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Conserved domains on  [gi|351720597|dbj|BAL04139|]
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gag-pol precursor polyprotein [Feline leukemia virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p30 pfam02093
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ...
 286-493 3.72e-150

Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.


:

Pssm-ID: 426597  Cd Length: 208  Bit Score: 459.52  E-value: 3.72e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   286 QYWPFSASDLYNWKSHNPPFSQDPVALTNLIESILVTHQPTWDDCQQLLQTLLTAEERQRVLLEARKQVPGEDGRPTQLP 365
Cdd:pfam02093    1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   366 NVIDEAFPLTRPNWDFATPAGREHLRLYRQLLLAGLRGAARRPTNLAQVKQVVQGKEETPAAFLERLKEAYRMYTPYDPE 445
Cdd:pfam02093   81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 351720597   446 DPGQAASVILSFIYQSSPDIRNKLQRLEGLQGFTLSDLLKEAEKIYNK 493
Cdd:pfam02093  161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 208
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 762-975 1.69e-108

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


:

Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 343.95  E-value: 1.69e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  762 PISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCRSPWNTPLLPVKKPGTGDYRPVQDLREVNKRVEDIHPTVPNPYNLLS 841
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  842 TLPPSHPWYTVLDLKDAFFCLRLHPESQLLFAFEWKDpeiglsGQLTWTRLPQGFKNSPTLFDEALHSDLADFRVRYPTL 921
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 351720597  922 VLLQYVDDLLLAAATRTECLEGTKALLKTLGSKGYRASAKKAQICLQKVTYLGY 975
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 ...
 1224-1364 8.56e-54

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: 184.46  E-value: 8.56e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1224 TWYTDGSSFirngerKAGAAVTTESEVIWAASLPPGTSAQRAELIALTQALKMAKGKKLTVYTDSRYAFATAHVHGEIYR 1303
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 351720597 1304 RRGLLtsegKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAA 1364
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 79-175 6.70e-41

Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.


:

Pssm-ID: 426076 [Multi-domain]  Cd Length: 126  Bit Score: 147.14  E-value: 6.70e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597    79 GQTVTTPLSLTLDHWSEVRTRAHNQGVEVRKKKWITLCEAEWVMMNVGWPREGTFSLDNISQVEKKIFAPGPCGHPDQVP 158
Cdd:pfam01140    1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                           90
                   ....*....|....*..
gi 351720597   159 YITTWRSLASDPPSWVR 175
Cdd:pfam01140   81 YIVTWEALAADPPPWVR 97
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1700-1788 2.18e-35

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: 129.95  E-value: 2.18e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1700 HPFKPGDSVWVRRHQTKNLEPRWKGPHIVLLTTPTALKVDGVAAWIHASHVKAAgptanqDPSDDPSSEDPSrWKVQRT- 1778
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPA------DPHAVLEDFIPS-WQVQKDr 73

                           90
                   ....*....|
gi 351720597  1779 QNPLKIRLSR 1788
Cdd:pfam18697   74 DNPLKLRLRR 83
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 594-686 7.50e-26

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: 103.22  E-value: 7.50e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   594 PEPRITLKIGGQPVTFLVDTGAQHSVLTRPDGPLS----DRTALVQGATGSKNYRWTTDRRVQLATGKVTH--SFLYVPE 667
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpkqKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                           90
                   ....*....|....*....
gi 351720597   668 CPYPLLGRDLLTKLKAQIH 686
Cdd:pfam00077   83 CPVNIIGRDLLQQLGGRLT 101
zf-H2C2 super family cl07828
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1387-1479 2.28e-25

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 pfam16721:

Pssm-ID: 447530  Cd Length: 96  Bit Score: 101.73  E-value: 2.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1387 WEYDDSDLDLVQKLKAHYEPKRGTWEYQGKTIMPEKFAKELISHLHKLTHLSAKKMKTLLEREETGFYLPNRDLHLRQVT 1466
Cdd:pfam16721    3 FHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|...
gi 351720597  1467 ESCRACAQINAGK 1479
Cdd:pfam16721   83 ETCKACAQVNASK 95
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1493-1588 9.64e-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: 9.64e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1493 PGAHWEVDFTEIK-PGMYGYKYLLVFIDTFSGWAEAYPAKRETAKVVAKKLLEEIFPRYGI-PQVLGSDNGPAFVSQVSQ 1570
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 351720597  1571 SVATLLGINWKLHCAYRP 1588
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) ...
 1065-1170 1.01e-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: 77.17  E-value: 1.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1065 DITKPFELFIDeSSGFAKG-VLVQKL-GPWKRPVAYLSKKLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSH 1142
Cdd:pfam17917    1 DPSKPFILETD-ASDYGIGaVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 351720597  1143 PVEALVRQPpnrWLSNARMTHYQAMLLD 1170
Cdd:pfam17917   80 KPLKYLFTP---KELNGRLARWALFLQE 104
ZnF_C2HC smart00343
zinc finger;
552-568 1.97e-03

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.04  E-value: 1.97e-03
                            10
                    ....*....|....*..
gi 351720597    552 QCAYCKEKGHWVRDCPK 568
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
Gag_p30 pfam02093
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ...
 286-493 3.72e-150

Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.


