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Conserved domains on  [gi|327391639|gb|AEA72809|]
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putative gag-pol polyprotein [XMRV-like mouse endogenous retrovirus mERV-XL]

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 ...
 224-431 1.92e-146

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: 448.73  E-value: 1.92e-146
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   224 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLITHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 303
Cdd:pfam02093    1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   304 NEVNAAFPLERPDWDYTTTEGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGSNESPSAFLERLKEAYRRYTPYDPE 383
Cdd:pfam02093   81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 327391639   384 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 431
Cdd:pfam02093  161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 208
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 715-930 1.45e-119

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: 374.76  E-value: 1.45e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  715 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVGDIHPTVPNPYNLLS 794
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  795 GLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDL 874
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 327391639  875 ILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLL 930
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 2-124 5.46e-58

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: 196.06  E-value: 5.46e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639     2 GQTVTTPLSLTLQHWGDVQRIASNQSVDVKKRRWVTFCSAEWPTFNVGWPQDGTFNLGIISQVKSRVFCPGPHGHPDQVP 81
Cdd:pfam01140    1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 327391639    82 YIVTWEALAYDPPPWVKPFVSPKPPPLPTAPVL---PPGPSAQPPS 124
Cdd:pfam01140   81 YIVTWEALAADPPPWVRPFLTPKPPPPQPPAAPglrPPLPPASAPP 126
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1177-1317 3.15e-56

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: 191.01  E-value: 3.15e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1177 TWYTDGSSYlhegqrRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHGEIYR 1256
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 327391639 1257 RRGLLtsegKEIKNKSEILALLKALFLPKRLSIIHCPGHQRGNSAEARGNRMADQAAREAA 1317
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Gag_p12 pfam01141
Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. ...
 130-213 1.17e-49

Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus.


:

Pssm-ID: 279483 [Multi-domain]  Cd Length: 85  Bit Score: 170.70  E-value: 1.17e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   130 PALTPSIKSKPPKPQVLPDSGGPLIDLLTEDPPPY-GAQPSSSARENNEEEAATTSEVSPPSPMVSRLRGRRDPPAADST 208
Cdd:pfam01141    1 PALTPSIGAKPPKPQVLPDSGGPLIDLLTEDPPPYrDAQPPPSARDGNEEEAAPAGEAPDPSPMASRLRGRRDPPAADST 80


                   ....*
gi 327391639   209 TSQAF 213
Cdd:pfam01141   81 TSQAF 85
zf-H2C2 super family cl07828
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1340-1433 1.27e-43

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: 153.73  E-value: 1.27e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1340 FHYTETDKRDLDTLGAAYDETKRYWVFQGKPVMPSQDTFELLDFLHQLTHLSYQKMRALLDRKESPYYMLNKDKILHEVA 1419
Cdd:pfam16721    3 FHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|....
gi 327391639  1420 ESCQACVQVNASKA 1433
Cdd:pfam16721   83 ETCKACAQVNASKS 96
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1653-1734 4.11e-39

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: 140.35  E-value: 4.11e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1653 HPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAATTPPAGTASGPTWKVQRS-QNPLKIR 1731
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEDFIPSWQVQKDrDNPLKLR 80


                   ...
gi 327391639  1732 LTR 1734
Cdd:pfam18697   81 LRR 83
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 546-638 2.65e-30

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: 115.93  E-value: 2.65e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   546 PEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLS----DKSAWVQGATGGKRYRWTTDRKVHLATGKVTH--SFLHVPD 619
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpkqKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                           90
                   ....*....|....*....
gi 327391639   620 CPYPLLGRDLLTKLKAQIH 638
Cdd:pfam00077   83 CPVNIIGRDLLQQLGGRLT 101
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1446-1541 6.97e-25

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: 100.47  E-value: 6.97e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1446 PGTHWEIDFTEVK-PGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFISQVSQ 1523
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 327391639  1524 SVAKLLGIDWKLHCAYRP 1541
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1018-1123 4.12e-17

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: 78.32  E-value: 4.12e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1018 DLTKPFELFVDEKqGYAKG-VLTQKL-GPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPH 1095
Cdd:pfam17917    1 DPSKPFILETDAS-DYGIGaVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 327391639  1096 AVEALVKQPpdrWLSNARMTHYQAMLLD 1123
Cdd:pfam17917   80 KPLKYLFTP---KELNGRLARWALFLQE 104
ZnF_C2HC smart00343
zinc finger;
501-517 4.72e-04

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 4.72e-04
                            10
                    ....*....|....*..
gi 327391639    501 QCAYCKEKGHWAKDCPK 517
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 ...
 224-431 1.92e-146

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: 448.73  E-value: 1.92e-146
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   224 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLITHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 303
Cdd:pfam02093    1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   304 NEVNAAFPLERPDWDYTTTEGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGSNESPSAFLERLKEAYRRYTPYDPE 383
Cdd:pfam02093   81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 327391639   384 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 431
Cdd:pfam02093  161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 208
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 715-930 1.45e-119

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: 374.76  E-value: 1.45e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  715 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVGDIHPTVPNPYNLLS 794
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  795 GLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDL 874
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 327391639  875 ILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLL 930
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 2-124 5.46e-58

