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Conserved domains on  [gi|5802814|gb|AAD51793|]
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Gag-Pro-Pol-Env protein [Homo sapiens]

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 ...
 956-1168 1.37e-131

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: 410.91  E-value: 1.37e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   956 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNALIQPMGPLQPGLPSPAMI 1035
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1036 PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYI 1115
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1116 IHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQI 1168
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
HERV-K_env_2 pfam13804
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ...
 1798-1966 1.43e-119

Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins.


:

Pssm-ID: 290518  Cd Length: 169  Bit Score: 374.47  E-value: 1.43e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1798 PVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 1877
Cdd:pfam13804    1 AVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1878 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKKIPKESKNTEVLVWEECVDNSAVILQNNEFGTIIDWAPRGQFYHN 1957
Cdd:pfam13804   81 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 160


                   ....*....
gi 5802814    1958 CSGQTQSCP 1966
Cdd:pfam13804  161 CSGQTQSCP 169
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 306-434 1.99e-47

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: 166.30  E-value: 1.99e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     306 RYKSFSIKMLKDMKEGVKQYGPNSPYMRTLLDSIAYGHRLIPYDWEILAKSSLSPSQFLQFKTWWIDGVQEQVRRNRAAN 385
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 5802814     386 PPVNIDADQLLGIGQnWSTISQQALMQNEAIEQVRAICLRAWEKIQDPG 434
Cdd:pfam00607   81 PDRGITLDMLTGTGQ-YATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1388-1512 8.79e-40

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: 144.40  E-value: 8.79e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1388 TVFTDGSS--NGKAAYTGPkERVIKTPYQ---SAQRAELVAVITVLQDF-DQPINIISDSAYVVQATRDVETALIKYSM- 1460
Cdd:cd09273    1 TVFTDGSSfkAGYAIVSGT-EIVEAQPLPpgtSAQRAELIALIQALELAkGKPVNIYTDSAYAVHALHLLETIGIERGFl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1461 -DDQLNQLFNLLQQTVrKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSAL 1512
Cdd:cd09273   80 kSIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 785-884 1.87e-39

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: 142.51  E-value: 1.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     785 SENRPVCKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVTGLVGIGTASEVYQSTEILHCLGPDNQESTVQPMIT 864
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|.
gi 5802814     865 S-IPLNLWGRDLLQQWGAEIT 884
Cdd:pfam00077   81 PtCPVNIIGRDLLQQLGGRLT 101
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1175-1240 1.57e-33

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: 124.35  E-value: 1.57e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5802814    1175 PQKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRILTPEATKEIK 1240
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 11-93 6.46e-33

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: 123.22  E-value: 6.46e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814      11 KYASYLSFIKILLKRGGVKVSTKNLIKLFQIIEQFCPWFPEQGTLDLKDWKRIGKELK-QAGRKG-NIIPLTVWNDWAII 88
Cdd:pfam02337    1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKtQATEHGpKNIPVDTWPIWALI 80


                   ....*
gi 5802814      89 KAALE 93
Cdd:pfam02337   81 RAVLD 85
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 434-512 1.16e-32

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: 122.20  E-value: 1.16e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 5802814     434 GSTCPSFNTVRQGSKEPYPDFVARLQDVAQKSIADEKAHKVIVELMAYENANPECQSAIKPLKGKvpagsDVISEYVKA 512
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-----GTLSDMIRA 74
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1569-1662 1.53e-27

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: 108.17  E-value: 1.53e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1569 PNALWQMDVTHVPSF--GRLSYVHVTVDTYSHFIWATCQTGE-STSHVKKHLLSCFAVMG-VPEKIKTDNGPGYCSKAFQ 1644
Cdd:pfam00665    1 PNQLWQGDFTYIRIPggGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 5802814    1645 KFLSQWKISHTTGIPYNS 1662
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 2184-2278 1.98e-27

heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic.


:

Pssm-ID: 197369  Cd Length: 128  Bit Score: 109.02  E-value: 1.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  2184 VNDWQKNSTRLWNSQSSIDQ--KLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTsDFCITPQIYNESEHHWDMVRRH 2261
Cdd:cd09909    1 VQARQLLVTRVQQQQSLIDAieKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNL-WGCVTKQPYCHTDVPWNRSWNH 79

                         90
                 ....*....|....*..
gi 5802814  2262 LQGREDNLTLDISKIKR 2278
Cdd:cd09909   80 LQGNDNWISLTWQEWEN 96
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 667-751 4.43e-20

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: 86.78  E-value: 4.43e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   667 VDLC---TIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLKGVQIHTS-VVDSDYKGEIQLVIS--SSIPWSA 740
Cdd:cd07557    3 YDLRlgeDFEGIVLPPGET-VLVPTGEAIELPEGYVGLVFPRSSLARKGITVHNAgVIDPGYRGEITLELYnlGPEPVVI 81

                         90
                 ....*....|.
gi 5802814   741 SPGDRIAQLLL 751
Cdd:cd07557   82 KKGDRIAQLVF 92
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
578-613 7.52e-17

GAG-polyprotein viral zinc-finger;


:

Pssm-ID: 373297  Cd Length: 36  Bit Score: 75.67  E-value: 7.52e-17
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 5802814     578 PPDLCPRCKKGKHWASQCRSKFDKNGQPLSGNEQRG 613
Cdd:pfam14787    1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1517-1552 7.79e-14

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: 67.01  E-value: 7.79e-14
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 5802814    1517 ELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQV 1552
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 890-934 1.28e-13

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: 66.76  E-value: 1.28e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 5802814     890 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQEREGIGYP 934
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
PRK10263 super family cl35903
DNA translocase FtsK; Provisional
 172-313 1.78e-07

DNA translocase FtsK; Provisional


The actual alignment was detected with superfamily member PRK10263:

Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 57.02  E-value: 1.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    172 GPSES--KPrGTSPLPAGQVPVRLQPQKQVKENKTQPPVAY----QYWPPAElQYRPP-----PESQYGYPGMPPAPQGR 240
Cdd:PRK10263  739 GPHEPlfTP-IVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYqqpqQPVAPQP-QYQQPqqpvaPQPQYQQPQQPVAPQPQ 816

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    241 APYP------QPPTRRLNPTAPPSRQGSELHEIIdksRKEGDTEAWQFPITLEPM------PPGE------GAQEGEPPT 302
Cdd:PRK10263  817 YQQPqqpvapQPQYQQPQQPVAPQPQDTLLHPLL---MRNGDSRPLHKPTTPLPSldlltpPPSEvepvdtFALEQMARL 893

                         170
                  ....*....|.
gi 5802814    303 VEARYKSFSIK 313
Cdd:PRK10263  894 VEARLADFRIK 904
AIR1 super family cl34894
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 545-601 9.19e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


The actual alignment was detected with superfamily member COG5082:

Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 48.69  E-value: 9.19e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814   545 KCYNCGQIGHLKKNCPVLNKQNITIQATTTGREP-PDLCPRCKKGKHWASQCRSKFDK 601
Cdd:COG5082   62 VCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPkPKKCYNCGETGHLSRDCNPSKDQ 119
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1738-1778 2.77e-03

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.


