQGA 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 218-388 1.77e-33

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: 127.80  E-value: 1.77e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  218 VKKPGTNDYRPV----QDLREVNKRVQD-IHPTVPNPYNL-----LSSLPPSHTWYTVLDLKDAFFCLKLHPNSQPLFAF 287
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQpgfrpGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  288 ------EWRDPEKGHtGQLTWTRLPQGFKNSPTLFDEALHRDLASFRASnPQVVLLQYVDDLLVAAPTYEDCKEGTQKLL 361
Cdd:pfam00078   81 ttppinINWNGELSG-GRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                          170       180
                   ....*....|....*....|....*....
gi 1841786952  362 QELSNLGYRVSAKKAQLC--QKEVTYLGY 388
Cdd:pfam00078  159 EWLKESGLKINPEKTQFFlkSKEVKYLGV 187
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1081-1154 1.73e-29

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: 112.62  E-value: 1.73e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1841786952 1081 HSFQVGDRVLVRRHRPSSLEPRWKGPYLVLLTTPTAVKVDGIAAWIHASHLKPAPPLAPDE----SWELEKT-DHPLKL 1154
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEdfipSWQVQKDrDNPLKL 79
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 13-94 2.09e-28

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: 109.34  E-value: 2.09e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEPLGKVG---PRRTVVEGATGSKVYPWTTQR-LLRVGHKQVTHSFLVIPECPAPLL 88
Cdd:cd06095      1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQelsTTSVLIRGVSGQSQQPVTTYRtLVDLGGHTVSHSFLVVPNCPDPLL 80


                   ....*.
gi 1841786952   89 GRDLLT 94
Cdd:cd06095     81 GRDLLS 86
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 876-971 7.03e-23

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: 94.30  E-value: 7.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  876 PGVYWEVDFTEVK-PGRYGNKYLLVFIDTFSGWVEAFPTKTETALTVCKKILEEIL-PRFGIPKVLGSDNGPAFVAQVSQ 953
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1841786952  954 GLATQLGIDWKLHCAYRP 971
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 9-100 5.26e-18

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: 80.49  E-value: 5.26e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952    9 PEPRVTLTVEGTPINFLVDTGAEHSVLTEplgKVGPRR-------TVVEGATGSKVYPWTTQRLLRVGHKQVTH--SFLV 79
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQ---NDWPTNwpkqkatTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLI 79

                           90       100
                   ....*....|....*....|.
gi 1841786952   80 IPECPAPLLGRDLLTKLKAQI 100
Cdd:pfam00077   80 LPTCPVNIIGRDLLQQLGGRL 100
transpos_IS481 NF033577
IS481 family transposase; null
 798-986 1.61e-16

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 81.48  E-value: 1.61e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  798 KTRPGELTLDQgEDFIRRLHQLTHLGPEKLLQLASRTSLRIPSlqSVVREVtgqCQACAMTNAVTTYREAGKRQRGDR-- 875
Cdd:NF033577    53 HRSPRRTSPET-EARILALRRELRLGPRRIAYELERQGPGVSR--STVHRI---LRRHGLSRLRALDRKTGKVKRYERah 126

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  876 PGVYWEVDFTEVKPGRYGNK-YLLVFIDTFSGWVEAFPTKTETALTVCKkILEEILPRFGIP--KVLgSDNGPAFVA--- 949
Cdd:NF033577   127 PGELWHIDIKKLGRIPDVGRlYLHTAIDDHSRFAYAELYPDETAETAAD-FLRRAFAEHGIPirRVL-TDNGSEFRSrah 204

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1841786952  950 QVSQGLAtQLGIDWKLHCAYRPQSSGQVERMNRTLKE 986
Cdd:NF033577   205 GFELALA-ELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 478-583 9.94e-16