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: 196.06  E-value: 5.46e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639     2 GQTVTTPLSLTLQHWGDVQRIASNQSVDVKKRRWVTFCSAEWPTFNVGWPQDGTFNLGIISQVKSRVFCPGPHGHPDQVP 81
Cdd:pfam01140    1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 327391639    82 YIVTWEALAYDPPPWVKPFVSPKPPPLPTAPVL---PPGPSAQPPS 124
Cdd:pfam01140   81 YIVTWEALAADPPPWVRPFLTPKPPPPQPPAAPglrPPLPPASAPP 126
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1177-1317 3.15e-56

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: 191.01  E-value: 3.15e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1177 TWYTDGSSYlhegqrRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHGEIYR 1256
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 327391639 1257 RRGLLtsegKEIKNKSEILALLKALFLPKRLSIIHCPGHQRGNSAEARGNRMADQAAREAA 1317
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Gag_p12 pfam01141
Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. ...
 130-213 1.17e-49

Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus.


Pssm-ID: 279483 [Multi-domain]  Cd Length: 85  Bit Score: 170.70  E-value: 1.17e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   130 PALTPSIKSKPPKPQVLPDSGGPLIDLLTEDPPPY-GAQPSSSARENNEEEAATTSEVSPPSPMVSRLRGRRDPPAADST 208
Cdd:pfam01141    1 PALTPSIGAKPPKPQVLPDSGGPLIDLLTEDPPPYrDAQPPPSARDGNEEEAAPAGEAPDPSPMASRLRGRRDPPAADST 80


                   ....*
gi 327391639   209 TSQAF 213
Cdd:pfam01141   81 TSQAF 85
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 1340-1433 1.27e-43

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: 153.73  E-value: 1.27e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1340 FHYTETDKRDLDTLGAAYDETKRYWVFQGKPVMPSQDTFELLDFLHQLTHLSYQKMRALLDRKESPYYMLNKDKILHEVA 1419
Cdd:pfam16721    3 FHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|....
gi 327391639  1420 ESCQACVQVNASKA 1433
Cdd:pfam16721   83 ETCKACAQVNASKS 96
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1653-1734 4.11e-39

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: 140.35  E-value: 4.11e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1653 HPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAATTPPAGTASGPTWKVQRS-QNPLKIR 1731
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEDFIPSWQVQKDrDNPLKLR 80


                   ...
gi 327391639  1732 LTR 1734
Cdd:pfam18697   81 LRR 83
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1177-1317 9.52e-37

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: 135.97  E-value: 9.52e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1177 TWYTDGSSYLHEGQRRAGAAVTTETEvIWARALPAGTSAQRAELIALTQALK-MAEGKKLNVYTDSRYAFATAH--VHGE 1253
Cdd:pfam00075    5 TVYTDGSCLGNPGPGGAGAVLYRGHE-NISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwVHGW 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 327391639  1254 IYRRRGlLTSEGKEIKNKsEILALLKALFLPKRLSIIHCPGHQrGNSaearGNRMADQAAREAA 1317
Cdd:pfam00075   84 KKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGHA-GNP----GNEMADRLAKQGA 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 758-928 2.08e-34

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: 130.89  E-value: 2.08e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   758 VKKPGTNDYRPV----QDLREVNKRV-GDIHPTVPNPYNLlSGLPP------SHQWYTVLDLKDAFFCLRLHPTSQPLFA 826
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIvKRLKPENLDSPPQ-PGFRPglaklkKAKWFLKLDLKKAFDQVPLDELDRKLTA 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   827 F----EWRDPEMGISGQL-TWTRLPQGFKNSPTLFDEALHRDLADFRiQHPDLILLQYVDDLLLAATSEQDCQRGTRALL 901
Cdd:pfam00078   80 FttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                          170       180
                   ....*....|....*....|....*....
gi 327391639   902 QTLGNLGYRASAKKAQIC--QKQVKYLGY 928
Cdd:pfam00078  159 EWLKESGLKINPEKTQFFlkSKEVKYLGV 187
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 546-638 2.65e-30

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: 115.93  E-value: 2.65e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   546 PEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLS----DKSAWVQGATGGKRYRWTTDRKVHLATGKVTH--SFLHVPD 619
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpkqKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                           90
                   ....*....|....*....
gi 327391639   620 CPYPLLGRDLLTKLKAQIH 638
Cdd:pfam00077   83 CPVNIIGRDLLQQLGGRLT 101
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1446-1541 6.97e-25

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: 100.47  E-value: 6.97e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1446 PGTHWEIDFTEVK-PGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFISQVSQ 1523
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 327391639  1524 SVAKLLGIDWKLHCAYRP 1541
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 550-631 1.02e-23

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: 96.63  E-value: 1.02e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  550 ITLKVGGQPVTFLVDTGAQHSVLTQNPGP---LSDKSAWVQGATGGKRYRWTTDRK-VHLATGKVTHSFLHVPDCPYPLL 625
Cdd:cd06095     1 VTITVEGVPIVFLVDTGATHSVLKSDLGPkqeLSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                  ....*.
gi 327391639  626 GRDLLT 631
Cdd:cd06095    81 GRDLLS 86
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1018-1123 4.12e-17