The actual alignment was detected with superfamily member pfam00552:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 37.76  E-value: 2.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 5802814    1738 WKDNKNKTWE-IGKVITWGRGFACVsPGENQLPVWLPTRHLK 1778
Cdd:pfam00552    3 WKDLLNGLWKgPDPLLWWGRGAVCV-PQDASDPQWVPERLLK 43
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 956-1168 1.37e-131

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: 410.91  E-value: 1.37e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   956 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNALIQPMGPLQPGLPSPAMI 1035
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1036 PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYI 1115
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1116 IHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQI 1168
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
HERV-K_env_2 pfam13804
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ...
 1798-1966 1.43e-119

Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins.


Pssm-ID: 290518  Cd Length: 169  Bit Score: 374.47  E-value: 1.43e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1798 PVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 1877
Cdd:pfam13804    1 AVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1878 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKKIPKESKNTEVLVWEECVDNSAVILQNNEFGTIIDWAPRGQFYHN 1957
Cdd:pfam13804   81 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 160


                   ....*....
gi 5802814    1958 CSGQTQSCP 1966
Cdd:pfam13804  161 CSGQTQSCP 169
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 306-434 1.99e-47

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: 166.30  E-value: 1.99e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     306 RYKSFSIKMLKDMKEGVKQYGPNSPYMRTLLDSIAYGHRLIPYDWEILAKSSLSPSQFLQFKTWWIDGVQEQVRRNRAAN 385
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 5802814     386 PPVNIDADQLLGIGQnWSTISQQALMQNEAIEQVRAICLRAWEKIQDPG 434
Cdd:pfam00607   81 PDRGITLDMLTGTGQ-YATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 999-1168 7.81e-46

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: 164.01  E-value: 7.81e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     999 IQKKS-GKWRML----TDLRAVNALIQP-------MGPLQPGLPSPAM-IPKDWPLIIIDLKDCFFTIPLAEQDCEKFAF 1065
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1066 TIPAINNK----EPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFsDCYIIHYIDDILCAAETKDKLIDCYTFLQA 1141
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 5802814    1142 EVANAGLAIASDKIQ---TSTPFHYLGMQI 1168
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 ...
 1388-1512 8.79e-40

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: 144.40  E-value: 8.79e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1388 TVFTDGSS--NGKAAYTGPkERVIKTPYQ---SAQRAELVAVITVLQDF-DQPINIISDSAYVVQATRDVETALIKYSM- 1460
Cdd:cd09273    1 TVFTDGSSfkAGYAIVSGT-EIVEAQPLPpgtSAQRAELIALIQALELAkGKPVNIYTDSAYAVHALHLLETIGIERGFl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1461 -DDQLNQLFNLLQQTVrKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSAL 1512
Cdd:cd09273   80 kSIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 785-884 1.87e-39

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: 142.51  E-value: 1.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     785 SENRPVCKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVTGLVGIGTASEVYQSTEILHCLGPDNQESTVQPMIT 864
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|.
gi 5802814     865 S-IPLNLWGRDLLQQWGAEIT 884
Cdd:pfam00077   81 PtCPVNIIGRDLLQQLGGRLT 101
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1175-1240 1.57e-33

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: 124.35  E-value: 1.57e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5802814    1175 PQKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRILTPEATKEIK 1240
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 11-93 6.46e-33

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: 123.22  E-value: 6.46e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814      11 KYASYLSFIKILLKRGGVKVSTKNLIKLFQIIEQFCPWFPEQGTLDLKDWKRIGKELK-QAGRKG-NIIPLTVWNDWAII 88
Cdd:pfam02337    1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKtQATEHGpKNIPVDTWPIWALI 80


                   ....*
gi 5802814      89 KAALE 93
Cdd:pfam02337   81 RAVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 434-512 1.16e-32

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: 122.20  E-value: 1.16e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 5802814     434 GSTCPSFNTVRQGSKEPYPDFVARLQDVAQKSIADEKAHKVIVELMAYENANPECQSAIKPLKGKvpagsDVISEYVKA 512
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-----GTLSDMIRA 74
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 791-877 4.05e-30

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: 115.06  E-value: 4.05e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   791 CKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVTGLVGIGTASEVYQST-EILHCLGpDNQESTVQPMITSIPLN 869
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSvLLLEIDG-EGHLGTILVYVLSLPVN 79


                 ....*...
gi 5802814   870 LWGRDLLQ 877
Cdd:cd05482   80 LWGRDILS 87
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1384-1513 1.87e-28

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: 112.47  E-value: 1.87e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1384 ENALTVFTDGSSN-----GKAAYTGPKERV-IKTPY---QSAQRAELVAVITVLQD--FDQPINIISDSAYVVQ-ATRDV 1451
Cdd:pfam00075    1 PKAVTVYTDGSCLgnpgpGGAGAVLYRGHEnISAPLpgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGgITQWV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 5802814    1452 ETAlIKYSMDDQLNQ-------LFNLLQQTVRKRNfpFYITHIRAHTNLPGpltkaNEQADLLVSSALI 1513
Cdd:pfam00075   81 HGW-KKNGWPTTSEGkpvknkdLWQLLKALCKKHQ--VYWQWVKGHAGNPG-----NEMADRLAKQGAE 141
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1569-1662 1.53e-27

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: 108.17  E-value: 1.53e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1569 PNALWQMDVTHVPSF--GRLSYVHVTVDTYSHFIWATCQTGE-STSHVKKHLLSCFAVMG-VPEKIKTDNGPGYCSKAFQ 1644
Cdd:pfam00665    1 PNQLWQGDFTYIRIPggGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 5802814    1645 KFLSQWKISHTTGIPYNS 1662
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 2184-2278 1.98e-27

heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic.


