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Conserved domains on  [gi|9627214|ref|NP_056891|]
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RT-IN [Mason-Pfizer monkey virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 935-1147 4.01e-123

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: 385.10  E-value: 4.01e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   935 PVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLPSPVAI 1014
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1015 PQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPSTNFKEPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQMYI 1094
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9627214  1095 IHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEKVQLQDPYTYLGFEL 1147
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 314-438 2.11e-48

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


:

Pssm-ID: 459864  Cd Length: 128  Bit Score: 168.61  E-value: 2.11e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     314 HHNGFDFAVIKELKTAASQYGATAPYTLAIVESVAD-NWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAG 392
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASsNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9627214     393 N--GWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKG 438
Cdd:pfam00607   81 PdrGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1366-1491 6.16e-38

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: 139.01  E-value: 6.16e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1366 LVFTDGSSTGMAAYTLTDTTIKFQTNLN---SAQLVELQALIAVLSAFPNQPLNIYTDSAYLAHSIPLLETVAQIK---H 1439
Cdd:cd09273    1 TVFTDGSSFKAGYAIVSGTEIVEAQPLPpgtSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIERgflK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9627214  1440 ISETAKLFLQCQQLIYnRSIPFYIGHVRAHSGLPGPIAQGNQRADLATKIVA 1491
Cdd:cd09273   81 SIKNLSLFLQLLEAVQ-RPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 771-858 1.72e-35

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: 130.08  E-value: 1.72e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   771 LTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPnLPVN 850
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS-LPVN 79


                 ....*...
gi 9627214   851 LWGRDLLS 858
Cdd:cd05482   80 LWGRDILS 87
trimeric_dUTPase super family cl00493
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 638-756 1.17e-30

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


The actual alignment was detected with superfamily member pfam00692:

Pssm-ID: 444938 [Multi-domain]  Cd Length: 129  Bit Score: 118.16  E-value: 1.17e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     638 LTRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVN 717
Cdd:pfam00692    6 PTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 9627214     718 N-IVTVSQGNRIAQLILLP----LIETDNKVQQPYRGQGSFGSS 756
Cdd:pfam00692   85 KsDFTIKKGDRIAQLIFEPilhpELEPVETLDNTDRGDGGFGSS 128
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1155-1219 7.75e-30

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 113.18  E-value: 7.75e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9627214    1155 QKAVIRKDKLQTLNDFQKLLGDINWLRPYLKLTTGDLKPLFDTLKGDSDPNSHRSLSKEALASLE 1219
Cdd:pfam06817    2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1554-1647 8.98e-24

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 97.38  E-value: 8.98e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1554 PNMIWQMDVTHYSEFGN--LKYIHVSIDTFSGFLLATLQTGETTKHVITHLLHCFSII--GLPKQIKTDNGPGYTSKNFQ 1629
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 9627214    1630 EFCSTLQIKHITGIPYNP 1647
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Gag_p10 super family cl03546
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-91 2.03e-23

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


The actual alignment was detected with superfamily member pfam02337:

Pssm-ID: 426727  Cd Length: 85  Bit Score: 95.88  E-value: 2.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214       8 HERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIK 87
Cdd:pfam02337    2 KQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALIR 81


                   ....
gi 9627214      88 ELID 91
Cdd:pfam02337   82 AVLD 85
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 443-510 1.28e-22

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


The actual alignment was detected with superfamily member pfam19317:

Pssm-ID: 466038  Cd Length: 74  Bit Score: 92.93  E-value: 1.28e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214     443 SLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR 510
Cdd:pfam19317    6 SLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIR 73
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1516-1710 2.84e-14

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


The actual alignment was detected with superfamily member COG2801:

Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.57  E-value: 2.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1516 RLMfnipREQARQIVKQCPICVTYLPVPHLGVNPRGLF----PNMIWQMDVTH-YSEFGNLkYIHVSIDTFSGFLLA-TL 1589
Cdd:COG2801  110 RLM----RELGLQARRRRKKKYTTYSGHGGPIAPNLLFtataPNQVWVTDITYiPTAEGWL-YLAAVIDLFSREIVGwSV 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1590 QTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNFQEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtieki 1667
Cdd:COG2801  185 SDSMDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY----- 259

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 9627214  1668 kkgEWYPRKgtprnilnhalfilNFLNLDDQNKSAAD-RFWHNN 1710
Cdd:COG2801  260 ---ELLYRR--------------RFESLEEAREAIEEyIEFYNH 286
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
575-609 7.54e-14

GAG-polyprotein viral zinc-finger;


:

Pssm-ID: 373297  Cd Length: 36  Bit Score: 66.81  E-value: 7.54e-14
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9627214     575 PGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGNR 609
Cdd:pfam14787    2 PGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1718-1763 1.46e-13

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 66.27  E-value: 1.46e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 9627214    1718 VKWKDPLDNTWHGPDPVLIWGRGSVCVySQTYDAARWLPERLVRQV 1763
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCV-PQDASDPQWVPERLLKRI 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 865-911 1.05e-12

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


:

Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 64.10  E-value: 1.05e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 9627214      865 CSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF 911
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
ZnF_C2HC smart00343
zinc finger;
548-562 4.91e-04

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 4.91e-04
                            10
                    ....*....|....*
gi 9627214      548 CCFKCGKKGHFAKNC 562
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 935-1147 4.01e-123

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: 385.10  E-value: 4.01e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   935 PVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLPSPVAI 1014
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1015 PQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPSTNFKEPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQMYI 1094
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9627214  1095 IHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEKVQLQDPYTYLGFEL 1147
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 314-438 2.11e-48

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 168.61  E-value: 2.11e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     314 HHNGFDFAVIKELKTAASQYGATAPYTLAIVESVAD-NWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAG 392
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASsNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9627214     393 N--GWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKG 438
Cdd:pfam00607   81 PdrGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 978-1147 1.01e-41