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: 74.08  E-value: 9.94e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  478 DLTKPFALYVDERD-GVArGVLTQTL-GPWRRPVAYLSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASH 555
Cdd:pfam17917    1 DPSKPFILETDASDyGIG-AVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*....
gi 1841786952  556 -SLESIVRQppdrWMTNARMTHYQSLLLN 583
Cdd:pfam17917   80 kPLKYLFTP----KELNGRLARWALFLQE 104
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
638-776 1.26e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.80  E-value: 1.26e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSSFITEGKRRAGAAIVDSKRTVWMS-SLPEGTSaQKAELIALTQALRLA---NGRDINIYTDSRYAF--ATAHIHG 711
Cdd:COG0328      6 YTDGACRGNPGPGGWGAVIRYGGEEKELSgGLGDTTN-NRAELTALIAALEALkelGPCEVEIYTDSQYVVnqITGWIHG 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1841786952  712 aiYRQRGLltsagKEIKNREEILALLEAIHlPRRVAIIHCPGHQkGNdpvaVGNRRADEAAKQAA 776
Cdd:COG0328     85 --WKKNGW-----KPVKNPDLWQRLDELLA-RHKVTFEWVKGHA-GH----PGNERADALANKAL 136
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 896-994 3.35e-11

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: 66.35  E-value: 3.35e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  896 YLLVFID--TfSGWVEAFPTKTETALTvCKKILEEILPRFGIPKVLGSDNGPAFVAQVSQGLA-----TQ-------LGI 961
Cdd:NF033594   148 TLLVAIDdaT-GRLMGLRFVESESTFG-YFEVTRQYLEKHGKPVAFYSDKHSVFRVNEEELAGkgdglTQfgralkeLGI 225

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1841786952  962 DWKlhCAYRPQSSGQVERMNRTLKETLTK-LALE 994
Cdd:NF033594   226 EII--CANSPQAKGRVERANQTLQDRLVKeLRLA 257
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
874-986 2.02e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 57.09  E-value: 2.02e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  874 DRPGVYWEVDFTEVkpgRYGNK--YLLVFIDTFS----GWVEAFPTKTETALTVckkiLEEILPRFGI--PKVLGSDNGP 945
Cdd:COG2801    146 TAPNQVWVTDITYI---PTAEGwlYLAAVIDLFSreivGWSVSDSMDAELVVDA----LEMAIERRGPpkPLILHSDNGS 218

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1841786952  946 AFVAQVSQGLATQLGIDWKLHCAYRPQSSGQVERMNRTLKE 986
Cdd:COG2801    219 QYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
11-104 3.49e-08

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 53.80  E-value: 3.49e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   11 PRVTLTVEGTPINFLVDTGAEHSVLTEP----LG---KVGPRRTVVEGATGSKVYPWTTQRLLRVGHKQVTH-SFLVIP- 81
Cdd:COG3577     42 FVVEGTINGQPVRFLVDTGASTVVLSESdarrLGldpEDLGRPVRVQTANGVVRAARVRLDSVRIGGITLRNvRAVVLPg 121

                           90       100
                   ....*....|....*....|....
gi 1841786952   82 -ECPAPLLGRDLLTKLKAQIQFST 104
Cdd:COG3577    122 gELDDGLLGMSFLGRLDFEIDGDR 145
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 817-856 3.14e-06

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: 45.01  E-value: 3.14e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1841786952  817 HQLTHLGPEKLLQLAsRTSLRIPSLQSVVREVTGQCQACA 856
Cdd:pfam09337    1 HALTHLGINKLTALL-ARKYHWLGIKETVSEVISSCVACQ 39
rnhA PRK00203
ribonuclease H; Reviewed
 678-776 1.85e-04

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 42.89  E-value: 1.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  678 ELIALTQALR-LANGRDINIYTDSRY---AFaTAHIHGaiYRQRGLLTSAGKEIKNREEILALLEAIHlPRRVAIIHCPG 753
Cdd:PRK00203    47 ELMAAIEALEaLKEPCEVTLYTDSQYvrqGI-TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKG 122

                           90       100
                   ....*....|....*....|...
gi 1841786952  754 HQkGNdpvaVGNRRADEAAKQAA 776
Cdd:PRK00203   123 HA-GH----PENERCDELARAGA 140
 