Pssm-ID: 197369  Cd Length: 128  Bit Score: 109.02  E-value: 1.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  2184 VNDWQKNSTRLWNSQSSIDQ--KLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTsDFCITPQIYNESEHHWDMVRRH 2261
Cdd:cd09909    1 VQARQLLVTRVQQQQSLIDAieKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNL-WGCVTKQPYCHTDVPWNRSWNH 79

                         90
                 ....*....|....*..
gi 5802814  2262 LQGREDNLTLDISKIKR 2278
Cdd:cd09909   80 LQGNDNWISLTWQEWEN 96
transpos_IS481 NF033577
IS481 family transposase; null
 1569-1690 4.29e-21

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 95.74  E-value: 4.29e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1569 PNALWQMDVTHVPSF---GRLsYVHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVP-EKIKTDNGPGYCSKA-- 1642
Cdd:NF033577  127 PGELWHIDIKKLGRIpdvGRL-YLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTDNGSEFRSRAhg 205

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 5802814   1643 FQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKE 1690
Cdd:NF033577  206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAE 253
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 667-751 4.43e-20

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: 86.78  E-value: 4.43e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   667 VDLC---TIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLKGVQIHTS-VVDSDYKGEIQLVIS--SSIPWSA 740
Cdd:cd07557    3 YDLRlgeDFEGIVLPPGET-VLVPTGEAIELPEGYVGLVFPRSSLARKGITVHNAgVIDPGYRGEITLELYnlGPEPVVI 81

                         90
                 ....*....|.
gi 5802814   741 SPGDRIAQLLL 751
Cdd:cd07557   82 KKGDRIAQLVF 92
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 668-754 4.23e-19

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 85.42  E-value: 4.23e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     668 DLCTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLKGVQIHTSVVDSDYKGEIQLVI--SSSIPWSASPGDR 745
Cdd:pfam00692   17 DLYAPYDLTVKPGGT-VLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLfnLGKSDFTIKKGDR 95


                   ....*....
gi 5802814     746 IAQLLLLPY 754
Cdd:pfam00692   96 IAQLIFEPI 104
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1569-1684 7.17e-18

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 86.75  E-value: 7.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1569 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTgESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 1644
Cdd:COG2801  148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSREIvgWSVSDS-MDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQ 226

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 5802814  1645 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKE 1684
Cdd:COG2801  227 ELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRR 266
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
578-613 7.52e-17

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 75.67  E-value: 7.52e-17
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 5802814     578 PPDLCPRCKKGKHWASQCRSKFDKNGQPLSGNEQRG 613
Cdd:pfam14787    1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
transpos_IS3 NF033516
IS3 family transposase;
1569-1683 2.02e-15

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 80.30  E-value: 2.02e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1569 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATcQTGESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 1644
Cdd:NF033516  215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSREIvgWSV-STSMSAELVLDALEMAIEWRGKPEGliLHSDNGSQYTSKAYR 293

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 5802814   1645 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQK 1683
Cdd:NF033516  294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRR 332
dut PRK00601
dUTP diphosphatase;
651-771 5.91e-14

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 71.35  E-value: 5.91e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    651 LPQYnncPSPQAAvqQVDL--CTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTSV--VDSDYK 725
Cdd:PRK00601   19 LPAY---ATEGSA--GLDLraCLDEPVTLAPGER-ALVPTGLAIHIPDGYEAQILPRSGLAHKhGIVLGNLPgtIDSDYR 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 5802814    726 GEIQ-LVIS-SSIPWSASPGDRIAQLLLLPYIKGGNSELKKI-------GGLGST 771
Cdd:PRK00601   93 GELKvSLWNrGQEPFTIEPGERIAQLVIVPVVQAEFEEVEEFdetergaGGFGST 147
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 650-771 6.33e-14

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: 70.82  E-value: 6.33e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   650 QLPQYNncpSPQAAvqQVDL--CTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTSV--VDSDY 724
Cdd:COG0756   12 PLPAYA---TPGSA--GLDLraALDEPVTLKPGER-ALVPTGLAIALPPGYEAQVRPRSGLALKhGITLLNSPgtIDSDY 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814   725 KGEIQlVI---SSSIPWSASPGDRIAQLLLLPYIKG--------GNSElKKIGGLGST 771
Cdd:COG0756   86 RGEIK-VIlinLGDEPFTIERGDRIAQLVIAPVVQAefeeveelDETE-RGAGGFGST 141
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 668-771 6.53e-14

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: 70.73  E-value: 6.53e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     668 DLCTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTS--VVDSDYKGEIQ--LVISSSIPWSASP 742
Cdd:TIGR00576   25 DLRAAEDVTIPPGER-ALVPTGIAIELPDGYYGRVAPRSGLALKhGVTIDNSpgVIDADYRGEIKviLINLGKEDFTVKK 103

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 5802814     743 GDRIAQLLLLPYIKGGNSELKKI--------GGLGST 771
Cdd:TIGR00576  104 GDRIAQLVVEKIVTEVEFEEVEEldetergeGGFGST 140
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1517-1552 7.79e-14

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: 67.01  E-value: 7.79e-14
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 5802814    1517 ELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQV 1552
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 890-934 1.28e-13

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: 66.76  E-value: 1.28e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 5802814     890 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQEREGIGYP 934
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 2177-2276 1.26e-11

Retroviral envelope protein; This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs).


Pssm-ID: 395415  Cd Length: 197  Bit Score: 65.77  E-value: 1.26e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    2177 SVQSVNFVNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQIYNESEhHWD 2256
Cdd:pfam00517    9 SIQAATLVDGLQYNVTKVMGTQQDIDKKLEARLSALEDVVRVLGEQVQSLKFRMKLQCHANYKWICVTKVPYNASD-PWD 87

                           90       100
                   ....*....|....*....|..
gi 5802814    2257 MVRRHLQG--REDNLTLDISKI 2276
Cdd:pfam00517   88 KVKKHLQGiwNNTEVSYDLLQL 109
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 890-933 1.79e-11

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: 60.64  E-value: 1.79e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 5802814      890 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQEREGIGY 933
Cdd:smart00443    3 TSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1385-1512 1.00e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 52.92  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1385 NALTVFTDGSSN---GKAAY-----TGPKERVIKTPYQSA--QRAELVAVITVLQ----DFDQPINIISDSAYVVQATRD 1450
Cdd:COG0328    1 KMIEIYTDGACRgnpGPGGWgavirYGGEEKELSGGLGDTtnNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITG 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1451 VETALIKYSMDDQLNQ-LFNLLQQTVRKRNFPFyiTHIRAHTNLPGpltkaNEQADLLVSSAL 1512
Cdd:COG0328   81 WIHGWKKNGWKPVKNPdLWQRLDELLARHKVTF--EWVKGHAGHPG-----NERADALANKAL 136
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 172-313 1.78e-07

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 57.02  E-value: 1.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    172 GPSES--KPrGTSPLPAGQVPVRLQPQKQVKENKTQPPVAY----QYWPPAElQYRPP-----PESQYGYPGMPPAPQGR 240
Cdd:PRK10263  739 GPHEPlfTP-IVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYqqpqQPVAPQP-QYQQPqqpvaPQPQYQQPQQPVAPQPQ 816

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    241 APYP------QPPTRRLNPTAPPSRQGSELHEIIdksRKEGDTEAWQFPITLEPM------PPGE------GAQEGEPPT 302
Cdd:PRK10263  817 YQQPqqpvapQPQYQQPQQPVAPQPQDTLLHPLL---MRNGDSRPLHKPTTPLPSldlltpPPSEvepvdtFALEQMARL 893