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: 152.07  E-value: 1.01e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     978 IKKKS-GKWRLL----QDLRAVNATMV-------LMGALQPGLPSPVAIPQGYLKII-IDLKDCFFSIPLHPSDQKRFAF 1044
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVkrlkpenLDSPPQPGFRPGLAKLKKAKWFLkLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1045 SLPSTNFK----EPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQmYIIHYMDDILIAGKDGQQVLQCFDQLKQ 1120
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGL-TLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 9627214    1121 ELTAAGLHIAPEKVQL---QDPYTYLGFEL 1147
Cdd:pfam00078  160 WLKESGLKINPEKTQFflkSKEVKYLGVTL 189
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1366-1491 6.16e-38

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: 139.01  E-value: 6.16e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1366 LVFTDGSSTGMAAYTLTDTTIKFQTNLN---SAQLVELQALIAVLSAFPNQPLNIYTDSAYLAHSIPLLETVAQIK---H 1439
Cdd:cd09273    1 TVFTDGSSFKAGYAIVSGTEIVEAQPLPpgtSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIERgflK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9627214  1440 ISETAKLFLQCQQLIYnRSIPFYIGHVRAHSGLPGPIAQGNQRADLATKIVA 1491
Cdd:cd09273   81 SIKNLSLFLQLLEAVQ-RPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 771-858 1.72e-35

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: 130.08  E-value: 1.72e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   771 LTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPnLPVN 850
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS-LPVN 79


                 ....*...
gi 9627214   851 LWGRDLLS 858
Cdd:cd05482   80 LWGRDILS 87
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 638-756 1.17e-30

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 118.16  E-value: 1.17e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     638 LTRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVN 717
Cdd:pfam00692    6 PTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 9627214     718 N-IVTVSQGNRIAQLILLP----LIETDNKVQQPYRGQGSFGSS 756
Cdd:pfam00692   85 KsDFTIKKGDRIAQLIFEPilhpELEPVETLDNTDRGDGGFGSS 128
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1155-1219 7.75e-30

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 113.18  E-value: 7.75e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9627214    1155 QKAVIRKDKLQTLNDFQKLLGDINWLRPYLKLTTGDLKPLFDTLKGDSDPNSHRSLSKEALASLE 1219
Cdd:pfam06817    2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 767-861 9.56e-28

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: 108.61  E-value: 9.56e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     767 QKPSLTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPN 846
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLILPT 82

                           90
                   ....*....|....*
gi 9627214     847 LPVNLWGRDLLSQMK 861
Cdd:pfam00077   83 CPVNIIGRDLLQQLG 97
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1554-1647 8.98e-24

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 97.38  E-value: 8.98e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1554 PNMIWQMDVTHYSEFGN--LKYIHVSIDTFSGFLLATLQTGETTKHVITHLLHCFSII--GLPKQIKTDNGPGYTSKNFQ 1629
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 9627214    1630 EFCSTLQIKHITGIPYNP 1647
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-91 2.03e-23

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 95.88  E-value: 2.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214       8 HERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIK 87
Cdd:pfam02337    2 KQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALIR 81


                   ....
gi 9627214      88 ELID 91
Cdd:pfam02337   82 AVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 443-510 1.28e-22

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 92.93  E-value: 1.28e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214     443 SLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR 510
Cdd:pfam19317    6 SLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIR 73
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 639-756 5.73e-22

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 93.84  E-value: 5.73e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     639 TRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKG---LQVYPGVIDNDYTGEIK-IMAK 714
Cdd:TIGR00576   15 TYATEGAAGYDLRAAEDVTIPP-GERALVPTGIAIELPDGYYGRVAPRSGLALKHgvtIDNSPGVIDADYRGEIKvILIN 93

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9627214     715 AVNNIVTVSQGNRIAQLILLPlIETDNKVQQPY------RGQGSFGSS 756
Cdd:TIGR00576   94 LGKEDFTVKKGDRIAQLVVEK-IVTEVEFEEVEeldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 639-756 5.17e-20

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 88.15  E-value: 5.17e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   639 TRATPGSAGLDLCSTSH--TVLTPemGPQAL-STGIYGPLPPNTFGLILGRSSITMK-GLQVY--PGVIDNDYTGEIKIM 712
Cdd:COG0756   15 AYATPGSAGLDLRAALDepVTLKP--GERALvPTGLAIALPPGYEAQVRPRSGLALKhGITLLnsPGTIDSDYRGEIKVI 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214   713 akAVN---NIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:COG0756   93 --LINlgdEPFTIERGDRIAQLVIAPvvqaefeeveeLDETE-------RGAGGFGST 141
transpos_IS481 NF033577
IS481 family transposase; null
 1554-1662 3.82e-19

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 89.57  E-value: 3.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1554 PNMIWQMDVTHYsefGNLK-----YIHVSIDTFSGFLLATLQTGETTKHVITHLLHCFSIIGLP-KQIKTDNGPGYTSK- 1626
Cdd:NF033577  127 PGELWHIDIKKL---GRIPdvgrlYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTDNGSEFRSRa 203

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 9627214   1627 -NFQEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKT 1662
Cdd:NF033577  204 hGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 646-733 6.06e-19

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 83.31  E-value: 6.06e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   646 AGLDLCS---TSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVY-PGVIDNDYTGEIKIMAKAVNNI-V 720
Cdd:cd07557    1 AGYDLRLgedFEGIVLPP-GETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpV 79

                         90
                 ....*....|...
gi 9627214   721 TVSQGNRIAQLIL 733
Cdd:cd07557   80 VIKKGDRIAQLVF 92
dut PRK00601
dUTP diphosphatase;
639-756 1.29e-17

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 81.36  E-value: 1.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    639 TRATPGSAGLDLCSTSHTVLTPEMGPQAL-STGIYGPLPPNTFGLILGRS------SITMKGLqvyPGVIDNDYTGEIK- 710
Cdd:PRK00601   21 AYATEGSAGLDLRACLDEPVTLAPGERALvPTGLAIHIPDGYEAQILPRSglahkhGIVLGNL---PGTIDSDYRGELKv 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627214    711 IMAKAVNNIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:PRK00601   98 SLWNRGQEPFTIEPGERIAQLVIVPvvqaefeeveeFDETE-------RGAGGFGST 147
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1362-1492 1.42e-15