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: 78.32  E-value: 4.12e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1018 DLTKPFELFVDEKqGYAKG-VLTQKL-GPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPH 1095
Cdd:pfam17917    1 DPSKPFILETDAS-DYGIGaVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 327391639  1096 AVEALVKQPpdrWLSNARMTHYQAMLLD 1123
Cdd:pfam17917   80 KPLKYLFTP---KELNGRLARWALFLQE 104
transpos_IS481 NF033577
IS481 family transposase; null
 1425-1594 9.18e-17

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 82.64  E-value: 9.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1425 CVQVNASKAKVGPGVRVRGHRPGTHWEIDFTEVKPGLY-GYKYLLVFVDTFSGWVEAFPTKHETAkVVTKKLLEEIFPRF 1503
Cdd:NF033577  106 LSRLRALDRKTGKVKRYERAHPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAYAELYPDETA-ETAADFLRRAFAEH 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1504 GMP--QVLgTDNGPAFISQVS--QSVAKLLGIDWKLHCAYRPQSSGQVERMNRTIKETLTKLTLATGARDWVLLLP--LA 1577
Cdd:NF033577  185 GIPirRVL-TDNGSEFRSRAHgfELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAELQAALDewLH 263

                         170       180
                  ....*....|....*....|.
gi 327391639 1578 LYrarNTPGPH----GLTPYE 1594
Cdd:NF033577  264 HY---NHHRPHsalgGKTPAE 281
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1179-1317 6.21e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 64.87  E-value: 6.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1179 YTDGSSYLHEGQRRAGAAVTTETEVIW-ARALPAGTSaQRAELIALTQALKMAE---GKKLNVYTDSRYAFATAHVHGEI 1254
Cdd:COG0328     6 YTDGACRGNPGPGGWGAVIRYGGEEKElSGGLGDTTN-NRAELTALIAALEALKelgPCEVEIYTDSQYVVNQITGWIHG 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 327391639 1255 YRRRGLltsegKEIKNKsEILALLKALFLPKRLSIIHCPGHQrGNsaeaRGNRMADQAAREAA 1317
Cdd:COG0328    85 WKKNGW-----KPVKNP-DLWQRLDELLARHKVTFEWVKGHA-GH----PGNERADALANKAL 136
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1360-1556 2.18e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 57.86  E-value: 2.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1360 TKRYWVFQGKPVMPSQDTFELLDFLHQLTHLS----YQKMRALLDRKespYYMLNKDKILHEVAESCQACVQVNASK--- 1432
Cdd:COG2801    53 SRRRRRLRRPRSYRADEDAELLERIKEIFAESprygYRRITAELRRE---GIAVNRKRVRRLMRELGLQARRRRKKKytt 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1433 -----AKVGPGVRVRGHRPGTHWEIDFTEVkPGLYGYKYLLVFVDTFS----GWVEAfptKHETAKVVtKKLLEEIFPRF 1503
Cdd:COG2801   130 ysghgGPIAPNLLFTATAPNQVWVTDITYI-PTAEGWLYLAAVIDLFSreivGWSVS---DSMDAELV-VDALEMAIERR 204

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 327391639 1504 GMPQ--VLGTDNGPAFISQVSQSVAKLLGIDWKLHCAYRPQSSGQVERMNRTIKE 1556
Cdd:COG2801   205 GPPKplILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
548-637 3.04e-06

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 48.79  E-value: 3.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  548 PRITLKVGGQPVTFLVDTGAQHSVLTQ--------NPGPLsDKSAWVQGATGGKRYRWTTDRKVHLATGKVTH---SFLH 616
Cdd:COG3577    42 FVVEGTINGQPVRFLVDTGASTVVLSEsdarrlglDPEDL-GRPVRVQTANGVVRAARVRLDSVRIGGITLRNvraVVLP 120

                          90       100
                  ....*....|....*....|.
gi 327391639  617 VPDCPYPLLGRDLLTKLKAQI 637
Cdd:COG3577   121 GGELDDGLLGMSFLGRLDFEI 141
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1445-1560 1.60e-05

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 49.11  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1445 RPGtHWEIDfteVKPGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKL--LEEIFPRFgMPQVLGTDNGPAFiSQvS 1522
Cdd:COG2826   171 EPG-HWEGD---LIIGKRGKSALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEF-AD-H 243

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 327391639 1523 QSVAKLLGIDwklhcAY--RPQSS---GQVERMNRTIKETLTK 1560
Cdd:COG2826   244 KEIEAALGIK-----VYfaDPYSPwqrGTNENTNGLLRQYFPK 281
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 115-223 4.12e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 48.56  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  115 PPGPSAQPPSRSALYPALTPSIKSKPPKPQVLPDSGGPLIDLLTEDPPPYGAQPSSSARENNEEEAATTSEVSPPSPMVS 194
Cdd:PRK14951  388 APAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVA 467

                          90       100
                  ....*....|....*....|....*....
gi 327391639  195 RLRGRRDPPAADSTTSQAFPLRMGGDGQL 223
Cdd:PRK14951  468 PEPAVASAAPAPAAAPAAARLTPTEEGDV 496
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 1466-1560 6.10e-05