                         170
                  ....*....|.
gi 5802814    303 VEARYKSFSIK 313
Cdd:PRK10263  894 VEARLADFRIK 904
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1569-1743 5.29e-07

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 53.72  E-value: 5.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1569 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTGESTsHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 1644
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIvgWRVSSSMDTD-FVLDALEQALWARGRPGGliHHSDKGSQYVSLAYT 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1645 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKEcttpqmqlnLALYTLNFLNIYRNQTTTSAEQHLT 1724
Cdd:PHA02517  188 QRLKEAGIRASTGSRGDSYDNAPAESINGLYKAEVIHRVSWKNREE---------VELATLEWVAWYNNRRLHERLGYTP 258

                         170
                  ....*....|....*....
gi 5802814   1725 gkknsPHEGKLIWWKDNKN 1743
Cdd:PHA02517  259 -----PAEAEKAYYASIGN 272
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 545-601 9.19e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 48.69  E-value: 9.19e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814   545 KCYNCGQIGHLKKNCPVLNKQNITIQATTTGREP-PDLCPRCKKGKHWASQCRSKFDK 601
Cdd:COG5082   62 VCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPkPKKCYNCGETGHLSRDCNPSKDQ 119
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 544-560 6.35e-05

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: 41.74  E-value: 6.35e-05
                           10
                   ....*....|....*..
gi 5802814     544 GKCYNCGQIGHLKKNCP 560
Cdd:pfam00098    1 GKCYNCGEPGHIARDCP 17
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 117-305 8.00e-05

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 47.75  E-value: 8.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   117 ENTRKKSQKETESLHCEYVAEPVMAQSTQNVDYNQLQEVIYPETLKLEGKGPELVGPSESKPRGTSPLPAGQVPVRLQP- 195
Cdd:COG5180  216 DLTGGADHPRPEAASSPKVDPPSTSEARSRPATVDAQPEMRPPADAKERRRAAIGDTPAAEPPGLPVLEAGSEPQSDAPe 295

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   196 -----QKQVKENKTQPPVAYQYWPPAEL--QYRPPPESQYGYP-GMPPApqgRAPYPQPPT-----RRLNPTAP-----P 257
Cdd:COG5180  296 aetarPIDVKGVASAPPATRPVRPPGGArdPGTPRPGQPTERPaGVPEA---ASDAGQPPSayppaEEAVPGKPleqgaP 372

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814   258 SRQGSELHEIIDKSRKEGDTEAWQFPITL-EPMPPGEGAQ----EGEPPTVEA 305
Cdd:COG5180  373 RPGSSGGDGAPFQPPNGAPQPGLGRRGAPgPPMGAGDLVQaaldGGGRETASL 425
ZnF_C2HC smart00343
zinc finger;
545-560 3.17e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 3.17e-04
                            10
                    ....*....|....*.
gi 5802814      545 KCYNCGQIGHLKKNCP 560
Cdd:smart00343    1 KCYNCGKEGHIARDCP 16
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 544-598 7.18e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.10  E-value: 7.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 5802814    544 GKCYNCGQIGHLKKNCPvlnkqnitiQATTTGREpPDLCPRCKKGKHWASQCRSK 598
Cdd:PTZ00368  104 RACYNCGGEGHISRDCP---------NAGKRPGG-DKTCYNCGQTGHLSRDCPDK 148
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1738-1778 2.77e-03

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: 37.76  E-value: 2.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 5802814    1738 WKDNKNKTWE-IGKVITWGRGFACVsPGENQLPVWLPTRHLK 1778
Cdd:pfam00552    3 WKDLLNGLWKgPDPLLWWGRGAVCV-PQDASDPQWVPERLLK 43
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 956-1168 1.37e-131

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: 410.91  E-value: 1.37e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   956 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNALIQPMGPLQPGLPSPAMI 1035
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1036 PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYI 1115
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1116 IHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQI 1168
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
HERV-K_env_2 pfam13804
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ...
 1798-1966 1.43e-119

Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins.


Pssm-ID: 290518  Cd Length: 169  Bit Score: 374.47  E-value: 1.43e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1798 PVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 1877
Cdd:pfam13804    1 AVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1878 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKKIPKESKNTEVLVWEECVDNSAVILQNNEFGTIIDWAPRGQFYHN 1957
Cdd:pfam13804   81 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 160


                   ....*....
gi 5802814    1958 CSGQTQSCP 1966
Cdd:pfam13804  161 CSGQTQSCP 169
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 306-434 1.99e-47

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: 166.30  E-value: 1.99e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     306 RYKSFSIKMLKDMKEGVKQYGPNSPYMRTLLDSIAYGHRLIPYDWEILAKSSLSPSQFLQFKTWWIDGVQEQVRRNRAAN 385
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 5802814     386 PPVNIDADQLLGIGQnWSTISQQALMQNEAIEQVRAICLRAWEKIQDPG 434
Cdd:pfam00607   81 PDRGITLDMLTGTGQ-YATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 999-1168 7.81e-46

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: 164.01  E-value: 7.81e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     999 IQKKS-GKWRML----TDLRAVNALIQP-------MGPLQPGLPSPAM-IPKDWPLIIIDLKDCFFTIPLAEQDCEKFAF 1065
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1066 TIPAINNK----EPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFsDCYIIHYIDDILCAAETKDKLIDCYTFLQA 1141
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 5802814    1142 EVANAGLAIASDKIQ---TSTPFHYLGMQI 1168
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 ...
 1388-1512 8.79e-40

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: 144.40  E-value: 8.79e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1388 TVFTDGSS--NGKAAYTGPkERVIKTPYQ---SAQRAELVAVITVLQDF-DQPINIISDSAYVVQATRDVETALIKYSM- 1460
Cdd:cd09273    1 TVFTDGSSfkAGYAIVSGT-EIVEAQPLPpgtSAQRAELIALIQALELAkGKPVNIYTDSAYAVHALHLLETIGIERGFl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1461 -DDQLNQLFNLLQQTVrKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSAL 1512
Cdd:cd09273   80 kSIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 785-884 1.87e-39

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: 142.51  E-value: 1.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     785 SENRPVCKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVTGLVGIGTASEVYQSTEILHCLGPDNQESTVQPMIT 864
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|.
gi 5802814     865 S-IPLNLWGRDLLQQWGAEIT 884
Cdd:pfam00077   81 PtCPVNIIGRDLLQQLGGRLT 101
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 956-1168 1.12e-35

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: 135.94  E-value: 1.12e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   956 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSG-KWRMLTDLRAVNaliQPMGPLQPGLPSPAM 1034
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVN---QAVLPIHPAVPNPYT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1035 I-----PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAinnkepaTRFQWKVLPQGMLNSPTICQTFVGRALQPVREK 1109
Cdd:cd03715   78 LlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG-------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLE 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1110 FSDCYIIHYIDDILCAAETKDKLIDCYTFLQAEVANAGLAIASDKIQ-TSTPFHYLGMQI 1168
Cdd:cd03715  151 HEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQiCRAEVKFLGVVW 210
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1175-1240 1.57e-33