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 ...
 175-390 4.52e-113

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: 350.49  E-value: 4.52e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  175 PVAVRQYPMSREAQEGIRPHIQRFLDLGVLVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLS 254
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  255 SLPPSHTWYTVLDLKDAFFCLKLHPNSQPLFAFEWRDpekghtGQLTWTRLPQGFKNSPTLFDEALHRDLASFRASNPQV 334
Cdd:cd03715     81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1841786952  335 VLLQYVDDLLVAAPTYEDCKEGTQKLLQELSNLGYRVSAKKAQLCQKEVTYLGYLL 390
Cdd:cd03715    155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 637-776 4.35e-53

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: 181.77  E-value: 4.35e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  637 WYTDGSSFitegkrRAGAAIVDSKRTVWMSSLPEGTSAQKAELIALTQALRLANGRDINIYTDSRYAFATAHIHGAIYRQ 716
Cdd:cd09273      2 VFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIE 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  717 RGLLtsagKEIKNREEILALLEAIHLPRRVAIIHCPGHQKGNDPVAVGNRRADEAAKQAA 776
Cdd:cd09273     76 RGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 175-390 9.15e-42

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: 152.44  E-value: 9.15e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  175 PVAVRQYPMSREAQEGIRPHIQRFLDLGVLVPCQSPWNTPLLPVKKPgTNDYRPVQDLREVNKRVQD---IHPTVPNPyn 251
Cdd:cd01645      1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK-SGKWRLLHDLRAVNAQTQDmgaLQPGLPHP-- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  252 llsSLPPSHTWYTVLDLKDAFFCLKLHPNSQPLFAFEWRDPE-KGHTGQLTWTRLPQGFKNSPTLFDEALHRDLASFRAS 330
Cdd:cd01645     78 ---AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQ 154

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  331 NPQVVLLQYVDDLLVAAPTYEDCKEGTQKLLQELSNLGYRVSAKKAQLcQKEVTYLGYLL 390
Cdd:cd01645    155 YPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQYLGYEL 213
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 202-389 1.74e-39

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: 144.66  E-value: 1.74e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  202 GVLVPCQSPWNTPLLPVKKPGtNDYRPVQDLREVNKR-VQDIHPtVPNPYNLLSSLPPSHtWYTVLDLKDAFFCLKLHPN 280
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKD-GKLRLCVDYRKLNKVtIKDRYP-LPTIDELLEELAGAK-VFSKLDLRSGYHQIPLAEE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  281 SQPLFAFewrdpeKGHTGQLTWTRLPQGFKNSPTLF----DEALHRDLASFrasnpqvvLLQYVDDLLVAAPTYEDCKEG 356
Cdd:cd01647     78 SRPKTAF------RTPFGLYEYTRMPFGLKNAPATFqrlmNKILGDLLGDF--------VEVYLDDILVYSKTEEEHLEH 143

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1841786952  357 TQKLLQELSNLGYRVSAKKAQLCQKEVTYLGYL 389
Cdd:cd01647    144 LREVLERLREAGLKLNPEKCEFGVPEVEFLGHI 176
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 637-776 9.91e-35

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: 129.42  E-value: 9.91e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  637 WYTDGSSFITEGKRRAGAaIVDSKRTVWMSSLPEGTSAQKAELIALTQALR-LANGRDINIYTDSRYAFATAH--IHGAI 713
Cdd:pfam00075    6 VYTDGSCLGNPGPGGAGA-VLYRGHENISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwVHGWK 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1841786952  714 YRQRGlLTSAGKEIKNReEILALLEAIHLPRRVAIIHCPGHqKGNdpvaVGNRRADEAAKQAA 776
Cdd:pfam00075   85 KNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGN----PGNEMADRLAKQGA 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 218-388 1.77e-33

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: 127.80  E-value: 1.77e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  218 VKKPGTNDYRPV----QDLREVNKRVQD-IHPTVPNPYNL-----LSSLPPSHTWYTVLDLKDAFFCLKLHPNSQPLFAF 287
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQpgfrpGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  288 ------EWRDPEKGHtGQLTWTRLPQGFKNSPTLFDEALHRDLASFRASnPQVVLLQYVDDLLVAAPTYEDCKEGTQKLL 361
Cdd:pfam00078   81 ttppinINWNGELSG-GRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                          170       180
                   ....*....|....*....|....*....
gi 1841786952  362 QELSNLGYRVSAKKAQLC--QKEVTYLGY 388
Cdd:pfam00078  159 EWLKESGLKINPEKTQFFlkSKEVKYLGV 187
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1081-1154 1.73e-29