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: 47.48  E-value: 6.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1466 YLLVFVD--TfSGWVEAFPTKHETAK---VVTKKLLEeifpRFGMPQVLGTDNGPAFISQVSQSVAKL------------ 1528
Cdd:NF033594  148 TLLVAIDdaT-GRLMGLRFVESESTFgyfEVTRQYLE----KHGKPVAFYSDKHSVFRVNEEELAGKGdgltqfgralke 222

                          90       100       110
                  ....*....|....*....|....*....|..
gi 327391639 1529 LGIDWKlhCAYRPQSSGQVERMNRTIKETLTK 1560
Cdd:NF033594  223 LGIEII--CANSPQAKGRVERANQTLQDRLVK 252
ZnF_C2HC smart00343
zinc finger;
501-517 4.72e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 4.72e-04
                            10
                    ....*....|....*..
gi 327391639    501 QCAYCKEKGHWAKDCPK 517
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 500-517 2.39e-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: 36.74  E-value: 2.39e-03
                           10
                   ....*....|....*...
gi 327391639   500 DQCAYCKEKGHWAKDCPK 517
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 ...
 224-431 1.92e-146

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: 448.73  E-value: 1.92e-146
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   224 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLITHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 303
Cdd:pfam02093    1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   304 NEVNAAFPLERPDWDYTTTEGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGSNESPSAFLERLKEAYRRYTPYDPE 383
Cdd:pfam02093   81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 327391639   384 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 431
Cdd:pfam02093  161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNK 208
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 715-930 1.45e-119

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: 374.76  E-value: 1.45e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  715 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVGDIHPTVPNPYNLLS 794
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  795 GLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDL 874
Cdd:cd03715    81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGT 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 327391639  875 ILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQICQKQVKYLGYLL 930
Cdd:cd03715   155 ILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 2-124 5.46e-58

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: 196.06  E-value: 5.46e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639     2 GQTVTTPLSLTLQHWGDVQRIASNQSVDVKKRRWVTFCSAEWPTFNVGWPQDGTFNLGIISQVKSRVFCPGPHGHPDQVP 81
Cdd:pfam01140    1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 327391639    82 YIVTWEALAYDPPPWVKPFVSPKPPPLPTAPVL---PPGPSAQPPS 124
Cdd:pfam01140   81 YIVTWEALAADPPPWVRPFLTPKPPPPQPPAAPglrPPLPPASAPP 126
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1177-1317 3.15e-56

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: 191.01  E-value: 3.15e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1177 TWYTDGSSYlhegqrRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHGEIYR 1256
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 327391639 1257 RRGLLtsegKEIKNKSEILALLKALFLPKRLSIIHCPGHQRGNSAEARGNRMADQAAREAA 1317
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
Gag_p12 pfam01141
Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. ...
 130-213 1.17e-49

Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus.


Pssm-ID: 279483 [Multi-domain]  Cd Length: 85  Bit Score: 170.70  E-value: 1.17e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   130 PALTPSIKSKPPKPQVLPDSGGPLIDLLTEDPPPY-GAQPSSSARENNEEEAATTSEVSPPSPMVSRLRGRRDPPAADST 208
Cdd:pfam01141    1 PALTPSIGAKPPKPQVLPDSGGPLIDLLTEDPPPYrDAQPPPSARDGNEEEAAPAGEAPDPSPMASRLRGRRDPPAADST 80


                   ....*
gi 327391639   209 TSQAF 213
Cdd:pfam01141   81 TSQAF 85
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
 1340-1433 1.27e-43

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: 153.73  E-value: 1.27e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1340 FHYTETDKRDLDTLGAAYDETKRYWVFQGKPVMPSQDTFELLDFLHQLTHLSYQKMRALLDRKESPYYMLNKDKILHEVA 1419
Cdd:pfam16721    3 FHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNIT 82

                           90
                   ....*....|....
gi 327391639  1420 ESCQACVQVNASKA 1433
Cdd:pfam16721   83 ETCKACAQVNASKS 96
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 715-930 2.23e-43

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: 157.83  E-value: 2.23e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  715 PVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPgTNDYRPVQDLREVNKRV---GDIHPTVPNPyn 791
Cdd:cd01645     1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK-SGKWRLLHDLRAVNAQTqdmGALQPGLPHP-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  792 llSGLPpsHQWY-TVLDLKDAFFCLRLHPTSQPLFAFEWrdPEMGISG---QLTWTRLPQGFKNSPTLFDEALHRDLADF 867
Cdd:cd01645    78 --AALP--KGWPlIVLDLKDCFFSIPLHPDDRERFAFTV--PSINNKGpakRYQWKVLPQGMKNSPTICQSFVAQALEPF 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 327391639  868 RIQHPDLILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRASAKKAQIcQKQVKYLGYLL 930
Cdd:cd01645   152 RKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQYLGYEL 213
MLVIN_C pfam18697
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ...
 1653-1734 4.11e-39