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: 124.35  E-value: 1.57e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5802814    1175 PQKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRILTPEATKEIK 1240
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 11-93 6.46e-33

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: 123.22  E-value: 6.46e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814      11 KYASYLSFIKILLKRGGVKVSTKNLIKLFQIIEQFCPWFPEQGTLDLKDWKRIGKELK-QAGRKG-NIIPLTVWNDWAII 88
Cdd:pfam02337    1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKtQATEHGpKNIPVDTWPIWALI 80


                   ....*
gi 5802814      89 KAALE 93
Cdd:pfam02337   81 RAVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 434-512 1.16e-32

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: 122.20  E-value: 1.16e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 5802814     434 GSTCPSFNTVRQGSKEPYPDFVARLQDVAQKSIADEKAHKVIVELMAYENANPECQSAIKPLKGKvpagsDVISEYVKA 512
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-----GTLSDMIRA 74
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 791-877 4.05e-30

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: 115.06  E-value: 4.05e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   791 CKAIIQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVTGLVGIGTASEVYQST-EILHCLGpDNQESTVQPMITSIPLN 869
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSvLLLEIDG-EGHLGTILVYVLSLPVN 79


                 ....*...
gi 5802814   870 LWGRDLLQ 877
Cdd:cd05482   80 LWGRDILS 87
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1384-1513 1.87e-28

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: 112.47  E-value: 1.87e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1384 ENALTVFTDGSSN-----GKAAYTGPKERV-IKTPY---QSAQRAELVAVITVLQD--FDQPINIISDSAYVVQ-ATRDV 1451
Cdd:pfam00075    1 PKAVTVYTDGSCLgnpgpGGAGAVLYRGHEnISAPLpgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGgITQWV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 5802814    1452 ETAlIKYSMDDQLNQ-------LFNLLQQTVRKRNfpFYITHIRAHTNLPGpltkaNEQADLLVSSALI 1513
Cdd:pfam00075   81 HGW-KKNGWPTTSEGkpvknkdLWQLLKALCKKHQ--VYWQWVKGHAGNPG-----NEMADRLAKQGAE 141
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1569-1662 1.53e-27

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: 108.17  E-value: 1.53e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    1569 PNALWQMDVTHVPSF--GRLSYVHVTVDTYSHFIWATCQTGE-STSHVKKHLLSCFAVMG-VPEKIKTDNGPGYCSKAFQ 1644
Cdd:pfam00665    1 PNQLWQGDFTYIRIPggGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 5802814    1645 KFLSQWKISHTTGIPYNS 1662
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 2184-2278 1.98e-27

heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic.


Pssm-ID: 197369  Cd Length: 128  Bit Score: 109.02  E-value: 1.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  2184 VNDWQKNSTRLWNSQSSIDQ--KLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTsDFCITPQIYNESEHHWDMVRRH 2261
Cdd:cd09909    1 VQARQLLVTRVQQQQSLIDAieKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNL-WGCVTKQPYCHTDVPWNRSWNH 79

                         90
                 ....*....|....*..
gi 5802814  2262 LQGREDNLTLDISKIKR 2278
Cdd:cd09909   80 LQGNDNWISLTWQEWEN 96
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 983-1130 1.14e-26

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: 108.84  E-value: 1.14e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   983 GHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNALIQPM-GPlqpgLPSP----AMIPKDWPLIIIDLKDCFFTIPLAE 1057
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDrYP----LPTIdellEELAGAKVFSKLDLRSGYHQIPLAE 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1058 QDCEKFAFTIpainnkePATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFsdcyIIHYIDDILCAAETKD 1130
Cdd:cd01647   77 ESRPKTAFRT-------PFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF----VEVYLDDILVYSKTEE 138
transpos_IS481 NF033577
IS481 family transposase; null
 1569-1690 4.29e-21

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 95.74  E-value: 4.29e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1569 PNALWQMDVTHVPSF---GRLsYVHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVP-EKIKTDNGPGYCSKA-- 1642
Cdd:NF033577  127 PGELWHIDIKKLGRIpdvGRL-YLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTDNGSEFRSRAhg 205

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 5802814   1643 FQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKE 1690
Cdd:NF033577  206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAE 253
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 667-751 4.43e-20

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: 86.78  E-value: 4.43e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   667 VDLC---TIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLKGVQIHTS-VVDSDYKGEIQLVIS--SSIPWSA 740
Cdd:cd07557    3 YDLRlgeDFEGIVLPPGET-VLVPTGEAIELPEGYVGLVFPRSSLARKGITVHNAgVIDPGYRGEITLELYnlGPEPVVI 81

                         90
                 ....*....|.
gi 5802814   741 SPGDRIAQLLL 751
Cdd:cd07557   82 KKGDRIAQLVF 92
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 668-754 4.23e-19

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 85.42  E-value: 4.23e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     668 DLCTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLKGVQIHTSVVDSDYKGEIQLVI--SSSIPWSASPGDR 745
Cdd:pfam00692   17 DLYAPYDLTVKPGGT-VLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLfnLGKSDFTIKKGDR 95


                   ....*....
gi 5802814     746 IAQLLLLPY 754
Cdd:pfam00692   96 IAQLIFEPI 104
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1569-1684 7.17e-18

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 86.75  E-value: 7.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1569 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTgESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 1644
Cdd:COG2801  148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSREIvgWSVSDS-MDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQ 226

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 5802814  1645 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKE 1684
Cdd:COG2801  227 ELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRR 266
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
578-613 7.52e-17

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 75.67  E-value: 7.52e-17
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 5802814     578 PPDLCPRCKKGKHWASQCRSKFDKNGQPLSGNEQRG 613
Cdd:pfam14787    1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
transpos_IS3 NF033516
IS3 family transposase;
1569-1683 2.02e-15

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 80.30  E-value: 2.02e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1569 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATcQTGESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 1644
Cdd:NF033516  215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSREIvgWSV-STSMSAELVLDALEMAIEWRGKPEGliLHSDNGSQYTSKAYR 293

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 5802814   1645 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQK 1683
Cdd:NF033516  294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRR 332
dut PRK00601
dUTP diphosphatase;
651-771 5.91e-14

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 71.35  E-value: 5.91e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    651 LPQYnncPSPQAAvqQVDL--CTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTSV--VDSDYK 725
Cdd:PRK00601   19 LPAY---ATEGSA--GLDLraCLDEPVTLAPGER-ALVPTGLAIHIPDGYEAQILPRSGLAHKhGIVLGNLPgtIDSDYR 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 5802814    726 GEIQ-LVIS-SSIPWSASPGDRIAQLLLLPYIKGGNSELKKI-------GGLGST 771
Cdd:PRK00601   93 GELKvSLWNrGQEPFTIEPGERIAQLVIVPVVQAEFEEVEEFdetergaGGFGST 147
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 650-771 6.33e-14