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: 112.62  E-value: 1.73e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1841786952 1081 HSFQVGDRVLVRRHRPSSLEPRWKGPYLVLLTTPTAVKVDGIAAWIHASHLKPAPPLAPDE----SWELEKT-DHPLKL 1154
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEdfipSWQVQKDrDNPLKL 79
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 13-94 2.09e-28

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: 109.34  E-value: 2.09e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEPLGKVG---PRRTVVEGATGSKVYPWTTQR-LLRVGHKQVTHSFLVIPECPAPLL 88
Cdd:cd06095      1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQelsTTSVLIRGVSGQSQQPVTTYRtLVDLGGHTVSHSFLVVPNCPDPLL 80


                   ....*.
gi 1841786952   89 GRDLLT 94
Cdd:cd06095     81 GRDLLS 86
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 876-971 7.03e-23

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: 94.30  E-value: 7.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  876 PGVYWEVDFTEVK-PGRYGNKYLLVFIDTFSGWVEAFPTKTETALTVCKKILEEIL-PRFGIPKVLGSDNGPAFVAQVSQ 953
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1841786952  954 GLATQLGIDWKLHCAYRP 971
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 638-776 1.06e-18

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 83.77  E-value: 1.06e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSsFITEGKR--RAGAAIV---DSKRTVWMSSLPEGTSAQKAELIALTQALRLA---NGRDINIYTDSRYAFATAHI 709
Cdd:cd09280      3 YTDGS-CLNNGKPgaRAGIGVYfgpGDPRNVSEPLPGRKQTNNRAELLAVIHALEQApeeGIRKLEIRTDSKYAINCITK 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1841786952  710 HGAIYRQRGLLTSAGKEIKNREEILALLEAIH-LPRRVAIIHCPGHQkgNDPvavGNRRADEAAKQAA 776
Cdd:cd09280     82 WIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRkRGIKVKFEHVKGHS--GDP---GNEEADRLAREGA 144
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 9-100 5.26e-18

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: 80.49  E-value: 5.26e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952    9 PEPRVTLTVEGTPINFLVDTGAEHSVLTEplgKVGPRR-------TVVEGATGSKVYPWTTQRLLRVGHKQVTH--SFLV 79
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQ---NDWPTNwpkqkatTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLI 79

                           90       100
                   ....*....|....*....|.
gi 1841786952   80 IPECPAPLLGRDLLTKLKAQI 100
Cdd:pfam00077   80 LPTCPVNIIGRDLLQQLGGRL 100
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 638-776 2.52e-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: 79.83  E-value: 2.52e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSSFITEGKRRAGAAIVDSKRTVWMSSLPEGTSAQKAELIALTQALR-LANGRDINIYTDSRYAF--ATAHIHGaiY 714
Cdd:cd09278      5 YTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEaLKEPCPVTIYTDSQYVIngITKWIKG--W 82

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1841786952  715 RQRGLLTSAGKEIKNREEILALLEAIhLPRRVAIIHCPGHQkGNdpvaVGNRRADEAAKQAA 776
Cdd:cd09278     83 KKNGWKTADGKPVKNRDLWQELDALL-AGHKVTWEWVKGHA-GH----PGNERADRLANKAA 138
transpos_IS481 NF033577
IS481 family transposase; null
 798-986 1.61e-16

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 81.48  E-value: 1.61e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  798 KTRPGELTLDQgEDFIRRLHQLTHLGPEKLLQLASRTSLRIPSlqSVVREVtgqCQACAMTNAVTTYREAGKRQRGDR-- 875
Cdd:NF033577    53 HRSPRRTSPET-EARILALRRELRLGPRRIAYELERQGPGVSR--STVHRI---LRRHGLSRLRALDRKTGKVKRYERah 126

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  876 PGVYWEVDFTEVKPGRYGNK-YLLVFIDTFSGWVEAFPTKTETALTVCKkILEEILPRFGIP--KVLgSDNGPAFVA--- 949
Cdd:NF033577   127 PGELWHIDIKKLGRIPDVGRlYLHTAIDDHSRFAYAELYPDETAETAAD-FLRRAFAEHGIPirRVL-TDNGSEFRSrah 204