Pssm-ID: 426597  Cd Length: 208  Bit Score: 459.52  E-value: 3.72e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   286 QYWPFSASDLYNWKSHNPPFSQDPVALTNLIESILVTHQPTWDDCQQLLQTLLTAEERQRVLLEARKQVPGEDGRPTQLP 365
Cdd:pfam02093    1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   366 NVIDEAFPLTRPNWDFATPAGREHLRLYRQLLLAGLRGAARRPTNLAQVKQVVQGKEETPAAFLERLKEAYRMYTPYDPE 445
Cdd:pfam02093   81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 351720597   446 DPGQAASVILSFIYQSSPDIRNKLQRLEGLQGFTLSDLLKEAEKIYNK 493
Cdd:pfam02093  161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 208
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 762-975 1.69e-108

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 343.95  E-value: 1.69e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  762 PISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCRSPWNTPLLPVKKPGTGDYRPVQDLREVNKRVEDIHPTVPNPYNLLS 841
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  842 TLPPSHPWYTVLDLKDAFFCLRLHPESQLLFAFEWKDpeiglsGQLTWTRLPQGFKNSPTLFDEALHSDLADFRVRYPTL 921
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 351720597  922 VLLQYVDDLLLAAATRTECLEGTKALLKTLGSKGYRASAKKAQICLQKVTYLGY 975
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 ...
 1224-1364 8.56e-54

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: 184.46  E-value: 8.56e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1224 TWYTDGSSFirngerKAGAAVTTESEVIWAASLPPGTSAQRAELIALTQALKMAKGKKLTVYTDSRYAFATAHVHGEIYR 1303
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 351720597 1304 RRGLLtsegKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAA 1364
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 79-175 6.70e-41

Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.


Pssm-ID: 426076 [Multi-domain]  Cd Length: 126  Bit Score: 147.14  E-value: 6.70e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597    79 GQTVTTPLSLTLDHWSEVRTRAHNQGVEVRKKKWITLCEAEWVMMNVGWPREGTFSLDNISQVEKKIFAPGPCGHPDQVP 158
Cdd:pfam01140    1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                           90
                   ....*....|....*..
gi 351720597   159 YITTWRSLASDPPSWVR 175
Cdd:pfam01140   81 YIVTWEALAADPPPWVR 97
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1220-1364 2.83e-36

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: 134.43  E-value: 2.83e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1220 DADLTWYTDGSSFIRNGERKAGAAVTTESEvIWAASLPPGTSAQRAELIALTQALKMAK-GKKLTVYTDSRYAFATAH-- 1296
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHE-NISAPLPGRTTNNRAELQAVIEALKALKsPSKVNIYTDSQYVIGGITqw 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 351720597  1297 VHGEIYRRRGlLTSEGKEIKNKnEILALLEALFLPKRLSIIHCPGHqKGDspqaKGNRLADDTAKKAA 1364
Cdd:pfam00075   80 VHGWKKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGN----PGNEMADRLAKQGA 140
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1700-1788 2.18e-35

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: 129.95  E-value: 2.18e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1700 HPFKPGDSVWVRRHQTKNLEPRWKGPHIVLLTTPTALKVDGVAAWIHASHVKAAgptanqDPSDDPSSEDPSrWKVQRT- 1778
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPA------DPHAVLEDFIPS-WQVQKDr 73

                           90
                   ....*....|
gi 351720597  1779 QNPLKIRLSR 1788
Cdd:pfam18697   74 DNPLKLRLRR 83
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 805-977 2.95e-32

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: 124.72  E-value: 2.95e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   805 VKKPGTGDYRPV----QDLREVNKRVED-IHPTVPNPYNLLSTLPPSHP-----WYTVLDLKDAFFCLRLHPESQLLFAF 874
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQPGFRPGLAKlkkakWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   875 EWKDPEIGLSGQL-----TWTRLPQGFKNSPTLFDEALHSDLADFRVRYpTLVLLQYVDDLLLAAATRTECLEGTKALLK 949
Cdd:pfam00078   81 TTPPININWNGELsggryEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 351720597   950 TLGSKGYRASAKKAQICLQK--VTYLGYSL 977
Cdd:pfam00078  160 WLKESGLKINPEKTQFFLKSkeVKYLGVTL 189
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 594-686 7.50e-26

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: 103.22  E-value: 7.50e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   594 PEPRITLKIGGQPVTFLVDTGAQHSVLTRPDGPLS----DRTALVQGATGSKNYRWTTDRRVQLATGKVTH--SFLYVPE 667
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpkqKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                           90
                   ....*....|....*....
gi 351720597   668 CPYPLLGRDLLTKLKAQIH 686
Cdd:pfam00077   83 CPVNIIGRDLLQQLGGRLT 101
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 598-679 2.01e-25