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: 70.82  E-value: 6.33e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   650 QLPQYNncpSPQAAvqQVDL--CTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTSV--VDSDY 724
Cdd:COG0756   12 PLPAYA---TPGSA--GLDLraALDEPVTLKPGER-ALVPTGLAIALPPGYEAQVRPRSGLALKhGITLLNSPgtIDSDY 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814   725 KGEIQlVI---SSSIPWSASPGDRIAQLLLLPYIKG--------GNSElKKIGGLGST 771
Cdd:COG0756   86 RGEIK-VIlinLGDEPFTIERGDRIAQLVIAPVVQAefeeveelDETE-RGAGGFGST 141
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 668-771 6.53e-14

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: 70.73  E-value: 6.53e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814     668 DLCTIQAVSLLPGEPpQKIPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTS--VVDSDYKGEIQ--LVISSSIPWSASP 742
Cdd:TIGR00576   25 DLRAAEDVTIPPGER-ALVPTGIAIELPDGYYGRVAPRSGLALKhGVTIDNSpgVIDADYRGEIKviLINLGKEDFTVKK 103

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 5802814     743 GDRIAQLLLLPYIKGGNSELKKI--------GGLGST 771
Cdd:TIGR00576  104 GDRIAQLVVEKIVTEVEFEEVEEldetergeGGFGST 140
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1517-1552 7.79e-14

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: 67.01  E-value: 7.79e-14
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 5802814    1517 ELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQV 1552
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 890-934 1.28e-13

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: 66.76  E-value: 1.28e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 5802814     890 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQEREGIGYP 934
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 2177-2276 1.26e-11

Retroviral envelope protein; This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs).


Pssm-ID: 395415  Cd Length: 197  Bit Score: 65.77  E-value: 1.26e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    2177 SVQSVNFVNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQIYNESEhHWD 2256
Cdd:pfam00517    9 SIQAATLVDGLQYNVTKVMGTQQDIDKKLEARLSALEDVVRVLGEQVQSLKFRMKLQCHANYKWICVTKVPYNASD-PWD 87

                           90       100
                   ....*....|....*....|..
gi 5802814    2257 MVRRHLQG--REDNLTLDISKI 2276
Cdd:pfam00517   88 KVKKHLQGiwNNTEVSYDLLQL 109
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 890-933 1.79e-11

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: 60.64  E-value: 1.79e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 5802814      890 YSPTSQKIMTKRGYIPGKGLGKNEDGIKIPFEAKINQEREGIGY 933
Cdd:smart00443    3 TSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1388-1507 1.84e-10

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: 61.04  E-value: 1.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1388 TVFTDGSS--NGKAA-------YTGPK------ERVIKtPYQSAQRAELVAVITVLQDFDQ----PINIISDSAYVVQA- 1447
Cdd:cd09280    1 VVYTDGSClnNGKPGaragigvYFGPGdprnvsEPLPG-RKQTNNRAELLAVIHALEQAPEegirKLEIRTDSKYAINCi 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 5802814  1448 TRDVETALIKYSMDDQLNQLFN--LLQQTV---RKRNFPFYITHIRAHTNLPGpltkaNEQADLL 1507
Cdd:cd09280   80 TKWIPKWKKNGWKTSKGKPVKNqdLIKELDkllRKRGIKVKFEHVKGHSGDPG-----NEEADRL 139
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1385-1512 1.00e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 52.92  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1385 NALTVFTDGSSN---GKAAY-----TGPKERVIKTPYQSA--QRAELVAVITVLQ----DFDQPINIISDSAYVVQATRD 1450
Cdd:COG0328    1 KMIEIYTDGACRgnpGPGGWgavirYGGEEKELSGGLGDTtnNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITG 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1451 VETALIKYSMDDQLNQ-LFNLLQQTVRKRNFPFyiTHIRAHTNLPGpltkaNEQADLLVSSAL 1512
Cdd:COG0328   81 WIHGWKKNGWKPVKNPdLWQRLDELLARHKVTF--EWVKGHAGHPG-----NERADALANKAL 136
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 172-313 1.78e-07

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 57.02  E-value: 1.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    172 GPSES--KPrGTSPLPAGQVPVRLQPQKQVKENKTQPPVAY----QYWPPAElQYRPP-----PESQYGYPGMPPAPQGR 240
Cdd:PRK10263  739 GPHEPlfTP-IVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYqqpqQPVAPQP-QYQQPqqpvaPQPQYQQPQQPVAPQPQ 816

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    241 APYP------QPPTRRLNPTAPPSRQGSELHEIIdksRKEGDTEAWQFPITLEPM------PPGE------GAQEGEPPT 302
Cdd:PRK10263  817 YQQPqqpvapQPQYQQPQQPVAPQPQDTLLHPLL---MRNGDSRPLHKPTTPLPSldlltpPPSEvepvdtFALEQMARL 893

                         170
                  ....*....|.
gi 5802814    303 VEARYKSFSIK 313
Cdd:PRK10263  894 VEARLADFRIK 904
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1044-1168 3.19e-07

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: 50.43  E-value: 3.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1044 IDLKDCFFTIPLaeqdcekfaftipainnkepatrfqwkvlPQGMLNSPTICQTFVGRALQPVREKFSDCYIIHYIDDIL 1123
Cdd:cd00304    1 FDVKSFFTSIPL-----------------------------PQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 5802814  1124 CAAETKDKLIDCYTFLQAEvANAGLAIASDKIQTST---PFHYLGMQI 1168
Cdd:cd00304   52 VIAKSEQQAVKKRELEEFL-ARLGLNLSDEKTQFTEkekKFKFLGILV 98
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1569-1743 5.29e-07

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 53.72  E-value: 5.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1569 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTGESTsHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 1644
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIvgWRVSSSMDTD-FVLDALEQALWARGRPGGliHHSDKGSQYVSLAYT 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   1645 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKEcttpqmqlnLALYTLNFLNIYRNQTTTSAEQHLT 1724
Cdd:PHA02517  188 QRLKEAGIRASTGSRGDSYDNAPAESINGLYKAEVIHRVSWKNREE---------VELATLEWVAWYNNRRLHERLGYTP 258

                         170
                  ....*....|....*....
gi 5802814   1725 gkknsPHEGKLIWWKDNKN 1743
Cdd:PHA02517  259 -----PAEAEKAYYASIGN 272
PHA03094 PHA03094
dUTPase; Provisional
 694-772 6.17e-07