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 75.49  E-value: 1.42e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1362 NNALLVFTDGSS-----TGMAAYTL--TDTTIKFQTNL-NSAQLVELQALIAVLSAFP-NQPLNIYTDSAYLAHSIPLLE 1432
Cdd:pfam00075    1 PKAVTVYTDGSClgnpgPGGAGAVLyrGHENISAPLPGrTTNNRAELQAVIEALKALKsPSKVNIYTDSQYVIGGITQWV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214    1433 TVAQIKHISETAK--------LFLQCQQLIynRSIPFYIGHVRAHSGLPgpiaqGNQRADLATKIVAS 1492
Cdd:pfam00075   81 HGWKKNGWPTTSEgkpvknkdLWQLLKALC--KKHQVYWQWVKGHAGNP-----GNEMADRLAKQGAE 141
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1516-1710 2.84e-14

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.57  E-value: 2.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1516 RLMfnipREQARQIVKQCPICVTYLPVPHLGVNPRGLF----PNMIWQMDVTH-YSEFGNLkYIHVSIDTFSGFLLA-TL 1589
Cdd:COG2801  110 RLM----RELGLQARRRRKKKYTTYSGHGGPIAPNLLFtataPNQVWVTDITYiPTAEGWL-YLAAVIDLFSREIVGwSV 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1590 QTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNFQEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtieki 1667
Cdd:COG2801  185 SDSMDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY----- 259

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 9627214  1668 kkgEWYPRKgtprnilnhalfilNFLNLDDQNKSAAD-RFWHNN 1710
Cdd:COG2801  260 ---ELLYRR--------------RFESLEEAREAIEEyIEFYNH 286
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
575-609 7.54e-14

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 66.81  E-value: 7.54e-14
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9627214     575 PGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGNR 609
Cdd:pfam14787    2 PGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1718-1763 1.46e-13

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 66.27  E-value: 1.46e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 9627214    1718 VKWKDPLDNTWHGPDPVLIWGRGSVCVySQTYDAARWLPERLVRQV 1763
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCV-PQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1503-1538 2.93e-13

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 65.09  E-value: 2.93e-13
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 9627214    1503 NAHTLHHLNAQTLRLMFNIPREQARQIVKQCPICVT 1538
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 865-911 1.05e-12

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 64.10  E-value: 1.05e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 9627214      865 CSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF 911
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
transpos_IS3 NF033516
IS3 family transposase;
1554-1677 7.06e-11

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 66.05  E-value: 7.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1554 PNMIWQMDVTH--YSEfGNLkYIHVSIDTFSGFLLA-TLQTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNF 1628
Cdd:NF033516  215 PNQVWVTDITYirTAE-GWL-YLAVVLDLFSREIVGwSVSTSMSAELVLDALEMAIEWRGKPEGliLHSDNGSQYTSKAY 292

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 9627214   1629 QEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtiekikkgEWYPRKG 1677
Cdd:NF033516  293 REWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR--------ECLYRRR 333
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 875-909 2.00e-08

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 51.74  E-value: 2.00e-08
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9627214     875 MLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFG 909
Cdd:pfam01585    9 LQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLG 43
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1367-1488 1.95e-06

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 49.07  E-value: 1.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1367 VFTDGSS---TGMAAY----TLTDTTIKF------QTNlNSAqlvELQALIAVLSA---FPNQPLNIYTDSAYLAHSI-- 1428
Cdd:COG0328    5 IYTDGACrgnPGPGGWgaviRYGGEEKELsgglgdTTN-NRA---ELTALIAALEAlkeLGPCEVEIYTDSQYVVNQItg 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9627214  1429 --PLLETVA--QIKHisetAKLFLQCQQLIYNRSIPFYigHVRAHSGLPgpiaqGNQRAD-LATK 1488
Cdd:COG0328   81 wiHGWKKNGwkPVKN----PDLWQRLDELLARHKVTFE--WVKGHAGHP-----GNERADaLANK 134
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1554-1677 2.69e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 44.86  E-value: 2.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1554 PNMIWQMDVTHYSEFGNLKYIHVSIDTFSGFLLA-TLQTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNFQE 1630
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGwRVSSSMDTDFVLDALEQALWARGRPGGliHHSDKGSQYVSLAYTQ 188

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 9627214   1631 FCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtiekikkgEWYPRKG 1677
Cdd:PHA02517  189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA--------EVIHRVS 227
ZnF_C2HC smart00343
zinc finger;
548-562 4.91e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 4.91e-04
                            10
                    ....*....|....*
gi 9627214      548 CCFKCGKKGHFAKNC 562
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 542-594 2.49e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 2.49e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627214    542 NKEKGGC----CFKCGKKGHFAKNCHEHAHNNAEPKvpgLCPRCKRGKHWANECKSK 594
Cdd:PTZ00368   95 NRAKGGAarraCYNCGGEGHISRDCPNAGKRPGGDK---TCYNCGQTGHLSRDCPDK 148
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 549-562 3.47e-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: 36.35  E-value: 3.47e-03
                           10
                   ....*....|....
gi 9627214     549 CFKCGKKGHFAKNC 562
Cdd:pfam00098    3 CYNCGEPGHIARDC 16
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 1556-1660 4.47e-03

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


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 41.31  E-value: 4.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1556 MIWQMDVTHYSEFGNLK---YIHVSID----------------TFSGFllatlqtgETTKHVITHllHcfsiiGLPKQIK 1616
Cdd:NF033594  128 ELIQIDGSPHDWFEGRGpkcTLLVAIDdatgrlmglrfvesesTFGYF--------EVTRQYLEK--H-----GKPVAFY 192

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214   1617 TDNGP--------------GYTskNFQEFCSTLQIKHITGipYNPQGQGIVERAHLSL 1660
Cdd:NF033594  193 SDKHSvfrvneeelagkgdGLT--QFGRALKELGIEIICA--NSPQAKGRVERANQTL 246
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 935-1147 4.01e-123