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: 140.35  E-value: 4.11e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1653 HPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAATTPPAGTASGPTWKVQRS-QNPLKIR 1731
Cdd:pfam18697    1 HRYQPGDWVFVRRHQQKTLEPRWKGPYVVVLTTPTALKVDGIAAWVHYTHVRPADPHAVLEDFIPSWQVQKDrDNPLKLR 80


                   ...
gi 327391639  1732 LTR 1734
Cdd:pfam18697   81 LRR 83
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1177-1317 9.52e-37

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: 135.97  E-value: 9.52e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1177 TWYTDGSSYLHEGQRRAGAAVTTETEvIWARALPAGTSAQRAELIALTQALK-MAEGKKLNVYTDSRYAFATAH--VHGE 1253
Cdd:pfam00075    5 TVYTDGSCLGNPGPGGAGAVLYRGHE-NISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwVHGW 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 327391639  1254 IYRRRGlLTSEGKEIKNKsEILALLKALFLPKRLSIIHCPGHQrGNSaearGNRMADQAAREAA 1317
Cdd:pfam00075   84 KKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGHA-GNP----GNEMADRLAKQGA 140
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 742-929 9.65e-35

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: 131.56  E-value: 9.65e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  742 GILVPCQSPWNTPLLPVKKPGtNDYRPVQDLREVNKRVG-DIHPtVPNPYNLLSGLPPSHqWYTVLDLKDAFFCLRLHPT 820
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKD-GKLRLCVDYRKLNKVTIkDRYP-LPTIDELLEELAGAK-VFSKLDLRSGYHQIPLAEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  821 SQPLFAFEWRDpemgisGQLTWTRLPQGFKNSPTLF----DEALHRDLADFriqhpdliLLQYVDDLLLAATSEQDCQRG 896
Cdd:cd01647    78 SRPKTAFRTPF------GLYEYTRMPFGLKNAPATFqrlmNKILGDLLGDF--------VEVYLDDILVYSKTEEEHLEH 143

                         170       180       190
                  ....*....|....*....|....*....|...
gi 327391639  897 TRALLQTLGNLGYRASAKKAQICQKQVKYLGYL 929
Cdd:cd01647   144 LREVLERLREAGLKLNPEKCEFGVPEVEFLGHI 176
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 758-928 2.08e-34

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: 130.89  E-value: 2.08e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   758 VKKPGTNDYRPV----QDLREVNKRV-GDIHPTVPNPYNLlSGLPP------SHQWYTVLDLKDAFFCLRLHPTSQPLFA 826
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIvKRLKPENLDSPPQ-PGFRPglaklkKAKWFLKLDLKKAFDQVPLDELDRKLTA 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   827 F----EWRDPEMGISGQL-TWTRLPQGFKNSPTLFDEALHRDLADFRiQHPDLILLQYVDDLLLAATSEQDCQRGTRALL 901
Cdd:pfam00078   80 FttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNELLRPLR-KRAGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                          170       180
                   ....*....|....*....|....*....
gi 327391639   902 QTLGNLGYRASAKKAQIC--QKQVKYLGY 928
Cdd:pfam00078  159 EWLKESGLKINPEKTQFFlkSKEVKYLGV 187
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 546-638 2.65e-30

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: 115.93  E-value: 2.65e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   546 PEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLS----DKSAWVQGATGGKRYRWTTDRKVHLATGKVTH--SFLHVPD 619
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNwpkqKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                           90
                   ....*....|....*....
gi 327391639   620 CPYPLLGRDLLTKLKAQIH 638
Cdd:pfam00077   83 CPVNIIGRDLLQQLGGRLT 101
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1446-1541 6.97e-25

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: 100.47  E-value: 6.97e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1446 PGTHWEIDFTEVK-PGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFISQVSQ 1523
Cdd:pfam00665    1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 327391639  1524 SVAKLLGIDWKLHCAYRP 1541
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 550-631 1.02e-23

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: 96.63  E-value: 1.02e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  550 ITLKVGGQPVTFLVDTGAQHSVLTQNPGP---LSDKSAWVQGATGGKRYRWTTDRK-VHLATGKVTHSFLHVPDCPYPLL 625
Cdd:cd06095     1 VTITVEGVPIVFLVDTGATHSVLKSDLGPkqeLSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                  ....*.
gi 327391639  626 GRDLLT 631
Cdd:cd06095    81 GRDLLS 86
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1179-1317 2.01e-20

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


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 89.16  E-value: 2.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1179 YTDGSSyLHEGQR--RAGAAVtteteviW---------ARALP--AGTSaQRAELIALTQALKMA---EGKKLNVYTDSR 1242
Cdd:cd09280     3 YTDGSC-LNNGKPgaRAGIGV-------YfgpgdprnvSEPLPgrKQTN-NRAELLAVIHALEQApeeGIRKLEIRTDSK 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 327391639 1243 YAFATAHVHGEIYRRRGLLTSEGKEIKNKSEILALLKAL-FLPKRLSIIHCPGHQrGNsaeaRGNRMADQAAREAA 1317
Cdd:cd09280    74 YAINCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLrKRGIKVKFEHVKGHS-GD----PGNEEADRLAREGA 144
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 844-930 1.73e-17