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: 101.64  E-value: 2.01e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  598 ITLKIGGQPVTFLVDTGAQHSVLTRPDGP---LSDRTALVQGATGSKNYRWTTDRR-VQLATGKVTHSFLYVPECPYPLL 673
Cdd:cd06095     1 VTITVEGVPIVFLVDTGATHSVLKSDLGPkqeLSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                  ....*.
gi 351720597  674 GRDLLT 679
Cdd:cd06095    81 GRDLLS 86
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 1387-1479 2.28e-25

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: 101.73  E-value: 2.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1387 WEYDDSDLDLVQKLKAHYEPKRGTWEYQGKTIMPEKFAKELISHLHKLTHLSAKKMKTLLEREETGFYLPNRDLHLRQVT 1466
Cdd:pfam16721    3 FHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|...
gi 351720597  1467 ESCRACAQINAGK 1479
Cdd:pfam16721   83 ETCKACAQVNASK 95
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1493-1588 9.64e-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: 9.64e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1493 PGAHWEVDFTEIK-PGMYGYKYLLVFIDTFSGWAEAYPAKRETAKVVAKKLLEEIFPRYGI-PQVLGSDNGPAFVSQVSQ 1570
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 351720597  1571 SVATLLGINWKLHCAYRP 1588
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1065-1170 1.01e-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: 77.17  E-value: 1.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1065 DITKPFELFIDeSSGFAKG-VLVQKL-GPWKRPVAYLSKKLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSH 1142
Cdd:pfam17917    1 DPSKPFILETD-ASDYGIGaVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 351720597  1143 PVEALVRQPpnrWLSNARMTHYQAMLLD 1170
Cdd:pfam17917   80 KPLKYLFTP---KELNGRLARWALFLQE 104
transpos_IS481 NF033577
IS481 family transposase; null
 1491-1641 1.54e-15

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 79.17  E-value: 1.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1491 HRPGAHWEVDFTEIKPGMY-GYKYLLVFIDTFSGWA--EAYPAKRetaKVVAKKLLEEIFPRYGIP--QVLgSDNGPAFV 1565
Cdd:NF033577  125 AHPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAyaELYPDET---AETAADFLRRAFAEHGIPirRVL-TDNGSEFR 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1566 SQVSQSVATL--LGINWKLHCAYRPQSSGQVERMNRSIKETLTKLTLETGSKDWVLLLP--LVLYrvrNTPGPH----GL 1637
Cdd:NF033577  201 SRAHGFELALaeLGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAELQAALDewLHHY---NHHRPHsalgGK 277


                  ....
gi 351720597 1638 TPFE 1641
Cdd:NF033577  278 TPAE 281
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1226-1364 3.45e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 65.64  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1226 YTDGSSfiRNGERKAGAAV---TTESEVIWAASLPPGTSaQRAELIALTQALKMAK---GKKLTVYTDSRYAFATAHVHG 1299
Cdd:COG0328     6 YTDGAC--RGNPGPGGWGAvirYGGEEKELSGGLGDTTN-NRAELTALIAALEALKelgPCEVEIYTDSQYVVNQITGWI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 351720597 1300 EIYRRRGLltsegKEIKNKnEILALLEALFLPKRLSIIHCPGHQkGDspqaKGNRLADDTAKKAA 1364
Cdd:COG0328    83 HGWKKNGW-----KPVKNP-DLWQRLDELLARHKVTFEWVKGHA-GH----PGNERADALANKAL 136
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1398-1603 6.00e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 6.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1398 QKLKAHYEPKRGTWEYQGKTIMPEKFAKELISHLHKLTHLS----AKKMKTLLEREetgFYLPNRD--------LHLRQV 1465
Cdd:COG2801    44 RLLRRRRARSRRRRRLRRPRSYRADEDAELLERIKEIFAESprygYRRITAELRRE---GIAVNRKrvrrlmreLGLQAR 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1466 TESCRACAQINAGKIKFGPDVRARGHRPGAHWEVDFTEIkPGMYGYKYLLVFIDTFS----GWAeayPAKRETAKVVaKK 1541
Cdd:COG2801   121 RRRKKKYTTYSGHGGPIAPNLLFTATAPNQVWVTDITYI-PTAEGWLYLAAVIDLFSreivGWS---VSDSMDAELV-VD 195

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 351720597 1542 LLEEIFPRYGIPQ--VLGSDNGPAFVSQVSQSVATLLGINWKLHCAYRPQSSGQVERMNRSIKE 1603
Cdd:COG2801   196 ALEMAIERRGPPKplILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
596-685 5.10e-08

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 53.80  E-value: 5.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  596 PRITLKIGGQPVTFLVDTGAQHSVLTRPD-------GPLSDRTALVQGATGSKNYRWTTDRRVQLATGKVTH---SFLYV 665
Cdd:COG3577    42 FVVEGTINGQPVRFLVDTGASTVVLSESDarrlgldPEDLGRPVRVQTANGVVRAARVRLDSVRIGGITLRNvraVVLPG 121