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 50.92  E-value: 6.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    694 LPKGTVGLILGRSSLNLK-GVQIHTSVVDSDYKGEIQLVI--SSSIPWSASPGDRIAQLLllpYIKGGNSELKKIGGLGS 770
Cdd:PHA03094   54 IPKFCYGRIAPRSGLSLNyGIDIGGGVIDEDYRGNIGVIFinNGKCTFNIKTGDRIAQII---FERIEYPELKEVQSLDS 130


                  ..
gi 5802814    771 TD 772
Cdd:PHA03094  131 TD 132
PLN02547 PLN02547
dUTP pyrophosphatase
 686-771 6.39e-07

dUTP pyrophosphatase


Pssm-ID: 215302  Cd Length: 157  Bit Score: 51.33  E-value: 6.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    686 IPTGVYGPLPKGTVGLILGRSSLNLK-GVQIHTSVVDSDYKGEIQLVI--SSSIPWSASPGDRIAQLLLLPYIKGGNSEL 762
Cdd:PLN02547   57 VPTDLSIAIPEGTYARIAPRSGLAWKhSIDVGAGVIDADYRGPVGVILfnHSDVDFEVKVGDRIAQLILEKIVTPEVVEV 136

                          90
                  ....*....|....*.
gi 5802814    763 KKI-------GGLGST 771
Cdd:PLN02547  137 EDLdatvrgaGGFGST 152
PHA03379 PHA03379
EBNA-3A; Provisional
 178-324 9.90e-07

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 54.29  E-value: 9.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    178 PRGTSPLPAGQVPVRLQPQKQVKEN--KTQPPVAYQYWPPAELQYRPPPESQYgYPGMPPAP------QGRAPYPQPPTR 249
Cdd:PHA03379  580 PRSPSQMSVRDRLARLRAEAQPYQAsvEVQPPQLTQVSPQQPMEYPLEPEQQM-FPGSPFSQvadvmrAGGVPAMQPQYF 658

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    250 RLnPTAPPSRQGSEL----HEIIDKSRKEGDTEAWqFPITL-EPMPPGEGAQEG------EPPTVEARYKSFSIKMLKDM 318
Cdd:PHA03379  659 DL-PLQQPISQGAPLaplrASMGPVPPVPATQPQY-FDIPLtEPINQGASAAHFlpqqpmEGPLVPERWMFQGATLSQSV 736


                  ....*.
gi 5802814    319 KEGVKQ 324
Cdd:PHA03379  737 RPGVAQ 742
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 545-601 9.19e-06

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 48.69  E-value: 9.19e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814   545 KCYNCGQIGHLKKNCPVLNKQNITIQATTTGREP-PDLCPRCKKGKHWASQCRSKFDK 601
Cdd:COG5082   62 VCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPkPKKCYNCGETGHLSRDCNPSKDQ 119
Dcd COG0717
dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway ...
 694-759 3.44e-05

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


Pssm-ID: 440481  Cd Length: 180  Bit Score: 46.74  E-value: 3.44e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814   694 LPKGTVGLILGRSSLNLKGVQIHTS--VVDSDYKGEIQLVISSSIPWSA--SPGDRIAQLLLL--------PYIKGGN 759
Cdd:COG0717   88 LPDDLVAFLEGRSSLARLGLFVHTTagVIDPGFEGRITLELSNTGPLPIklYPGMRIAQLVFFrlsgpaerPYGRGGK 165
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1044-1168 4.60e-05

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: 45.03  E-value: 4.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1044 IDLKDCFFTIPLAEQ--DCEKFAFTIPAinnkepatrFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDcyIIHYIDD 1121
Cdd:cd03714    1 VDLKDAYFHIPILPRsrDLLGFAWQGET---------YQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVR--IFSYLDD 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1122 ILCAAET---KDKLIDCytFLQAEVANAGLAIASDKiQTSTPFH---YLGMQI 1168
Cdd:cd03714   70 LLIIASSiktSEAVLRH--LRATLLANLGFTLNLEK-SKLGPTQritFLGLEL 119
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 544-560 6.35e-05

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: 41.74  E-value: 6.35e-05
                           10
                   ....*....|....*..
gi 5802814     544 GKCYNCGQIGHLKKNCP 560
Cdd:pfam00098    1 GKCYNCGEPGHIARDCP 17
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 795-877 7.99e-05

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: 43.09  E-value: 7.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   795 IQGKQFEGLVDTGADVSIIALNQWPKNWPKQKAVTgLVGIGTASEVYQSTEILHC-LGPdnqeSTVQP---MITSIPLNL 870
Cdd:cd06095    5 VEGVPIVFLVDTGATHSVLKSDLGPKQELSTTSVL-IRGVSGQSQQPVTTYRTLVdLGG----HTVSHsflVVPNCPDPL 79


                 ....*..
gi 5802814   871 WGRDLLQ 877
Cdd:cd06095   80 LGRDLLS 86
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 117-305 8.00e-05

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 47.75  E-value: 8.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   117 ENTRKKSQKETESLHCEYVAEPVMAQSTQNVDYNQLQEVIYPETLKLEGKGPELVGPSESKPRGTSPLPAGQVPVRLQP- 195
Cdd:COG5180  216 DLTGGADHPRPEAASSPKVDPPSTSEARSRPATVDAQPEMRPPADAKERRRAAIGDTPAAEPPGLPVLEAGSEPQSDAPe 295

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814   196 -----QKQVKENKTQPPVAYQYWPPAEL--QYRPPPESQYGYP-GMPPApqgRAPYPQPPT-----RRLNPTAP-----P 257
Cdd:COG5180  296 aetarPIDVKGVASAPPATRPVRPPGGArdPGTPRPGQPTERPaGVPEA---ASDAGQPPSayppaEEAVPGKPleqgaP 372

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 5802814   258 SRQGSELHEIIDKSRKEGDTEAWQFPITL-EPMPPGEGAQ----EGEPPTVEA 305
Cdd:COG5180  373 RPGSSGGDGAPFQPPNGAPQPGLGRRGAPgPPMGAGDLVQaaldGGGRETASL 425
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1388-1511 1.44e-04

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: 43.75  E-value: 1.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1388 TVFTDGSSNGK---AAYTGPKERVIKT------PYQSAQRAELVAV------ITVLQDFDQPINIISDSAYVVQATRDVE 1452
Cdd:cd09276    1 VIYTDGSKLEGsvgAGFVIYRGGEVISrsyrlgTHASVFDAELEAIlealelALATARRARKVTIFTDSQSALQALRNPR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 5802814  1453 TalikySMDDQLNQLFNLLQQTVRKRNFPFYITHIRAHTNLPGpltkaNEQADLLVSSA 1511
Cdd:cd09276   81 R-----SSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEG-----NEAADRLAKEA 129
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 151-324 1.61e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 47.00  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    151 QLQEVIYPETLKLEGKGPELVGPSESKPRGTSPLPAGQVPVRLQPQKQVKENKTQPPVAYqYWPPAELQYRPPPESQYGY 230
Cdd:PRK10263  402 QPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQST-YQTEQTYQQPAAQEPLYQQ 480