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: 79.32  E-value: 1.73e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  844 RLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSEQdCQRGTRALLQTLGNLGYRASAKKAQ--ICQK 921
Cdd:cd00304    11 PLPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQ-QAVKKRELEEFLARLGLNLSDEKTQftEKEK 89


                  ....*....
gi 327391639  922 QVKYLGYLL 930
Cdd:cd00304    90 KFKFLGILV 98
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1018-1123 4.12e-17

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: 78.32  E-value: 4.12e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  1018 DLTKPFELFVDEKqGYAKG-VLTQKL-GPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPH 1095
Cdd:pfam17917    1 DPSKPFILETDAS-DYGIGaVLSQKDeDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDH 79

                           90       100
                   ....*....|....*....|....*...
gi 327391639  1096 AVEALVKQPpdrWLSNARMTHYQAMLLD 1123
Cdd:pfam17917   80 KPLKYLFTP---KELNGRLARWALFLQE 104
transpos_IS481 NF033577
IS481 family transposase; null
 1425-1594 9.18e-17

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 82.64  E-value: 9.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1425 CVQVNASKAKVGPGVRVRGHRPGTHWEIDFTEVKPGLY-GYKYLLVFVDTFSGWVEAFPTKHETAkVVTKKLLEEIFPRF 1503
Cdd:NF033577  106 LSRLRALDRKTGKVKRYERAHPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAYAELYPDETA-ETAADFLRRAFAEH 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1504 GMP--QVLgTDNGPAFISQVS--QSVAKLLGIDWKLHCAYRPQSSGQVERMNRTIKETLTKLTLATGARDWVLLLP--LA 1577
Cdd:NF033577  185 GIPirRVL-TDNGSEFRSRAHgfELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAELQAALDewLH 263

                         170       180
                  ....*....|....*....|.
gi 327391639 1578 LYrarNTPGPH----GLTPYE 1594
Cdd:NF033577  264 HY---NHHRPHsalgGKTPAE 281
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
993-1073 2.11e-16

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 76.38  E-value: 2.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   993 WGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVD-EKQGYAkGVLTQKL--GPWrRPVAYLSKKLDPVAAGWPPCLRM 1069
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDaSDYGIG-AVLSQEDddGGE-RPIAYASRKLSPAERNYSTTEKE 78


                   ....
gi 327391639  1070 VAAI 1073
Cdd:pfam17919   79 LLAI 82
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1178-1314 1.00e-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: 1.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1178 WYTDGSSylHEGQRRAGAAVT---TETEVIWARALPAGT-SAQRAELIALTQALKMA---EGKKLNVYTDSRYAFatahv 1250
Cdd:cd06222     1 INVDGSC--RGNPGPAGIGGVlrdHEGGWLGGFALKIGApTALEAELLALLLALELAldlGYLKVIIESDSKYVV----- 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 327391639 1251 hgeiyrrRGLLTSEGKEIKNKSEILALLKALFLPKRLSIIHCPGHqrgnsaearGNRMADQAAR 1314
Cdd:cd06222    74 -------DLINSGSFKWSPNILLIEDILLLLSRFWSVKISHVPRE---------GNQVADALAK 121
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1179-1317 1.26e-13

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 69.43  E-value: 1.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1179 YTDGSSylhegqRRA------GAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-EGKKLNVYTDSRYAF--ATAH 1249
Cdd:cd09278     5 YTDGAC------LGNpgpggwAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALkEPCPVTIYTDSQYVIngITKW 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 327391639 1250 VHGeiYRRRGLLTSEGKEIKNKSEILALLKALfLPKRLSIIHCPGHQrGNsaeaRGNRMADQAAREAA 1317
Cdd:cd09278    79 IKG--WKKNGWKTADGKPVKNRDLWQELDALL-AGHKVTWEWVKGHA-GH----PGNERADRLANKAA 138
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1179-1317 5.21e-13

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: 67.63  E-value: 5.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1179 YTDGSSYlhegQRRAGAAVTTETEVIWAR---ALPAGTSAQRAELIALTQALKMA-----EGKKLNVYTDSRYAFA---- 1246
Cdd:cd09276     3 YTDGSKL----EGSVGAGFVIYRGGEVISrsyRLGTHASVFDAELEAILEALELAlatarRARKVTIFTDSQSALQalrn 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 327391639 1247 TAHVHGEIYRRRGLLTSegKEIKNKseilallkalflPKRLSIIHCPGHQrgnsaEARGNRMADQAAREAA 1317
Cdd:cd09276    79 PRRSSGQVILIRILRLL--RLLKAK------------GVKVRLRWVPGHV-----GIEGNEAADRLAKEAA 130
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1385-1425 2.62e-12