                          90       100
                  ....*....|....*....|
gi 351720597  666 PECPYPLLGRDLLTKLKAQI 685
Cdd:COG3577   122 GELDDGLLGMSFLGRLDFEI 141
ZnF_C2HC smart00343
zinc finger;
552-568 1.97e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.04  E-value: 1.97e-03
                            10
                    ....*....|....*..
gi 351720597    552 QCAYCKEKGHWVRDCPK 568
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 1513-1599 5.61e-03

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: 40.93  E-value: 5.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1513 YLLVFID--TfSGWAEAYPAKRETA----KVvakklLEEIFPRYGIPQVLGSDNGPAF-------------VSQVSQSVA 1573
Cdd:NF033594  148 TLLVAIDdaT-GRLMGLRFVESESTfgyfEV-----TRQYLEKHGKPVAFYSDKHSVFrvneeelagkgdgLTQFGRALK 221

                          90       100
                  ....*....|....*....|....*.
gi 351720597 1574 TLlGINWKlhCAYRPQSSGQVERMNR 1599
Cdd:NF033594  222 EL-GIEII--CANSPQAKGRVERANQ 244
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 551-568 7.68e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.58  E-value: 7.68e-03
                           10
                   ....*....|....*...
gi 351720597   551 DQCAYCKEKGHWVRDCPK 568
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
Gag_p30 pfam02093
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ...
 286-493 3.72e-150

Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.


Pssm-ID: 426597  Cd Length: 208  Bit Score: 459.52  E-value: 3.72e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   286 QYWPFSASDLYNWKSHNPPFSQDPVALTNLIESILVTHQPTWDDCQQLLQTLLTAEERQRVLLEARKQVPGEDGRPTQLP 365
Cdd:pfam02093    1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   366 NVIDEAFPLTRPNWDFATPAGREHLRLYRQLLLAGLRGAARRPTNLAQVKQVVQGKEETPAAFLERLKEAYRMYTPYDPE 445
Cdd:pfam02093   81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 351720597   446 DPGQAASVILSFIYQSSPDIRNKLQRLEGLQGFTLSDLLKEAEKIYNK 493
Cdd:pfam02093  161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 208
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 762-975 1.69e-108

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 343.95  E-value: 1.69e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  762 PISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCRSPWNTPLLPVKKPGTGDYRPVQDLREVNKRVEDIHPTVPNPYNLLS 841
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  842 TLPPSHPWYTVLDLKDAFFCLRLHPESQLLFAFEWKDpeiglsGQLTWTRLPQGFKNSPTLFDEALHSDLADFRVRYPTL 921
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 351720597  922 VLLQYVDDLLLAAATRTECLEGTKALLKTLGSKGYRASAKKAQICLQKVTYLGY 975
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 ...
 1224-1364 8.56e-54

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: 184.46  E-value: 8.56e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1224 TWYTDGSSFirngerKAGAAVTTESEVIWAASLPPGTSAQRAELIALTQALKMAKGKKLTVYTDSRYAFATAHVHGEIYR 1303
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 351720597 1304 RRGLLtsegKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAA 1364
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 79-175 6.70e-41

Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.


Pssm-ID: 426076 [Multi-domain]  Cd Length: 126  Bit Score: 147.14  E-value: 6.70e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597    79 GQTVTTPLSLTLDHWSEVRTRAHNQGVEVRKKKWITLCEAEWVMMNVGWPREGTFSLDNISQVEKKIFAPGPCGHPDQVP 158
Cdd:pfam01140    1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                           90
                   ....*....|....*..
gi 351720597   159 YITTWRSLASDPPSWVR 175
Cdd:pfam01140   81 YIVTWEALAADPPPWVR 97
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 762-977 1.04e-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: 150.13  E-value: 1.04e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  762 PISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCRSPWNTPLLPVKKPgTGDYRPVQDLREVNKRVED---IHPTVPNPyn 838
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK-SGKWRLLHDLRAVNAQTQDmgaLQPGLPHP-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  839 llSTLPPSHPwYTVLDLKDAFFCLRLHPESQLLFAFEWkdPEIGLSG---QLTWTRLPQGFKNSPTLFDEALHSDLADFR 915
Cdd:cd01645    78 --AALPKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTV--PSINNKGpakRYQWKVLPQGMKNSPTICQSFVAQALEPFR 152

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 351720597  916 VRYPTLVLLQYVDDLLLAAATRTECLEGTKALLKTLGSKGYRASAKKAQIClQKVTYLGYSL 977
Cdd:cd01645   153 KQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKE-PPFQYLGYEL 213
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 789-975 2.61e-37

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: 138.88  E-value: 2.61e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  789 GILKPCRSPWNTPLLPVKKPGtGDYRPVQDLREVNKRVE-DIHPtVPNPYNLLSTLPPSHpWYTVLDLKDAFFCLRLHPE 867
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKD-GKLRLCVDYRKLNKVTIkDRYP-LPTIDELLEELAGAK-VFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  868 SQLLFAFewkdpeIGLSGQLTWTRLPQGFKNSPTLF----DEALHSDLADFrvryptlvLLQYVDDLLLAAATRTECLEG 943
Cdd:cd01647    78 SRPKTAF------RTPFGLYEYTRMPFGLKNAPATFqrlmNKILGDLLGDF--------VEVYLDDILVYSKTEEEHLEH 143