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: 385.10  E-value: 4.01e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   935 PVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLPSPVAI 1014
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1015 PQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPSTNFKEPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQMYI 1094
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9627214  1095 IHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEKVQLQDPYTYLGFEL 1147
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 314-438 2.11e-48

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 168.61  E-value: 2.11e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     314 HHNGFDFAVIKELKTAASQYGATAPYTLAIVESVAD-NWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAG 392
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASsNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9627214     393 N--GWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKG 438
Cdd:pfam00607   81 PdrGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 978-1147 1.01e-41

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: 152.07  E-value: 1.01e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     978 IKKKS-GKWRLL----QDLRAVNATMV-------LMGALQPGLPSPVAIPQGYLKII-IDLKDCFFSIPLHPSDQKRFAF 1044
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVkrlkpenLDSPPQPGFRPGLAKLKKAKWFLkLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1045 SLPSTNFK----EPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQmYIIHYMDDILIAGKDGQQVLQCFDQLKQ 1120
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGL-TLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 9627214    1121 ELTAAGLHIAPEKVQL---QDPYTYLGFEL 1147
Cdd:pfam00078  160 WLKESGLKINPEKTQFflkSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 935-1145 3.22e-38

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: 142.87  E-value: 3.22e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   935 PVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSG-KWRLLQDLRAVNATMVlmgALQPGLPSPVA 1013
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVL---PIHPAVPNPYT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1014 I-----PQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPStnfkepmQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHA 1088
Cdd:cd03715   78 LlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG-------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLE 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214  1089 WKQMYIIHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEKVQ-LQDPYTYLGF 1145
Cdd:cd03715  151 HEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQiCRAEVKFLGV 208
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1366-1491 6.16e-38

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: 139.01  E-value: 6.16e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1366 LVFTDGSSTGMAAYTLTDTTIKFQTNLN---SAQLVELQALIAVLSAFPNQPLNIYTDSAYLAHSIPLLETVAQIK---H 1439
Cdd:cd09273    1 TVFTDGSSFKAGYAIVSGTEIVEAQPLPpgtSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGIERgflK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9627214  1440 ISETAKLFLQCQQLIYnRSIPFYIGHVRAHSGLPGPIAQGNQRADLATKIVA 1491
Cdd:cd09273   81 SIKNLSLFLQLLEAVQ-RPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 771-858 1.72e-35

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: 130.08  E-value: 1.72e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   771 LTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPnLPVN 850
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS-LPVN 79


                 ....*...
gi 9627214   851 LWGRDLLS 858
Cdd:cd05482   80 LWGRDILS 87
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 962-1145 1.00e-30

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: 120.01  E-value: 1.00e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   962 GHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLPSPVAIPQGYLKI-IIDLKDCFFSIPLHPSDQK 1040
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFsKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1041 RFAFSLPStnfkepmQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWkqmyIIHYMDDILIAGK---DGQQVL-QCFD 1116
Cdd:cd01647   81 KTAFRTPF-------GLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF----VEVYLDDILVYSKteeEHLEHLrEVLE 149

                        170       180       190
                 ....*....|....*....|....*....|
gi 9627214  1117 QLKQeltaAGLHIAPEKVQLQDPY-TYLGF 1145
Cdd:cd01647  150 RLRE----AGLKLNPEKCEFGVPEvEFLGH 175
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 638-756 1.17e-30

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 118.16  E-value: 1.17e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     638 LTRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVN 717
Cdd:pfam00692    6 PTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 9627214     718 N-IVTVSQGNRIAQLILLP----LIETDNKVQQPYRGQGSFGSS 756
Cdd:pfam00692   85 KsDFTIKKGDRIAQLIFEPilhpELEPVETLDNTDRGDGGFGSS 128
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1155-1219 7.75e-30

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 113.18  E-value: 7.75e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9627214    1155 QKAVIRKDKLQTLNDFQKLLGDINWLRPYLKLTTGDLKPLFDTLKGDSDPNSHRSLSKEALASLE 1219
Cdd:pfam06817    2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 767-861 9.56e-28

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: 108.61  E-value: 9.56e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     767 QKPSLTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPN 846
Cdd:pfam00077    3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLILPT 82

                           90
                   ....*....|....*
gi 9627214     847 LPVNLWGRDLLSQMK 861
Cdd:pfam00077   83 CPVNIIGRDLLQQLG 97
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1554-1647 8.98e-24

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 97.38  E-value: 8.98e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1554 PNMIWQMDVTHYSEFGN--LKYIHVSIDTFSGFLLATLQTGETTKHVITHLLHCFSII--GLPKQIKTDNGPGYTSKNFQ 1629
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrgGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 9627214    1630 EFCSTLQIKHITGIPYNP 1647
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-91 2.03e-23

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 95.88  E-value: 2.03e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214       8 HERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIK 87
Cdd:pfam02337    2 KQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALIR 81


                   ....
gi 9627214      88 ELID 91
Cdd:pfam02337   82 AVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 443-510 1.28e-22

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 92.93  E-value: 1.28e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214     443 SLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR 510
Cdd:pfam19317    6 SLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIR 73
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 639-756 5.73e-22

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 93.84  E-value: 5.73e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     639 TRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKG---LQVYPGVIDNDYTGEIK-IMAK 714
Cdd:TIGR00576   15 TYATEGAAGYDLRAAEDVTIPP-GERALVPTGIAIELPDGYYGRVAPRSGLALKHgvtIDNSPGVIDADYRGEIKvILIN 93

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9627214     715 AVNNIVTVSQGNRIAQLILLPlIETDNKVQQPY------RGQGSFGSS 756
Cdd:TIGR00576   94 LGKEDFTVKKGDRIAQLVVEK-IVTEVEFEEVEeldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 639-756 5.17e-20