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    231 PgmPPAPQGRAPYPQPPTRRLNPTAPPSRQGSELHEiiDKSRKEGDTEAWQFPItlePMPpgegAQEGEP--PTVEARYK 308
Cdd:PRK10263  481 P--QPVEQQPVVEPEPVVEETKPARPPLYYFEEVEE--KRAREREQLAAWYQPI---PEP----VKEPEPikSSLKAPSV 549

                         170       180
                  ....*....|....*....|.
gi 5802814    309 SF-----SIKMLKDMKEGVKQ 324
Cdd:PRK10263  550 AAvppveAAAAVSPLASGVKK 570
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1387-1447 1.87e-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: 43.63  E-value: 1.87e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5802814  1387 LTVFTDGSS---NGKAAY-----TGPKERVIKTPYQSA--QRAELVAVITVLQDF--DQPINIISDSAYVVQA 1447
Cdd:cd09278    2 IVIYTDGAClgnPGPGGWaavirYGDHEKELSGGEPGTtnNRMELTAAIEALEALkePCPVTIYTDSQYVING 74
PHA03247 PHA03247
large tegument protein UL36; Provisional
 158-261 2.43e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.86  E-value: 2.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    158 PETLKLEGK----GP-ELVGPSESKPrgTSPLPAGQVPVRLQPQKQVK---ENKTQPPVAYQYWPPAELQYRPPPESQYG 229
Cdd:PHA03247 2847 PPSLPLGGSvapgGDvRRRPPSRSPA--AKPAAPARPPVRRLARPAVSrstESFALPPDQPERPPQPQAPPPPQPQPQPP 2924

                          90       100       110
                  ....*....|....*....|....*....|..
gi 5802814    230 YPGMPPAPQGRAPYPQPPtrrLNPTAPPSRQG 261
Cdd:PHA03247 2925 PPPQPQPPPPPPPRPQPP---LAPTTDPAGAG 2953
ZnF_C2HC smart00343
zinc finger;
545-560 3.17e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 3.17e-04
                            10
                    ....*....|....*.
gi 5802814      545 KCYNCGQIGHLKKNCP 560
Cdd:smart00343    1 KCYNCGKEGHIARDCP 16
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 544-598 7.18e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.10  E-value: 7.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 5802814    544 GKCYNCGQIGHLKKNCPvlnkqnitiQATTTGREpPDLCPRCKKGKHWASQCRSK 598
Cdd:PTZ00368  104 RACYNCGGEGHISRDCP---------NAGKRPGG-DKTCYNCGQTGHLSRDCPDK 148
dnaA PRK14086
chromosomal replication initiator protein DnaA;
167-305 1.48e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 43.66  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    167 GPELVGPSESKPRGTSPLPAGQVPVRLQPQKQVKenkTQPPVAYQYWPPAELQYRPPPESQYGYPGMPPAPQGRAPYPQP 246
Cdd:PRK14086  107 EPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLP---TARPAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASP 183

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 5802814    247 --PTRRLNPTAPPSRQGSELHeiiDKSRKEGDTEA--WQFP-----ITLEPMPPGEGAQEGEPPTVEA 305
Cdd:PRK14086  184 asYAPEQERDREPYDAGRPEY---DQRRRDYDHPRpdWDRPrrdrtDRPEPPPGAGHVHRGGPGPPER 248
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 659-750 2.02e-03

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 41.12  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    659 SPQAAvqQVDLCTiQAVSLLPGEPPQKIPTGVYGPLPKGTVGLILGRSSLNLKG-VQIHTSVVDSDYKGEIQLVISS--S 735
Cdd:PHA02703   30 SPGAA--GLDLCS-ACDCIVPAGCRCVVFTDLLIKLPDGCYGRIAPRSGLAVKHfIDVGAGVIDADYRGNVGVVLFNfgH 106

                          90
                  ....*....|....*
gi 5802814    736 IPWSASPGDRIAQLL 750
Cdd:PHA02703  107 NDFEVKKGDRIAQLI 121
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1738-1778 2.77e-03

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: 37.76  E-value: 2.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 5802814    1738 WKDNKNKTWE-IGKVITWGRGFACVsPGENQLPVWLPTRHLK 1778
Cdd:pfam00552    3 WKDLLNGLWKgPDPLLWWGRGAVCV-PQDASDPQWVPERLLK 43
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 1389-1453 2.87e-03

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


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 40.64  E-value: 2.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814  1389 VFTDG--SSNGKAA-------YTGPK---------ERVIKTPyQSAQRAELVAVITVLQDFDQPIN----------IISD 1440
Cdd:cd13934    2 VYIDGacRNNGRPDaragygvYFGPDssynvsgrlEDTGGHP-QTSQRAELRAAIAALRFRSWIIDpdgeglktvvIATD 80

                         90
                 ....*....|....
gi 5802814  1441 SAYVVQ-ATRDVET 1453
Cdd:cd13934   81 SEYVVKgATEWIPK 94
PRK02253 PRK02253
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
 694-751 3.20e-03

deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional


Pssm-ID: 179395  Cd Length: 167  Bit Score: 40.70  E-value: 3.20e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    694 LPKGTVGLILGRSSLNLKGVQIHTSVVDSDY--KGEIQLVISSSIPWSASPGDRIAQLLL 751
Cdd:PRK02253   89 IPEDHVGFAYPRSSLLRNGCTLETAVWDAGYegRGEGLLVVHNPHGIRLERGARIAQLVF 148
PHA03124 PHA03124
dUTPase; Provisional
 668-752 3.23e-03

dUTPase; Provisional


Pssm-ID: 165396 [Multi-domain]  Cd Length: 418  Bit Score: 42.24  E-value: 3.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5802814    668 DLCTIQAVSLLPGEP-----PQKIPTGvygplpKGTVGLILGRSSLNLKGVQIH-TSVVDSDYkgeIQLVISSSIPWSAS 741
Cdd:PHA03124  294 DIRAPEDCTILPGGStriilPQKLACG------KFRAAFILGRSSMNLKGLLVDpEHVQDDDW---ISFNITNIRDAAAF 364

                          90
                  ....*....|...
gi 5802814    742 --PGDRIAQLLLL 752
Cdd:PHA03124  365 fhAGDRIAQLIAL 377
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1389-1447 6.86e-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: 6.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 5802814  1389 VFTDGSS---NGKAAY----TGPKERVI-----KTPYQSAQRAELVAVITVLQ----DFDQPINIISDSAYVVQA 1447
Cdd:cd06222    1 INVDGSCrgnPGPAGIggvlRDHEGGWLggfalKIGAPTALEAELLALLLALElaldLGYLKVIIESDSKYVVDL 75
 
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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