                         170       180       190
                  ....*....|....*....|....*....|..
gi 351720597  944 TKALLKTLGSKGYRASAKKAQICLQKVTYLGY 975
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 ...
 1220-1364 2.83e-36

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: 134.43  E-value: 2.83e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1220 DADLTWYTDGSSFIRNGERKAGAAVTTESEvIWAASLPPGTSAQRAELIALTQALKMAK-GKKLTVYTDSRYAFATAH-- 1296
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHE-NISAPLPGRTTNNRAELQAVIEALKALKsPSKVNIYTDSQYVIGGITqw 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 351720597  1297 VHGEIYRRRGlLTSEGKEIKNKnEILALLEALFLPKRLSIIHCPGHqKGDspqaKGNRLADDTAKKAA 1364
Cdd:pfam00075   80 VHGWKKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGN----PGNEMADRLAKQGA 140
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1700-1788 2.18e-35

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: 129.95  E-value: 2.18e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1700 HPFKPGDSVWVRRHQTKNLEPRWKGPHIVLLTTPTALKVDGVAAWIHASHVKAAgptanqDPSDDPSSEDPSrWKVQRT- 1778
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPA------DPHAVLEDFIPS-WQVQKDr 73

                           90
                   ....*....|
gi 351720597  1779 QNPLKIRLSR 1788
Cdd:pfam18697   74 DNPLKLRLRR 83
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 805-977 2.95e-32

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: 124.72  E-value: 2.95e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   805 VKKPGTGDYRPV----QDLREVNKRVED-IHPTVPNPYNLLSTLPPSHP-----WYTVLDLKDAFFCLRLHPESQLLFAF 874
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQPGFRPGLAKlkkakWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   875 EWKDPEIGLSGQL-----TWTRLPQGFKNSPTLFDEALHSDLADFRVRYpTLVLLQYVDDLLLAAATRTECLEGTKALLK 949
Cdd:pfam00078   81 TTPPININWNGELsggryEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 351720597   950 TLGSKGYRASAKKAQICLQK--VTYLGYSL 977
Cdd:pfam00078  160 WLKESGLKINPEKTQFFLKSkeVKYLGVTL 189
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 594-686 7.50e-26

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: 103.22  E-value: 7.50e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   594 PEPRITLKIGGQPVTFLVDTGAQHSVLTRPDGPLS----DRTALVQGATGSKNYRWTTDRRVQLATGKVTH--SFLYVPE 667
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpkqKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                           90
                   ....*....|....*....
gi 351720597   668 CPYPLLGRDLLTKLKAQIH 686
Cdd:pfam00077   83 CPVNIIGRDLLQQLGGRLT 101
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 598-679 2.01e-25

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: 101.64  E-value: 2.01e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  598 ITLKIGGQPVTFLVDTGAQHSVLTRPDGP---LSDRTALVQGATGSKNYRWTTDRR-VQLATGKVTHSFLYVPECPYPLL 673
Cdd:cd06095     1 VTITVEGVPIVFLVDTGATHSVLKSDLGPkqeLSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                  ....*.
gi 351720597  674 GRDLLT 679
Cdd:cd06095    81 GRDLLS 86
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 1387-1479 2.28e-25

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: 101.73  E-value: 2.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1387 WEYDDSDLDLVQKLKAHYEPKRGTWEYQGKTIMPEKFAKELISHLHKLTHLSAKKMKTLLEREETGFYLPNRDLHLRQVT 1466
Cdd:pfam16721    3 FHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|...
gi 351720597  1467 ESCRACAQINAGK 1479
Cdd:pfam16721   83 ETCKACAQVNASK 95
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1493-1588 9.64e-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: 9.64e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1493 PGAHWEVDFTEIK-PGMYGYKYLLVFIDTFSGWAEAYPAKRETAKVVAKKLLEEIFPRYGI-PQVLGSDNGPAFVSQVSQ 1570
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 351720597  1571 SVATLLGINWKLHCAYRP 1588
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1226-1364 7.97e-19

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: 84.92  E-value: 7.97e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1226 YTDGSsFIRNG--ERKAGAAVtteseviW---------AASLPPG--TSaQRAELIALTQALKMAK---GKKLTVYTDSR 1289
Cdd:cd09280     3 YTDGS-CLNNGkpGARAGIGV-------YfgpgdprnvSEPLPGRkqTN-NRAELLAVIHALEQAPeegIRKLEIRTDSK 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 351720597 1290 YAFATAHVHGEIYRRRGLLTSEGKEIKNKNEILALLEAL-FLPKRLSIIHCPGHQkGDspqaKGNRLADDTAKKAA 1364
Cdd:cd09280    74 YAINCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLrKRGIKVKFEHVKGHS-GD----PGNEEADRLAREGA 144
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1065-1170 1.01e-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: 77.17  E-value: 1.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1065 DITKPFELFIDeSSGFAKG-VLVQKL-GPWKRPVAYLSKKLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSH 1142
Cdd:pfam17917    1 DPSKPFILETD-ASDYGIGaVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 351720597  1143 PVEALVRQPpnrWLSNARMTHYQAMLLD 1170
Cdd:pfam17917   80 KPLKYLFTP---KELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1040-1138 7.20e-16