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 88.15  E-value: 5.17e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   639 TRATPGSAGLDLCSTSH--TVLTPemGPQAL-STGIYGPLPPNTFGLILGRSSITMK-GLQVY--PGVIDNDYTGEIKIM 712
Cdd:COG0756   15 AYATPGSAGLDLRAALDepVTLKP--GERALvPTGLAIALPPGYEAQVRPRSGLALKhGITLLnsPGTIDSDYRGEIKVI 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214   713 akAVN---NIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:COG0756   93 --LINlgdEPFTIERGDRIAQLVIAPvvqaefeeveeLDETE-------RGAGGFGST 141
transpos_IS481 NF033577
IS481 family transposase; null
 1554-1662 3.82e-19

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 89.57  E-value: 3.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1554 PNMIWQMDVTHYsefGNLK-----YIHVSIDTFSGFLLATLQTGETTKHVITHLLHCFSIIGLP-KQIKTDNGPGYTSK- 1626
Cdd:NF033577  127 PGELWHIDIKKL---GRIPdvgrlYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTDNGSEFRSRa 203

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 9627214   1627 -NFQEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKT 1662
Cdd:NF033577  204 hGFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 646-733 6.06e-19

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 83.31  E-value: 6.06e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   646 AGLDLCS---TSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVY-PGVIDNDYTGEIKIMAKAVNNI-V 720
Cdd:cd07557    1 AGYDLRLgedFEGIVLPP-GETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpV 79

                         90
                 ....*....|...
gi 9627214   721 TVSQGNRIAQLIL 733
Cdd:cd07557   80 VIKKGDRIAQLVF 92
dut PRK00601
dUTP diphosphatase;
639-756 1.29e-17

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 81.36  E-value: 1.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    639 TRATPGSAGLDLCSTSHTVLTPEMGPQAL-STGIYGPLPPNTFGLILGRS------SITMKGLqvyPGVIDNDYTGEIK- 710
Cdd:PRK00601   21 AYATEGSAGLDLRACLDEPVTLAPGERALvPTGLAIHIPDGYEAQILPRSglahkhGIVLGNL---PGTIDSDYRGELKv 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627214    711 IMAKAVNNIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:PRK00601   98 SLWNRGQEPFTIEPGERIAQLVIVPvvqaefeeveeFDETE-------RGAGGFGST 147
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 639-774 3.20e-16

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 78.10  E-value: 3.20e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    639 TRATPGSAGLDLCSTSHTVLtPEMGPQALSTGIYGPLPPNTFGLILGRSSITMKG-LQVYPGVIDNDYTGEIK-IMAKAV 716
Cdd:PHA02703   27 TRGSPGAAGLDLCSACDCIV-PAGCRCVVFTDLLIKLPDGCYGRIAPRSGLAVKHfIDVGAGVIDADYRGNVGvVLFNFG 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9627214    717 NNIVTVSQGNRIAQLIL----LPLIETDNKVQQPYRGQGSFGSSDIYwvqpiTCQKPSLTLW 774
Cdd:PHA02703  106 HNDFEVKKGDRIAQLICeraaFPAVEEVACLDDTDRGAGGFGSTGSG-----ACEGCGDTVW 162
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1362-1492 1.42e-15

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 75.49  E-value: 1.42e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    1362 NNALLVFTDGSS-----TGMAAYTL--TDTTIKFQTNL-NSAQLVELQALIAVLSAFP-NQPLNIYTDSAYLAHSIPLLE 1432
Cdd:pfam00075    1 PKAVTVYTDGSClgnpgPGGAGAVLyrGHENISAPLPGrTTNNRAELQAVIEALKALKsPSKVNIYTDSQYVIGGITQWV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214    1433 TVAQIKHISETAK--------LFLQCQQLIynRSIPFYIGHVRAHSGLPgpiaqGNQRADLATKIVAS 1492
Cdd:pfam00075   81 HGWKKNGWPTTSEgkpvknkdLWQLLKALC--KKHQVYWQWVKGHAGNP-----GNEMADRLAKQGAE 141
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1516-1710 2.84e-14

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.57  E-value: 2.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1516 RLMfnipREQARQIVKQCPICVTYLPVPHLGVNPRGLF----PNMIWQMDVTH-YSEFGNLkYIHVSIDTFSGFLLA-TL 1589
Cdd:COG2801  110 RLM----RELGLQARRRRKKKYTTYSGHGGPIAPNLLFtataPNQVWVTDITYiPTAEGWL-YLAAVIDLFSREIVGwSV 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1590 QTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNFQEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtieki 1667
Cdd:COG2801  185 SDSMDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY----- 259

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 9627214  1668 kkgEWYPRKgtprnilnhalfilNFLNLDDQNKSAAD-RFWHNN 1710
Cdd:COG2801  260 ---ELLYRR--------------RFESLEEAREAIEEyIEFYNH 286
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
575-609 7.54e-14

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 66.81  E-value: 7.54e-14
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9627214     575 PGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGNR 609
Cdd:pfam14787    2 PGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1718-1763 1.46e-13

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 66.27  E-value: 1.46e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 9627214    1718 VKWKDPLDNTWHGPDPVLIWGRGSVCVySQTYDAARWLPERLVRQV 1763
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCV-PQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1503-1538 2.93e-13

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 65.09  E-value: 2.93e-13
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 9627214    1503 NAHTLHHLNAQTLRLMFNIPREQARQIVKQCPICVT 1538
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
PLN02547 PLN02547
dUTP pyrophosphatase
 639-756 3.92e-13

dUTP pyrophosphatase


Pssm-ID: 215302  Cd Length: 157  Bit Score: 68.67  E-value: 3.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    639 TRATPGSAGLDLCSTSHTVLtPEMGPQALSTGIYGPLPPNTFGLILGRSSITMK-GLQVYPGVIDNDYTGEIK-IMAKAV 716
Cdd:PLN02547   30 SRGSALAAGYDLSSAYDTVV-PARGKALVPTDLSIAIPEGTYARIAPRSGLAWKhSIDVGAGVIDADYRGPVGvILFNHS 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 9627214    717 NNIVTVSQGNRIAQLIL----LPLIETDNKVQQPYRGQGSFGSS 756
Cdd:PLN02547  109 DVDFEVKVGDRIAQLILekivTPEVVEVEDLDATVRGAGGFGST 152
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 865-911 1.05e-12