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: 62.73  E-value: 2.62e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 327391639  1385 HQLTHLSYQKMRALLDRKespYYMLNKDKILHEVAESCQAC 1425
Cdd:pfam09337    1 HALTHLGINKLTALLARK---YHWLGIKETVSEVISSCVAC 38
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1179-1317 6.21e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 64.87  E-value: 6.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1179 YTDGSSYLHEGQRRAGAAVTTETEVIW-ARALPAGTSaQRAELIALTQALKMAE---GKKLNVYTDSRYAFATAHVHGEI 1254
Cdd:COG0328     6 YTDGACRGNPGPGGWGAVIRYGGEEKElSGGLGDTTN-NRAELTALIAALEALKelgPCEVEIYTDSQYVVNQITGWIHG 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 327391639 1255 YRRRGLltsegKEIKNKsEILALLKALFLPKRLSIIHCPGHQrGNsaeaRGNRMADQAAREAA 1317
Cdd:COG0328    85 WKKNGW-----KPVKNP-DLWQRLDELLARHKVTFEWVKGHA-GH----PGNERADALANKAL 136
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 806-927 1.77e-11

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: 62.75  E-value: 1.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  806 LDLKDAFFCLRLHPTSQPLFAFEWRDPemgisgQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILlqYVDDLLL 885
Cdd:cd03714     1 VDLKDAYFHIPILPRSRDLLGFAWQGE------TYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFS--YLDDLLI 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 327391639  886 AATSEQDCQRGTRALLQT-LGNLGYRASAKKAQIC-QKQVKYLG 927
Cdd:cd03714    73 IASSIKTSEAVLRHLRATlLANLGFTLNLEKSKLGpTQRITFLG 116
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1360-1556 2.18e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 57.86  E-value: 2.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1360 TKRYWVFQGKPVMPSQDTFELLDFLHQLTHLS----YQKMRALLDRKespYYMLNKDKILHEVAESCQACVQVNASK--- 1432
Cdd:COG2801    53 SRRRRRLRRPRSYRADEDAELLERIKEIFAESprygYRRITAELRRE---GIAVNRKRVRRLMRELGLQARRRRKKKytt 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1433 -----AKVGPGVRVRGHRPGTHWEIDFTEVkPGLYGYKYLLVFVDTFS----GWVEAfptKHETAKVVtKKLLEEIFPRF 1503
Cdd:COG2801   130 ysghgGPIAPNLLFTATAPNQVWVTDITYI-PTAEGWLYLAAVIDLFSreivGWSVS---DSMDAELV-VDALEMAIERR 204

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 327391639 1504 GMPQ--VLGTDNGPAFISQVSQSVAKLLGIDWKLHCAYRPQSSGQVERMNRTIKE 1556
Cdd:COG2801   205 GPPKplILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 550-630 2.27e-08

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: 52.96  E-value: 2.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   550 ITLKVGGQPVTFLVDTGAQHSVLTQN--------PGPLSDKsAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHV--PD 619
Cdd:pfam13975    1 VDVTINGRPVRFLVDTGASVTVISEAlaerlgldRLVDAYP-VTVRTANGTVRAARVRLDSVKIGGIELRNVPAVVlpGD 79

                           90
                   ....*....|.
gi 327391639   620 CPYPLLGRDLL 630
Cdd:pfam13975   80 LDDVLLGMDFL 90
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 550-631 3.09e-08

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: 52.72  E-value: 3.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  550 ITLKVGGQPVTFLVDTGAQHSVLTQN-------PGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGK--VTHSFLHVPDC 620
Cdd:cd00303     1 LKGKINGVPVRALVDSGASVNFISESlakklglPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGktFTVDFYVLDLL 80

                          90
                  ....*....|..
gi 327391639  621 PYP-LLGRDLLT 631
Cdd:cd00303    81 SYDvILGRPWLE 92
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1179-1317 1.15e-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: 49.39  E-value: 1.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1179 YTDGSSYLHEGQRRAGAAVTTETEVIWARALPAGTSAQ--RAELIALTQALKMAEG---KKLNVYTDSRyaFATAHVHGE 1253
Cdd:cd09279     4 YFDGASRGNPGPAGAGVVIYSPGGEVLELSERLGFPATnnEAEYEALIAGLELALElgaEKLEIYGDSQ--LVVNQLNGE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1254 IyrrrglltsegkEIKNK------SEILALLKALflpKRLSIIHCPGHQrgnsaeargNRMADQAAREAA 1317
Cdd:cd09279    82 Y------------KVKNErlkpllEKVLELLAKF---ELVELKWIPREQ---------NKEADALANQAL 127
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
548-637 3.04e-06

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 48.79  E-value: 3.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  548 PRITLKVGGQPVTFLVDTGAQHSVLTQ--------NPGPLsDKSAWVQGATGGKRYRWTTDRKVHLATGKVTH---SFLH 616
Cdd:COG3577    42 FVVEGTINGQPVRFLVDTGASTVVLSEsdarrlglDPEDL-GRPVRVQTANGVVRAARVRLDSVRIGGITLRNvraVVLP 120

                          90       100
                  ....*....|....*....|.
gi 327391639  617 VPDCPYPLLGRDLLTKLKAQI 637
Cdd:COG3577   121 GGELDDGLLGMSFLGRLDFEI 141
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 548-605 1.43e-05

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: 45.31  E-value: 1.43e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 327391639  548 PRITLKVGGQPVTFLVDTGAQHSVLTQ------NPGPLSDKSAWVQGATGGKRYRWTTDRKVHL 605
Cdd:cd05483     3 FVVPVTINGQPVRFLLDTGASTTVISEelaerlGLPLTLGGKVTVQTANGRVRAARVRLDSLQI 66
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1445-1560 1.60e-05