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 74.84  E-value: 7.20e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  1040 WGPDQQLAFENIKKALLSSPALGLPDITKPFELFIDeSSGFAKG-VLVQKL--GPWkRPVAYLSKKLDTVASGWPPCLRM 1116
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETD-ASDYGIGaVLSQEDddGGE-RPIAYASRKLSPAERNYSTTEKE 78

                           90       100
                   ....*....|....*....|..
gi 351720597  1117 VAAIAILVKDAGKLTLGQPLTI 1138
Cdd:pfam17919   79 LLAIVFALKKFRHYLLGRKFTV 100
transpos_IS481 NF033577
IS481 family transposase; null
 1491-1641 1.54e-15

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 79.17  E-value: 1.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1491 HRPGAHWEVDFTEIKPGMY-GYKYLLVFIDTFSGWA--EAYPAKRetaKVVAKKLLEEIFPRYGIP--QVLgSDNGPAFV 1565
Cdd:NF033577  125 AHPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAyaELYPDET---AETAADFLRRAFAEHGIPirRVL-TDNGSEFR 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1566 SQVSQSVATL--LGINWKLHCAYRPQSSGQVERMNRSIKETLTKLTLETGSKDWVLLLP--LVLYrvrNTPGPH----GL 1637
Cdd:NF033577  201 SRAHGFELALaeLGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAELQAALDewLHHY---NHHRPHsalgGK 277


                  ....
gi 351720597 1638 TPFE 1641
Cdd:NF033577  278 TPAE 281
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1226-1364 1.75e-15

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: 74.83  E-value: 1.75e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1226 YTDGSSfiRNGERKAG--AAVTTESEVIWAASLPPGTSAQRAELIALTQALKMAK-GKKLTVYTDSRYAF--ATAHVHGe 1300
Cdd:cd09278     5 YTDGAC--LGNPGPGGwaAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKePCPVTIYTDSQYVIngITKWIKG- 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 351720597 1301 iYRRRGLLTSEGKEIKNKNEILALLEALfLPKRLSIIHCPGHQkGDspqaKGNRLADDTAKKAA 1364
Cdd:cd09278    82 -WKKNGWKTADGKPVKNRDLWQELDALL-AGHKVTWEWVKGHA-GH----PGNERADRLANKAA 138
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1225-1361 1.07e-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: 72.35  E-value: 1.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1225 WYTDGSSfiRNGERKAGAAVT---TESEVIWAASLPPGT-SAQRAELIALTQALKMAKG---KKLTVYTDSRYAFatahv 1297
Cdd:cd06222     1 INVDGSC--RGNPGPAGIGGVlrdHEGGWLGGFALKIGApTALEAELLALLLALELALDlgyLKVIIESDSKYVV----- 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 351720597 1298 hgeiyrrRGLLTSEGKEIKNKNEILALLEALFLPKRLSIIHCPGhqkgdspqaKGNRLADDTAK 1361
Cdd:cd06222    74 -------DLINSGSFKWSPNILLIEDILLLLSRFWSVKISHVPR---------EGNQVADALAK 121
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 891-975 3.92e-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: 66.99  E-value: 3.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  891 RLPQGFKNSPTLFDEALHSDLADFRVRYPTLVLLQYVDDLLLaAATRTECLEGTKALLKTLGSKGYRASAKKAQ--ICLQ 968
Cdd:cd00304    11 PLPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVV-IAKSEQQAVKKRELEEFLARLGLNLSDEKTQftEKEK 89


                  ....*..
gi 351720597  969 KVTYLGY 975
Cdd:cd00304    90 KFKFLGI 96
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1226-1364 3.45e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 65.64  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1226 YTDGSSfiRNGERKAGAAV---TTESEVIWAASLPPGTSaQRAELIALTQALKMAK---GKKLTVYTDSRYAFATAHVHG 1299
Cdd:COG0328     6 YTDGAC--RGNPGPGGWGAvirYGGEEKELSGGLGDTTN-NRAELTALIAALEALKelgPCEVEIYTDSQYVVNQITGWI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 351720597 1300 EIYRRRGLltsegKEIKNKnEILALLEALFLPKRLSIIHCPGHQkGDspqaKGNRLADDTAKKAA 1364
Cdd:COG0328    83 HGWKKNGW-----KPVKNP-DLWQRLDELLARHKVTFEWVKGHA-GH----PGNERADALANKAL 136
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1432-1473 1.03e-11

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: 60.80  E-value: 1.03e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 351720597  1432 HKLTHLSAKKMKTLLEREetgFYLPNRDLHLRQVTESCRACA 1473
Cdd:pfam09337    1 HALTHLGINKLTALLARK---YHWLGIKETVSEVISSCVACQ 39
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1226-1365 2.93e-10