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 64.10  E-value: 1.05e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 9627214      865 CSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF 911
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
transpos_IS3 NF033516
IS3 family transposase;
1554-1677 7.06e-11

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 66.05  E-value: 7.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1554 PNMIWQMDVTH--YSEfGNLkYIHVSIDTFSGFLLA-TLQTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNF 1628
Cdd:NF033516  215 PNQVWVTDITYirTAE-GWL-YLAVVLDLFSREIVGwSVSTSMSAELVLDALEMAIEWRGKPEGliLHSDNGSQYTSKAY 292

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 9627214   1629 QEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtiekikkgEWYPRKG 1677
Cdd:NF033516  293 REWLKEHGITQSMSRPGNCWDNAVAESFFGTLKR--------ECLYRRR 333
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1023-1147 7.45e-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: 61.21  E-value: 7.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1023 IDLKDCFFSIPLHPSDQKRFAFSLPStnfkepmQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAwkQMYIIHYMDDIL 1102
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQG-------ETYQFKALPFGLSLAPRVFTKVVEALLAPLRLL--GVRIFSYLDDLL 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 9627214  1103 IAGKDGQQ---VLQCFdqLKQELTAAGLHIAPEKVQL--QDPYTYLGFEL 1147
Cdd:cd03714   72 IIASSIKTseaVLRHL--RATLLANLGFTLNLEKSKLgpTQRITFLGLEL 119
PHA03094 PHA03094
dUTPase; Provisional
 639-758 1.51e-10

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 60.93  E-value: 1.51e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    639 TRATPGSAGLDLCStSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRSSITMK-GLQVYPGVIDNDYTGEIK-IMAKAV 716
Cdd:PHA03094   19 TRSSPKSAGYDLYS-AYDYTVPPKERILVKTDISLSIPKFCYGRIAPRSGLSLNyGIDIGGGVIDEDYRGNIGvIFINNG 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 9627214    717 NNIVTVSQGNRIAQLIL----LPLIETDNKVQQPYRGQGSFGSSDI 758
Cdd:PHA03094   98 KCTFNIKTGDRIAQIIFerieYPELKEVQSLDSTDRGDQGFGSSGL 143
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 875-909 2.00e-08

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 51.74  E-value: 2.00e-08
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9627214     875 MLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFG 909
Cdd:pfam01585    9 LQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLG 43
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1389-1488 5.08e-08

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: 53.72  E-value: 5.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1389 QTNlNSAqlvELQALI-AVLSAF--PNQPLNIYTDSAYLAHSIplleTVAQIKHIS-----------ETAKLFLQCQQLI 1454
Cdd:cd09280   41 QTN-NRA---ELLAVIhALEQAPeeGIRKLEIRTDSKYAINCI----TKWIPKWKKngwktskgkpvKNQDLIKELDKLL 112

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 9627214  1455 YNRSIPFYIGHVRAHSGLPgpiaqGNQRAD-LATK 1488
Cdd:cd09280  113 RKRGIKVKFEHVKGHSGDP-----GNEEADrLARE 142
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1023-1147 1.20e-06

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: 48.50  E-value: 1.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1023 IDLKDCFFSIPLhpsdqkrfafslpstnfkepmqrfqwkvlPQGMANSPTLCQKYVATAIHKVRHAWKQMYIIHYMDDIL 1102
Cdd:cd00304    1 FDVKSFFTSIPL-----------------------------PQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 9627214  1103 IAGKDGQQVlQCFDQLKQELTAAGLHIAPEKVQL---QDPYTYLGFEL 1147
Cdd:cd00304   52 VIAKSEQQA-VKKRELEEFLARLGLNLSDEKTQFtekEKKFKFLGILV 98
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1367-1488 1.95e-06

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 49.07  E-value: 1.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1367 VFTDGSS---TGMAAY----TLTDTTIKF------QTNlNSAqlvELQALIAVLSA---FPNQPLNIYTDSAYLAHSI-- 1428
Cdd:COG0328    5 IYTDGACrgnPGPGGWgaviRYGGEEKELsgglgdTTN-NRA---ELTALIAALEAlkeLGPCEVEIYTDSQYVVNQItg 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9627214  1429 --PLLETVA--QIKHisetAKLFLQCQQLIYNRSIPFYigHVRAHSGLPgpiaqGNQRAD-LATK 1488
Cdd:COG0328   81 wiHGWKKNGwkPVKN----PDLWQRLDELLARHKVTFE--WVKGHAGHP-----GNERADaLANK 134
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 783-858 5.54e-06

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: 46.17  E-value: 5.54e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9627214   783 LIDTGADVTIIKlEDWPPNWPITDTLTNLRGI-GQSNNP-KQSSKYLTWRDKEnnsgLIKPF-VIPNLPVNLWGRDLLS 858
Cdd:cd06095   13 LVDTGATHSVLK-SDLGPKQELSTTSVLIRGVsGQSQQPvTTYRTLVDLGGHT----VSHSFlVVPNCPDPLLGRDLLS 86
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 1024-1180 1.10e-05

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 48.45  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1024 DLKDCFFSIPLHPSDQK--RFAFsLPSTNFKEPmQRFQWKVLPQGMANSPTLCQKyvATAIHKVRHAWKQMY-II---HY 1097
Cdd:cd01644   65 DIEKMFHQVKVRPEDRDvlRFLW-RKDGDEPKP-IEYRMTVVPFGAASAPFLANR--ALKQHAEDHPHEAAAkIIkrnFY 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1098 MDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPekvqlqdpytylgFELNGPKITNQKAVIRKDKLQTLNDFQKLLGdI 1177
Cdd:cd01644  141 VDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRK-------------WASNSQEVLDDLPEERVLLDRDSDVTEKTLG-L 206