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1841786952  950 QVSQGLAtQLGIDWKLHCAYRPQSSGQVERMNRTLKE 986
Cdd:NF033577   205 GFELALA-ELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 478-583 9.94e-16

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: 74.08  E-value: 9.94e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  478 DLTKPFALYVDERD-GVArGVLTQTL-GPWRRPVAYLSKKLDPVASGWPTCLKAVAAVALLLKDADKLTLGQNVTVIASH 555
Cdd:pfam17917    1 DPSKPFILETDASDyGIG-AVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*....
gi 1841786952  556 -SLESIVRQppdrWMTNARMTHYQSLLLN 583
Cdd:pfam17917   80 kPLKYLFTP----KELNGRLARWALFLQE 104
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 638-776 1.69e-15

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: 74.18  E-value: 1.69e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSSFitegKRRAGAAIVDSKRTVWMS---SLPEGTSAQKAELIALTQALRLA-----NGRDINIYTDSRyAfATAHI 709
Cdd:cd09276      3 YTDGSKL----EGSVGAGFVIYRGGEVISrsyRLGTHASVFDAELEAILEALELAlatarRARKVTIFTDSQ-S-ALQAL 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1841786952  710 HGAiyrqrgllTSAGKEIKNREEILALLEAIHLPRRVAIIHCPGHQKgndpVAvGNRRADEAAKQAA 776
Cdd:cd09276     77 RNP--------RRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVG----IE-GNEAADRLAKEAA 130
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
638-776 1.26e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 71.80  E-value: 1.26e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSSFITEGKRRAGAAIVDSKRTVWMS-SLPEGTSaQKAELIALTQALRLA---NGRDINIYTDSRYAF--ATAHIHG 711
Cdd:COG0328      6 YTDGACRGNPGPGGWGAVIRYGGEEKELSgGLGDTTN-NRAELTALIAALEALkelGPCEVEIYTDSQYVVnqITGWIHG 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1841786952  712 aiYRQRGLltsagKEIKNREEILALLEAIHlPRRVAIIHCPGHQkGNdpvaVGNRRADEAAKQAA 776
Cdd:COG0328     85 --WKKNGW-----KPVKNPDLWQRLDELLA-RHKVTFEWVKGHA-GH----PGNERADALANKAL 136
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 637-773 6.58e-14

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: 69.27  E-value: 6.58e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  637 WYTDGSSFITEGKRRAGAAIVDS--KRTVWMSSLPEGTSAQKAELIALTQALRLA---NGRDINIYTDSRYAFATAHIHG 711
Cdd:cd06222      1 INVDGSCRGNPGPAGIGGVLRDHegGWLGGFALKIGAPTALEAELLALLLALELAldlGYLKVIIESDSKYVVDLINSGS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1841786952  712 AIYRQRGLLtsagkeiknREEILALLEAIHlprRVAIIHCPGHqkgndpvavGNRRADEAAK 773
Cdd:cd06222     81 FKWSPNILL---------IEDILLLLSRFW---SVKISHVPRE---------GNQVADALAK 121
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 304-390 4.02e-13

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: 66.22  E-value: 4.02e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  304 RLPQGFKNSPTLFDEALHRDLASFRASNPQVVLLQYVDDLLVAApTYEDCKEGTQKLLQELSNLGYRVSAKKAQL--CQK 381
Cdd:cd00304     11 PLPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIA-KSEQQAVKKRELEEFLARLGLNLSDEKTQFteKEK 89


                   ....*....
gi 1841786952  382 EVTYLGYLL 390
Cdd:cd00304     90 KFKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 266-387 9.17e-13

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: 65.83  E-value: 9.17e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  266 LDLKDAFFCLKLHPNSQPLFAFEWRDPekghtgQLTWTRLPQGFKNSPTLFDEALHRDLASFRASNpqVVLLQYVDDLLV 345
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGE------TYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG--VRIFSYLDDLLI 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1841786952  346 AAPTYEDCKEGTQKLLQELS-NLGYRVSAKKAQLC-QKEVTYLG 387
Cdd:cd03714     73 IASSIKTSEAVLRHLRATLLaNLGFTLNLEKSKLGpTQRITFLG 116
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 896-994 3.35e-11