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: 59.92  E-value: 2.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1226 YTDGSSFirngERKAGAAVTTESEVIWAA---SLPPGTSAQRAELIALTQALKMAK-----GKKLTVYTDSRYAFA---- 1293
Cdd:cd09276     3 YTDGSKL----EGSVGAGFVIYRGGEVISrsyRLGTHASVFDAELEAILEALELALatarrARKVTIFTDSQSALQalrn 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 351720597 1294 TAHVHGEIYRRRGLLTSegKEIKNKneilallealflPKRLSIIHCPGHQKgdspqAKGNRLADDTAKKAAT 1365
Cdd:cd09276    79 PRRSSGQVILIRILRLL--RLLKAK------------GVKVRLRWVPGHVG-----IEGNEAADRLAKEAAS 131
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 853-974 3.45e-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: 3.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  853 LDLKDAFFCLRLHPESQLLFAFEWKDPeiglsgQLTWTRLPQGFKNSPTLFDEALHSDLAdfRVRYPTLVLLQYVDDLLL 932
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGE------TYQFKALPFGLSLAPRVFTKVVEALLA--PLRLLGVRIFSYLDDLLI 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 351720597  933 AAATRTECLEGTKALLKTLGSK-GYRASAKKAQICL-QKVTYLG 974
Cdd:cd03714    73 IASSIKTSEAVLRHLRATLLANlGFTLNLEKSKLGPtQRITFLG 116
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 598-679 2.79e-09

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: 55.81  E-value: 2.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  598 ITLKIGGQPVTFLVDTGAQHSVLTRP------DGPLSDRTAL-VQGATGSKNYRWTTDRRVQLATGK--VTHSFLYVPEC 668
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESlakklgLPPRLLPTPLkVKGANGSSVKTLGVILPVTIGIGGktFTVDFYVLDLL 80

                          90
                  ....*....|..
gi 351720597  669 PYP-LLGRDLLT 679
Cdd:cd00303    81 SYDvILGRPWLE 92
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 598-678 4.17e-09

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: 55.28  E-value: 4.17e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   598 ITLKIGGQPVTFLVDTGAQHSVLTRPDG------PLSD-RTALVQGATGSKNYRWTTDRRVQLATGKVTHSFLYV--PEC 668
Cdd:pfam13975    1 VDVTINGRPVRFLVDTGASVTVISEALAerlgldRLVDaYPVTVRTANGTVRAARVRLDSVKIGGIELRNVPAVVlpGDL 80

                           90
                   ....*....|
gi 351720597   669 PYPLLGRDLL 678
Cdd:pfam13975   81 DDVLLGMDFL 90
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1398-1603 6.00e-09

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 6.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1398 QKLKAHYEPKRGTWEYQGKTIMPEKFAKELISHLHKLTHLS----AKKMKTLLEREetgFYLPNRD--------LHLRQV 1465
Cdd:COG2801    44 RLLRRRRARSRRRRRLRRPRSYRADEDAELLERIKEIFAESprygYRRITAELRRE---GIAVNRKrvrrlmreLGLQAR 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1466 TESCRACAQINAGKIKFGPDVRARGHRPGAHWEVDFTEIkPGMYGYKYLLVFIDTFS----GWAeayPAKRETAKVVaKK 1541
Cdd:COG2801   121 RRRKKKYTTYSGHGGPIAPNLLFTATAPNQVWVTDITYI-PTAEGWLYLAAVIDLFSreivGWS---VSDSMDAELV-VD 195

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 351720597 1542 LLEEIFPRYGIPQ--VLGSDNGPAFVSQVSQSVATLLGINWKLHCAYRPQSSGQVERMNRSIKE 1603
Cdd:COG2801   196 ALEMAIERRGPPKplILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
596-685 5.10e-08

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 53.80  E-value: 5.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  596 PRITLKIGGQPVTFLVDTGAQHSVLTRPD-------GPLSDRTALVQGATGSKNYRWTTDRRVQLATGKVTH---SFLYV 665
Cdd:COG3577    42 FVVEGTINGQPVRFLVDTGASTVVLSESDarrlgldPEDLGRPVRVQTANGVVRAARVRLDSVRIGGITLRNvraVVLPG 121

                          90       100
                  ....*....|....*....|
gi 351720597  666 PECPYPLLGRDLLTKLKAQI 685
Cdd:COG3577   122 GELDDGLLGMSFLGRLDFEI 141
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 596-678 1.51e-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: 51.09  E-value: 1.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  596 PRITLKIGGQPVTFLVDTGAQHSVLTRPD------GPLSDRTALVQGATGSKNYRWTTDRRVQLatGKVTHSFLYVPECP 669
Cdd:cd05483     3 FVVPVTINGQPVRFLLDTGASTTVISEELaerlglPLTLGGKVTVQTANGRVRAARVRLDSLQI--GGITLRNVPAVVLP 80