                 ...
gi 9627214  1178 NWL 1180
Cdd:cd01644  207 RWN 209
PTZ00143 PTZ00143
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
 643-758 3.41e-05

deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional


Pssm-ID: 240288 [Multi-domain]  Cd Length: 155  Bit Score: 45.88  E-value: 3.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    643 PGSAGLDLCSTSHTVLTP------EMGPQ--ALSTGIYGPLPPNTFGLILGRSSITMKGLQVYP--GVIDNDYTGEIKIm 712
Cdd:PTZ00143   24 EGDSGLDLFIVKDQTIKPgetafiKLGIKaaAFQKDEDGSDGKNVSWLLFPRSSISKTPLRLANsiGLIDAGYRGELIA- 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 9627214    713 akAVNNI----VTVSQGNRIAQLILL---PL-IETDNKVQQPYRGQGSFGSSDI 758
Cdd:PTZ00143  103 --AVDNIkdepYTIKKGDRLVQLVSFdgePItFELVDELDETTRGEGGFGSTGR 154
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 1016-1147 1.00e-04

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 45.65  E-value: 1.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1016 QGYLKII-IDLKDCF---------FSIPLHPSDQKrfaFSLPSTNFKEPMQRFQWKV------LPQGMANSPTLC----- 1074
Cdd:cd01651   67 GGYTWVIeGDIKGFFdnidhdlllKILKRRIGDKR---VLRLIRKWLKAGVLEDGKLvetekgTPQGGVISPLLAniylh 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1075 --QKYVATAIHKVRHAWKQ----MYIIHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEKVQL----QDPYTYLG 1144
Cdd:cd01651  144 elDKFVEEKLKEYYDTSDPkfrrLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRIthfkSEGFDFLG 223


                 ...
gi 9627214  1145 FEL 1147
Cdd:cd01651  224 FTF 226
PHA03124 PHA03124
dUTPase; Provisional
 643-756 1.39e-04

dUTPase; Provisional


Pssm-ID: 165396 [Multi-domain]  Cd Length: 418  Bit Score: 46.47  E-value: 1.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    643 PGSAGLDLCSTSHTVLTPEMG-----PQALSTGiygplpPNTFGLILGRSSITMKGLQVYP-GVIDNDYtgeikiMAKAV 716
Cdd:PHA03124  288 AEDAGYDIRAPEDCTILPGGStriilPQKLACG------KFRAAFILGRSSMNLKGLLVDPeHVQDDDW------ISFNI 355

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9627214    717 NNI----VTVSQGNRIAQLILLP-----LIETD-------NKVQQ-----PYRGQGSFGSS 756
Cdd:PHA03124  356 TNIrdaaAFFHAGDRIAQLIALEdklefLGEPDalpwkivNSVQDekknlSSRGDGGFGSS 416
dCTP_deam TIGR02274
deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli ...
 675-752 1.79e-04

deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli monofunctional deoxycytidine triphosphate deaminase (dCTP deaminase) and a Methanocaldococcus jannaschii bifunctional dCTP deaminase (3.5.4.13)/dUTP diphosphatase (EC 3.6.1.23), which has the EC number 3.5.4.30 for the overall operation. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274062  Cd Length: 179  Bit Score: 44.23  E-value: 1.79e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214     675 LPPNTFGLILGRSSITMKGLQVYP--GVIDNDYTGEIKI-MAKAVNNIVTVSQGNRIAQLILLPLIEtdnKVQQPYRGQG 751
Cdd:TIGR02274   89 LPDDVVGFLEGRSSLARLGLFIHVtaGRIDPGFEGNITLeLFNAGKLPVKLRPGMRIAQLVFERLSS---PAERPYNGRS 165


                   .
gi 9627214     752 S 752
Cdd:TIGR02274  166 G 166
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 1024-1133 1.86e-04

RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 43.86  E-value: 1.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1024 DLKDCFFSIPLH----------PSDQKRFAFSLPSTNFKEPMQRFQWKV---LPQGMANSptlcqKYVATAI-----HKV 1085
Cdd:cd01646    2 DISNFYDSIYTHslpwalhgkiKAKQLLKLLRLLGNLLDLLLLSSQYGQtngLPIGPLTS-----RFLANIYlndvdHEL 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 9627214  1086 RHAWKQMYIIHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEK 1133
Cdd:cd01646   77 KSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSK 124
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1367-1488 2.28e-04

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: 42.86  E-value: 2.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1367 VFTDGSST------GMAAYTLTDTTIK-------FQTNlNSAqlvELQALIAVLSAFP-NQPLNIYTDSAYLAHSIplle 1432
Cdd:cd09278    4 IYTDGACLgnpgpgGWAAVIRYGDHEKelsggepGTTN-NRM---ELTAAIEALEALKePCPVTIYTDSQYVINGI---- 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9627214  1433 tvaqIKHISE-------TAK--------LFLQCQQLIYNRSIPFYigHVRAHSGLPgpiaqGNQRAD-LATK 1488
Cdd:cd09278   76 ----TKWIKGwkkngwkTADgkpvknrdLWQELDALLAGHKVTWE--WVKGHAGHP-----GNERADrLANK 136
Dcd COG0717
dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway ...
 675-752 2.38e-04

dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440481  Cd Length: 180  Bit Score: 43.66  E-value: 2.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   675 LPPNTFGLILGRSSITMKGL--QVYPGVIDNDYTGEIKIMAKAVNNI-VTVSQGNRIAQLIllpLIETDNKVQQPYRGQG 751
Cdd:COG0717   88 LPDDLVAFLEGRSSLARLGLfvHTTAGVIDPGFEGRITLELSNTGPLpIKLYPGMRIAQLV---FFRLSGPAERPYGRGG 164


                 .
gi 9627214   752 S 752
Cdd:COG0717  165 K 165
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1554-1677 2.69e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 44.86  E-value: 2.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1554 PNMIWQMDVTHYSEFGNLKYIHVSIDTFSGFLLA-TLQTGETTKHVITHLLHCFSIIGLPKQ--IKTDNGPGYTSKNFQE 1630
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGwRVSSSMDTDFVLDALEQALWARGRPGGliHHSDKGSQYVSLAYTQ 188