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: 66.35  E-value: 3.35e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  896 YLLVFID--TfSGWVEAFPTKTETALTvCKKILEEILPRFGIPKVLGSDNGPAFVAQVSQGLA-----TQ-------LGI 961
Cdd:NF033594   148 TLLVAIDdaT-GRLMGLRFVESESTFG-YFEVTRQYLEKHGKPVAFYSDKHSVFRVNEEELAGkgdglTQfgralkeLGI 225

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1841786952  962 DWKlhCAYRPQSSGQVERMNRTLKETLTK-LALE 994
Cdd:NF033594   226 EII--CANSPQAKGRVERANQTLQDRLVKeLRLA 257
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
453-551 1.74e-10

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 59.05  E-value: 1.74e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  453 WTEEHQKAFDCIKEALLTAPALALPDLTKPFALYVDERD-GVArGVLTQTL--GPWrRPVAYLSKKLDPVASGWPTCLKA 529
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDyGIG-AVLSQEDddGGE-RPIAYASRKLSPAERNYSTTEKE 78

                           90       100
                   ....*....|....*....|..
gi 1841786952  530 VAAVALLLKDADKLTLGQNVTV 551
Cdd:pfam17919   79 LLAIVFALKKFRHYLLGRKFTV 100
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 13-94 6.88e-10

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


Pssm-ID: 133136  Cd Length: 92  Bit Score: 56.96  E-value: 6.88e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEPLGK-------VGPRRTVVEGATGSKVYPWTTQRL--LRVGHKQVTHSFLVIPEC 83
Cdd:cd00303      1 LKGKINGVPVRALVDSGASVNFISESLAKklglpprLLPTPLKVKGANGSSVKTLGVILPvtIGIGGKTFTVDFYVLDLL 80

                           90
                   ....*....|..
gi 1841786952   84 PAP-LLGRDLLT 94
Cdd:cd00303     81 SYDvILGRPWLE 92
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 13-93 9.72e-10

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 56.43  E-value: 9.72e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEP----LG---KVGPRRTVVEGATGSKVYPWTTQRLLRVGHKQVTH-SFLVIP-EC 83
Cdd:pfam13975    1 VDVTINGRPVRFLVDTGASVTVISEAlaerLGldrLVDAYPVTVRTANGTVRAARVRLDSVKIGGIELRNvPAVVLPgDL 80

                           90
                   ....*....|
gi 1841786952   84 PAPLLGRDLL 93
Cdd:pfam13975   81 DDVLLGMDFL 90
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
874-986 2.02e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 57.09  E-value: 2.02e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  874 DRPGVYWEVDFTEVkpgRYGNK--YLLVFIDTFS----GWVEAFPTKTETALTVckkiLEEILPRFGI--PKVLGSDNGP 945
Cdd:COG2801    146 TAPNQVWVTDITYI---PTAEGwlYLAAVIDLFSreivGWSVSDSMDAELVVDA----LEMAIERRGPpkPLILHSDNGS 218

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1841786952  946 AFVAQVSQGLATQLGIDWKLHCAYRPQSSGQVERMNRTLKE 986
Cdd:COG2801    219 QYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
11-104 3.49e-08

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 53.80  E-value: 3.49e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   11 PRVTLTVEGTPINFLVDTGAEHSVLTEP----LG---KVGPRRTVVEGATGSKVYPWTTQRLLRVGHKQVTH-SFLVIP- 81
Cdd:COG3577     42 FVVEGTINGQPVRFLVDTGASTVVLSESdarrLGldpEDLGRPVRVQTANGVVRAARVRLDSVRIGGITLRNvRAVVLPg 121

                           90       100
                   ....*....|....*....|....
gi 1841786952   82 -ECPAPLLGRDLLTKLKAQIQFST 104
Cdd:COG3577    122 gELDDGLLGMSFLGRLDFEIDGDR 145
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 638-776 8.21e-08