                          90
                  ....*....|....*
gi 351720597  670 YP------LLGRDLL 678
Cdd:cd05483    81 GDalgvdgLLGMDFL 95
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 598-677 1.72e-06

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: 47.66  E-value: 1.72e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597   598 ITLKIGGQPVTFLVDTGAQHSVLTRP-------DGPLSDRTALVQGATGSKNYRWTTDRRVQLATGKVTHSFLYV---PE 667
Cdd:pfam13650    1 VPVTINGKPVRFLVDTGASGTVISPSlaerlglKVRGLAYTVRVSTAGGRVSAARVRLDSLRLGGLTLENVPALVldlGD 80

                           90
                   ....*....|
gi 351720597   668 CPYPLLGRDL 677
Cdd:pfam13650   81 LIDGLLGMDF 90
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1226-1364 9.63e-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: 46.70  E-value: 9.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1226 YTDGSSFIRNGERKAGAAVTTESEVIWAAS--LPPGTSAQRAELIALTQALKMAKG---KKLTVYTDSRyaFATAHVHGE 1300
Cdd:cd09279     4 YFDGASRGNPGPAGAGVVIYSPGGEVLELSerLGFPATNNEAEYEALIAGLELALElgaEKLEIYGDSQ--LVVNQLNGE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1301 IyrrrglltsegkEIKNKN------EILALLEALflpKRLSIIHCPGHQkgdspqakgNRLADDTAKKAA 1364
Cdd:cd09279    82 Y------------KVKNERlkplleKVLELLAKF---ELVELKWIPREQ---------NKEADALANQAL 127
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 598-679 1.08e-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: 42.64  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  598 ITLKIGGQPVTFLVDTGAQHSVLTRPDGPLSD-----RTAL--VQGATGSKNYR---WTTDRRVQLATGKVthsflYVPE 667
Cdd:cd05482     1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpaPSNLtgIGGAITPSQSSvllLEIDGEGHLGTILV-----YVLS 75

                          90
                  ....*....|..
gi 351720597  668 CPYPLLGRDLLT 679
Cdd:cd05482    76 LPVNLWGRDILS 87
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1420-1477 5.14e-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: 39.54  E-value: 5.14e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 351720597  1420 PEKFAKELISHLHKLT-HLSAKKMKTLLEREetgFYLPNRDLHLRQVTESCRACAQINA 1477
Cdd:pfam17921    2 PKSLRKEILKEAHDSGgHLGIEKTLARLRRR---YWWPGMRKDVKKYVKSCETCQRRKP 57
ZnF_C2HC smart00343
zinc finger;
552-568 1.97e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.04  E-value: 1.97e-03
                            10
                    ....*....|....*..
gi 351720597    552 QCAYCKEKGHWVRDCPK 568
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
retropepsin_like_LTR_2 cd05484
Retropepsins_like_LTR, pepsin-like aspartate proteases; Retropepsin of retrotransposons with ...
 598-678 3.08e-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: 38.73  E-value: 3.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  598 ITLKIGGQPVTFLVDTGAQHSVLTRPD------GPLSDRTALVQGATGSK-----------NYRwttdrrvqlatGKVTH 660
Cdd:cd05484     3 VTLLVNGKPLKFQLDTGSAITVISEKTwrklgsPPLKPTKKRLRTATGTKlsvlgqilvtvKYG-----------GKTKV 71

                          90
                  ....*....|....*....
gi 351720597  661 SFLYVPECPYP-LLGRDLL 678
Cdd:cd05484    72 LTLYVVKNEGLnLLGRDWL 90
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 854-952 4.70e-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: 40.37  E-value: 4.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597  854 DLKDAFFCLRLHPESQLLFAFEW-KDPEIGLSGQLTWTRLPQGFKNSPTLFDEALHSDLADFRVRYPTLVLLQ--YVDDL 930
Cdd:cd01644    65 DIEKMFHQVKVRPEDRDVLRFLWrKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRnfYVDDI 144

                          90       100
                  ....*....|....*....|....*
gi 351720597  931 LLAAATRTEC---LEGTKALLKTLG 952
Cdd:cd01644   145 LVSTDTLNEAvnvAKRLIALLKKGG 169
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 1513-1599 5.61e-03

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: 40.93  E-value: 5.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351720597 1513 YLLVFID--TfSGWAEAYPAKRETA----KVvakklLEEIFPRYGIPQVLGSDNGPAF-------------VSQVSQSVA 1573
Cdd:NF033594  148 TLLVAIDdaT-GRLMGLRFVESESTfgyfEV-----TRQYLEKHGKPVAFYSDKHSVFrvneeelagkgdgLTQFGRALK 221

                          90       100
                  ....*....|....*....|....*.
gi 351720597 1574 TLlGINWKlhCAYRPQSSGQVERMNR 1599
Cdd:NF033594  222 EL-GIEII--CANSPQAKGRVERANQ 244
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 551-568 7.68e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.58  E-value: 7.68e-03
                           10
                   ....*....|....*...
gi 351720597   551 DQCAYCKEKGHWVRDCPK 568
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
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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