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 9627214   1631 FCSTLQIKHITGIPYNPQGQGIVERAHLSLKTtiekikkgEWYPRKG 1677
Cdd:PHA02517  189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA--------EVIHRVS 227
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1368-1456 3.93e-04

DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 41.89  E-value: 3.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1368 FTDGSSTGMAAYtLTDTTIKF-----QTNLNSAQLvELQALIAVLSAFPNQPLN----IYTDS----AYLAH-----SIP 1429
Cdd:cd09275    3 FTDASLSGWGAY-LLNSRAHGpwsadERNKHINLL-ELKAVLLALQHFAAELKNrkilIRTDNttavAYINKqggtsSPP 80

                         90       100
                 ....*....|....*....|....*....
gi 9627214  1430 LLETVAQIKHISETAKLFLQCQQL--IYN 1456
Cdd:cd09275   81 LLALARQILLWCEQRNIWLRASHIpgVLN 109
ZnF_C2HC smart00343
zinc finger;
548-562 4.91e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.96  E-value: 4.91e-04
                            10
                    ....*....|....*
gi 9627214      548 CCFKCGKKGHFAKNC 562
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 542-594 2.49e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 2.49e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627214    542 NKEKGGC----CFKCGKKGHFAKNCHEHAHNNAEPKvpgLCPRCKRGKHWANECKSK 594
Cdd:PTZ00368   95 NRAKGGAarraCYNCGGEGHISRDCPNAGKRPGGDK---TCYNCGQTGHLSRDCPDK 148
dut PRK13956
dUTP diphosphatase;
640-757 2.64e-03

dUTP diphosphatase;


Pssm-ID: 184417 [Multi-domain]  Cd Length: 147  Bit Score: 40.16  E-value: 2.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    640 RATPGSAGLDLCSTSHTVLTPemGPQAL-STGIYGPLPPNTFGLILGRSS-ITMKGLQVYP--GVIDNDYTG----EIKI 711
Cdd:PRK13956   21 RETAHAAGYDLKVAERTVIAP--GEIKLvPTGVKAYMQPGEVLYLYDRSSnPRKKGLVLINsvGVIDGDYYGnpanEGHI 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 9627214    712 MAKAVN---NIVTVSQGNRIAQLILLPLIETDNKVQQPYRgQGSFGSSD 757
Cdd:PRK13956   99 FAQMKNitdQEVVLEVGERIVQGVFMPFLIADGDQADGER-TGGFGSTG 146
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 549-562 3.47e-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: 36.35  E-value: 3.47e-03
                           10
                   ....*....|....
gi 9627214     549 CFKCGKKGHFAKNC 562
Cdd:pfam00098    3 CYNCGEPGHIARDC 16
transpos_ISNCY_2 NF033594
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ...
 1556-1660 4.47e-03

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


Pssm-ID: 468103 [Multi-domain]  Cd Length: 367  Bit Score: 41.31  E-value: 4.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214   1556 MIWQMDVTHYSEFGNLK---YIHVSID----------------TFSGFllatlqtgETTKHVITHllHcfsiiGLPKQIK 1616
Cdd:NF033594  128 ELIQIDGSPHDWFEGRGpkcTLLVAIDdatgrlmglrfvesesTFGYF--------EVTRQYLEK--H-----GKPVAFY 192

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627214   1617 TDNGP--------------GYTskNFQEFCSTLQIKHITGipYNPQGQGIVERAHLSL 1660
Cdd:NF033594  193 SDKHSvfrvneeelagkgdGLT--QFGRALKELGIEIICA--NSPQAKGRVERANQTL 246
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1367-1488 4.73e-03

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: 38.83  E-value: 4.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1367 VFTDGSSTGM-----AAYTLTDTTIKFQ------TNLNSAQLVELQALIAVL---SAFPNQPLNIYTDSAYLahsIPLLE 1432
Cdd:cd06222    1 INVDGSCRGNpgpagIGGVLRDHEGGWLggfalkIGAPTALEAELLALLLALelaLDLGYLKVIIESDSKYV---VDLIN 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627214  1433 TvaQIKHISETAKLFLQCQQ-LIYNRSIPFYigHVrahsglPGPiaqGNQRADLATK 1488
Cdd:cd06222   78 S--GSFKWSPNILLIEDILLlLSRFWSVKIS--HV------PRE---GNQVADALAK 121
PHA03131 PHA03131
dUTPase; Provisional
 643-734 6.25e-03

dUTPase; Provisional


Pssm-ID: 222996 [Multi-domain]  Cd Length: 286  Bit Score: 40.75  E-value: 6.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214    643 PGSAGLDLCSTSHTVLTPEmgpQALSTGIYGPLP---PNTFGLILGRSSITMKGLQVYPGVIDND--------YTGEiki 711
Cdd:PHA03131  130 PDDAGFDVSLPQDLVIFPT---TTFTFTLSLCCPpisPHFVPVIFGRSGLASKGLTVKPTKWRRSglqlklynYTDE--- 203

                          90       100
                  ....*....|....*....|...
gi 9627214    712 makavnnIVTVSQGNRIAQLILL 734
Cdd:PHA03131  204 -------TIFLPAGSRICQVVFM 219
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1367-1488 9.21e-03

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: 38.35  E-value: 9.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627214  1367 VFTDGSST------GMAAYTlTDTTIKFQTNLNSAQLV---ELQAL-----IAVLSAFPNQPLNIYTDSAylahsiplle 1432
Cdd:cd09276    2 IYTDGSKLegsvgaGFVIYR-GGEVISRSYRLGTHASVfdaELEAIlealeLALATARRARKVTIFTDSQ---------- 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9627214  1433 tvAQIKHISETAK--------LFLQCQQLIYNRSIPFYIGHVRAHSGLPgpiaqGNQRADLATK 1488
Cdd:cd09276   71 --SALQALRNPRRssgqviliRILRLLRLLKAKGVKVRLRWVPGHVGIE-----GNEAADRLAK 127
 
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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