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: 52.97  E-value: 8.21e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSSfITEGK--RRAGAAIVDSKRTVWMSSLP-EGT-----SAQKAELIALTQALRLANGRDIN---------IYTDS 700
Cdd:cd13934      3 YIDGAC-RNNGRpdARAGYGVYFGPDSSYNVSGRlEDTgghpqTSQRAELRAAIAALRFRSWIIDPdgeglktvvIATDS 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  701 RYAF--ATAHIHGaiYRQRGLLTSAGKEIKNREEILALLEAI-------------HLPRRVaiihcpghqkgndpvavgN 765
Cdd:cd13934     82 EYVVkgATEWIPK--WKRNGWRTSKGKPVKNRDLFELLLDEIedleeggvevqfwHVPREL------------------N 141

                          170
                   ....*....|.
gi 1841786952  766 RRADEAAKQAA 776
Cdd:cd13934    142 KEADRLAKAAA 152
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 13-92 1.28e-07

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 50.36  E-value: 1.28e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEPLGK-------VGPRRTVVEGATGSKVYPWTTQRLLRVGHKQVTH-SFLVIP--E 82
Cdd:pfam13650    1 VPVTINGKPVRFLVDTGASGTVISPSLAErlglkvrGLAYTVRVSTAGGRVSAARVRLDSLRLGGLTLENvPALVLDlgD 80

                           90
                   ....*....|
gi 1841786952   83 CPAPLLGRDL 92
Cdd:pfam13650   81 LIDGLLGMDF 90
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 11-93 1.42e-07

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. 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 proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 50.32  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   11 PRVTLTVEGTPINFLVDTGAEHSVLTEPLGK------VGPRRTVVEGATGSKVYPWTTQRLLRVGHKQVTH-SFLVIPEC 83
Cdd:cd05483      3 FVVPVTINGQPVRFLLDTGASTTVISEELAErlglplTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNvPAVVLPGD 82

                           90
                   ....*....|...
gi 1841786952   84 PAP---LLGRDLL 93
Cdd:cd05483     83 ALGvdgLLGMDFL 95
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 638-776 1.91e-06

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: 48.24  E-value: 1.91e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  638 YTDGSSFITEGKRRAGAAIVDSKRTVWMSS--LPEGTSAQKAELIALTQALRLA---NGRDINIYTDSRyaFATAHIHGa 712
Cdd:cd09279      4 YFDGASRGNPGPAGAGVVIYSPGGEVLELSerLGFPATNNEAEYEALIAGLELAlelGAEKLEIYGDSQ--LVVNQLNG- 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  713 IYrqrglltsagkEIKN------REEILALLEAIhlpRRVAIIHCPGHQkgndpvavgNRRADEAAKQAA 776
Cdd:cd09279     81 EY-----------KVKNerlkplLEKVLELLAKF---ELVELKWIPREQ---------NKEADALANQAL 127
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 817-856 3.14e-06

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: 45.01  E-value: 3.14e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1841786952  817 HQLTHLGPEKLLQLAsRTSLRIPSLQSVVREVTGQCQACA 856
Cdd:pfam09337    1 HALTHLGINKLTALL-ARKYHWLGIKETVSEVISSCVACQ 39
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
865-986 6.25e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 49.49  E-value: 6.25e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  865 REAGKRQRgdrPGvYWEVDfteVKPGRYGNKYLLVFIDTFSGWVEAFPTKTETALTVCKKI--LEEILPRFgIPKVLGSD 942
Cdd:COG2826    164 AEVEDRAE---PG-HWEGD---LIIGKRGKSALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTD 235

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1841786952  943 NGPAFVAqvSQGLATQLGIDwklhcAY--RPQSS---GQVERMNRTLKE 986
Cdd:COG2826    236 NGKEFAD--HKEIEAALGIK-----VYfaDPYSPwqrGTNENTNGLLRQ 277
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 267-368 1.94e-05

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 46.91  E-value: 1.94e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  267 DLKDAFFCLKLHPNSQPLFAFEWRDPEKGHTGQ-LTWTRLPQGFKNSPTLFDEALHRDLASFRASNPQVVLLQ--YVDDL 343
Cdd:cd01644     65 DIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIeYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRnfYVDDI 144