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 49.11  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1445 RPGtHWEIDfteVKPGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKL--LEEIFPRFgMPQVLGTDNGPAFiSQvS 1522
Cdd:COG2826   171 EPG-HWEGD---LIIGKRGKSALLTLVERKSRFVILLKLPDKTAESVADALirLLRKLPAF-LRKSITTDNGKEF-AD-H 243

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 327391639 1523 QSVAKLLGIDwklhcAY--RPQSS---GQVERMNRTIKETLTK 1560
Cdd:COG2826   244 KEIEAALGIK-----VYfaDPYSPwqrGTNENTNGLLRQYFPK 281
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 115-223 4.12e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 48.56  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  115 PPGPSAQPPSRSALYPALTPSIKSKPPKPQVLPDSGGPLIDLLTEDPPPYGAQPSSSARENNEEEAATTSEVSPPSPMVS 194
Cdd:PRK14951  388 APAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVA 467

                          90       100
                  ....*....|....*....|....*....
gi 327391639  195 RLRGRRDPPAADSTTSQAFPLRMGGDGQL 223
Cdd:PRK14951  468 PEPAVASAAPAPAAAPAAARLTPTEEGDV 496
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 1466-1560 6.10e-05

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: 47.48  E-value: 6.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639 1466 YLLVFVD--TfSGWVEAFPTKHETAK---VVTKKLLEeifpRFGMPQVLGTDNGPAFISQVSQSVAKL------------ 1528
Cdd:NF033594  148 TLLVAIDdaT-GRLMGLRFVESESTFgyfEVTRQYLE----KHGKPVAFYSDKHSVFRVNEEELAGKGdgltqfgralke 222

                          90       100       110
                  ....*....|....*....|....*....|..
gi 327391639 1529 LGIDWKlhCAYRPQSSGQVERMNRTIKETLTK 1560
Cdd:NF033594  223 LGIEII--CANSPQAKGRVERANQTLQDRLVK 252
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 550-629 6.62e-05

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: 43.04  E-value: 6.62e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   550 ITLKVGGQPVTFLVDTGAQHSVLT-----QNPGPLSDKSAWVQGATGGKRyrwTTDRKVHLAT---GKVTHSFLHV---- 617
Cdd:pfam13650    1 VPVTINGKPVRFLVDTGASGTVISpslaeRLGLKVRGLAYTVRVSTAGGR---VSAARVRLDSlrlGGLTLENVPAlvld 77

                           90
                   ....*....|...
gi 327391639   618 -PDCPYPLLGRDL 629
Cdd:pfam13650   78 lGDLIDGLLGMDF 90
ZnF_C2HC smart00343
zinc finger;
501-517 4.72e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 4.72e-04
                            10
                    ....*....|....*..
gi 327391639    501 QCAYCKEKGHWAKDCPK 517
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 807-905 1.40e-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: 41.91  E-value: 1.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  807 DLKDAFFCLRLHPTSQPLFAFEWR-DPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFriQHPDL--ILLQ--YVD 881
Cdd:cd01644    65 DIEKMFHQVKVRPEDRDVLRFLWRkDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDH--PHEAAakIIKRnfYVD 142

                          90       100
                  ....*....|....*....|....*..
gi 327391639  882 DLLLAATSEQDCQ---RGTRALLQTLG 905
Cdd:cd01644   143 DILVSTDTLNEAVnvaKRLIALLKKGG 169
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 550-631 2.34e-03

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: 38.79  E-value: 2.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  550 ITLKVGGQPVTFLVDTGAQHSVLTQN--PGPLSDKSAW-----VQGATGGKRYR---WTTDRKVHLATGKVthsflHVPD 619
Cdd:cd05482     1 LTLYINGKLFEGLLDTGADVSIIAENdwPKNWPIQPAPsnltgIGGAITPSQSSvllLEIDGEGHLGTILV-----YVLS 75

                          90
                  ....*....|..
gi 327391639  620 CPYPLLGRDLLT 631
Cdd:cd05482    76 LPVNLWGRDILS 87
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 500-517 2.39e-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: 36.74  E-value: 2.39e-03
                           10
                   ....*....|....*...
gi 327391639   500 DQCAYCKEKGHWAKDCPK 517
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
PHA03247 PHA03247
large tegument protein UL36; Provisional
 71-216 4.48e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.23  E-value: 4.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639   71 PGPHGHPDQVPYIVTWEALAYD----PPPwvkPFVSPKPPPLPTAPVLPPGPSAQPPSRSALYPALTPSIKSKPPKPQVL 146
Cdd:PHA03247 2525 VGEPVHPRMLTWIRGLEELASDdagdPPP---PLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAP 2601

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 327391639  147 PDSGGPLI----------DLLTEDPPPYGAQPSSSARENNEEEAATTSEVSPPSPMVSRLRGRRDPPAADSTTSQAFPLR 216
Cdd:PHA03247 2602 VDDRGDPRgpappsplppDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQ 2681
 
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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