                           90       100
                   ....*....|....*....|....*
gi 1841786952  344 LVAAPTYEDCKEGTQKLLQELSNLG 368
Cdd:cd01644    145 LVSTDTLNEAVNVAKRLIALLKKGG 169
rnhA PRK00203
ribonuclease H; Reviewed
 678-776 1.85e-04

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 42.89  E-value: 1.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  678 ELIALTQALR-LANGRDINIYTDSRY---AFaTAHIHGaiYRQRGLLTSAGKEIKNREEILALLEAIHlPRRVAIIHCPG 753
Cdd:PRK00203    47 ELMAAIEALEaLKEPCEVTLYTDSQYvrqGI-TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKG 122

                           90       100
                   ....*....|....*....|...
gi 1841786952  754 HQkGNdpvaVGNRRADEAAKQAA 776
Cdd:PRK00203   123 HA-GH----PENERCDELARAGA 140
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 13-94 3.38e-04

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. 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: 133149  Cd Length: 87  Bit Score: 40.71  E-value: 3.38e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTE----PLGKVGPRRTVVEGATGSkVYPW-TTQRLLRVGHKQVTHSFLVIPEC-PAP 86
Cdd:cd05482      1 LTLYINGKLFEGLLDTGADVSIIAEndwpKNWPIQPAPSNLTGIGGA-ITPSqSSVLLLEIDGEGHLGTILVYVLSlPVN 79


                   ....*...
gi 1841786952   87 LLGRDLLT 94
Cdd:cd05482     80 LWGRDILS 87
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 810-860 6.25e-04

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 38.77  E-value: 6.25e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1841786952  810 EDFIRRLH-QLTHLGPEKLLQLASRTsLRIPSLQSVVREVTGQCQACAMTNA 860
Cdd:pfam17921    7 KEILKEAHdSGGHLGIEKTLARLRRR-YWWPGMRKDVKKYVKSCETCQRRKP 57
retropepsin_like_LTR_2 cd05484
Retropepsins_like_LTR, pepsin-like aspartate proteases; Retropepsin of retrotransposons with ...
 13-93 2.16e-03

Retropepsins_like_LTR, pepsin-like aspartate proteases; Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-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: 133151  Cd Length: 91  Bit Score: 38.34  E-value: 2.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952   13 VTLTVEGTPINFLVDTGAEHSVLTEP----LGK--VGPRRTVVEGATGSKVypwttqRLLRVGHKQVTH-------SFLV 79
Cdd:cd05484      3 VTLLVNGKPLKFQLDTGSAITVISEKtwrkLGSppLKPTKKRLRTATGTKL------SVLGQILVTVKYggktkvlTLYV 76

                           90
                   ....*....|....
gi 1841786952   80 IPECPAPLLGRDLL 93
Cdd:cd05484     77 VKNEGLNLLGRDWL 90
RP_Saci_like cd06094
RP_Saci_like, retropepsin family; Retropepsin on retrotransposons with long terminal repeats ...
 20-93 3.60e-03

RP_Saci_like, retropepsin family; Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. 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: 133158  Cd Length: 89  Bit Score: 37.60  E-value: 3.60e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1841786952   20 TPINFLVDTGAEHSVLTEPLGKVGPRRT--VVEGATGSKVYPW-TTQRLLRVGHKQVTHSFLVIPECPAPLLGRDLL 93
Cdd:cd06094      8 SGLRFLVDTGAAVSVLPASSTKKSLKPSplTLQAANGTPIATYgTRSLTLDLGLRRPFAWNFVVADVPHPILGADFL 84
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
 305-390 5.91e-03

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 39.58  E-value: 5.91e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841786952  305 LPQGFKNSPTLFD---EALHRDL---ASFRASNPQVVLLQYVDDLLVAAPTYEDCKEGTQKLLQE-LSNLGYRVSAKKAQ 377
Cdd:cd01650    107 VRQGDPLSPLLFNlalDDLLRLLnkeEEIKLGGPGITHLAYADDIVLFSEGKSRKLQELLQRLQEwSKESGLKINPSKSK 186

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1841786952  378 L---------------------CQKEVTYLGYLL 390
Cdd:cd01650    187 VmlignkkkrlkditlngtpieAVETFKYLGVTI 220
 
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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