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Conserved domains on  [gi|9626967|ref|NP_056880|]
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Pr160 [Mouse mammary tumor virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 881-1093 8.56e-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: 406.28  E-value: 8.56e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   881 PVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNATMHDMGALQPGLPSPVAV 960
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   961 PKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYI 1040
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9626967  1041 VHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHI 1093
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 284-409 8.19e-44

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: 155.52  E-value: 8.19e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     284 VWEPLPLKTLKELQSAVRTMGPSAPYTLQVVD-MVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQK--AAG 360
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEaLASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRnqRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 9626967     361 KRKGkVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPG 409
Cdd:pfam00607   81 PDRG-ITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 751-849 1.71e-38

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: 139.42  E-value: 1.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     751 SDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVI 829
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQiLILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|
gi 9626967     830 PTLPFTLWGRDIMKDIKVRL 849
Cdd:pfam00077   81 PTCPVNIIGRDLLQQLGGRL 100
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-92 6.24e-38

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: 137.09  E-value: 6.24e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967       8 GQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQL 87
Cdd:pfam02337    1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                   ....*
gi 9626967      88 REILT 92
Cdd:pfam02337   81 RAVLD 85
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 619-741 1.92e-35

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


:

Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 131.64  E-value: 1.92e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     619 TIHDLPRGTPGSAGLDLSSQKDLILSLeDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMV 698
Cdd:pfam00692    2 EAEIPTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9626967     699 KAAKNA-VIIHKGERIAQ----LLLLPYLKLPNPVIKEERGSEGFGST 741
Cdd:pfam00692   81 FNLGKSdFTIKKGDRIAQlifePILHPELEPVETLDNTDRGDGGFGSS 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 409-482 2.46e-34

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: 126.44  E-value: 2.46e-34
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9626967     409 GVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRA 482
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1100-1165 5.67e-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: 122.43  E-value: 5.67e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9626967    1100 YQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEILNGDSNPISTRKLTPEACKALQ 1165
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1312-1433 3.78e-29

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.


The actual alignment was detected with superfamily member cd09273:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 131  Bit Score: 113.97  E-value: 3.78e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1312 VIFTDGSANGRSVTYIQGREPIIKENTQ--NTAQQAEIVAVITAFEE-VSQPFNLYTDSKYVTGLFPEIETA----TLSP 1384
Cdd:cd09273    1 TVFTDGSSFKAGYAIVSGTEIVEAQPLPpgTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLLETIgierGFLK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 9626967  1385 RTKIYTELKHLQRLIhKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTR 1433
Cdd:cd09273   81 SIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAK 128
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1494-1587 7.69e-25

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


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 100.08  E-value: 7.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    1494 PRVLWQMDVTHVSEFGK--LKYVHVTVDTYSHFTFATARTGE-ATKDVLQHLAQSFAYMGI-PQKIKTDNAPAYVSRSIQ 1569
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 9626967    1570 EFLARWKISHVTGIPYNP 1587
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1655-1700 4.33e-17

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: 76.28  E-value: 4.33e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 9626967    1655 VMWKDLLTGSWKGPDVLITAGRGYACVfPQDAETPIWVPDRFIRPF 1700
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCV-PQDASDPQWVPERLLKRI 45
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
550-584 1.59e-16

GAG-polyprotein viral zinc-finger;


:

Pssm-ID: 373297  Cd Length: 36  Bit Score: 74.51  E-value: 1.59e-16
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9626967     550 PPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETN 584
Cdd:pfam14787    1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGN 35
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1443-1478 1.44e-15

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: 71.63  E-value: 1.44e-15
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 9626967    1443 ESHALHHQNAAALRFQFHITREQAREIVKLCPNCPD 1478
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
AIR1 super family cl34894
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 525-567 4.14e-05

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: 46.38  E-value: 4.14e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 9626967   525 PVCFSCGKTGHIRKDCkdekgskraPPGLCPRCKKGYHWKSEC 567
Cdd:COG5082   61 PVCFNCGQNGHLRRDC---------PHSICYNCSWDGHRSNHC 94
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 881-1093 8.56e-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: 406.28  E-value: 8.56e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   881 PVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNATMHDMGALQPGLPSPVAV 960
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   961 PKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYI 1040
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9626967  1041 VHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHI 1093
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 284-409 8.19e-44

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: 155.52  E-value: 8.19e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     284 VWEPLPLKTLKELQSAVRTMGPSAPYTLQVVD-MVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQK--AAG 360
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEaLASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRnqRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 9626967     361 KRKGkVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPG 409
Cdd:pfam00607   81 PDRG-ITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 924-1093 1.24e-43

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: 157.46  E-value: 1.24e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     924 IKKKS-GKWRLL----QDLRAVNATMHD-------MGALQPGLPSPVAVPKG-WEIIIIDLQDCFFNIKLHPEDCKRFAF 990
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKaKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     991 SVPSPNFK----RPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYqDSYIVHYMDDILLAHPSRSIVDEILTSMIQ 1066
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 9626967    1067 ALNKHGLVVSTEKIQ---KYDNLKYLGTHI 1093
Cdd:pfam00078  160 WLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 751-849 1.71e-38

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: 139.42  E-value: 1.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     751 SDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVI 829
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQiLILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|
gi 9626967     830 PTLPFTLWGRDIMKDIKVRL 849
Cdd:pfam00077   81 PTCPVNIIGRDLLQQLGGRL 100
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-92 6.24e-38

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: 137.09  E-value: 6.24e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967       8 GQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQL 87
Cdd:pfam02337    1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                   ....*
gi 9626967      88 REILT 92
Cdd:pfam02337   81 RAVLD 85
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 619-741 1.92e-35

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 131.64  E-value: 1.92e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     619 TIHDLPRGTPGSAGLDLSSQKDLILSLeDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMV 698
Cdd:pfam00692    2 EAEIPTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9626967     699 KAAKNA-VIIHKGERIAQ----LLLLPYLKLPNPVIKEERGSEGFGST 741
Cdd:pfam00692   81 FNLGKSdFTIKKGDRIAQlifePILHPELEPVETLDNTDRGDGGFGSS 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 409-482 2.46e-34

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: 126.44  E-value: 2.46e-34
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9626967     409 GVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRA 482
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1100-1165 5.67e-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: 122.43  E-value: 5.67e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9626967    1100 YQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEILNGDSNPISTRKLTPEACKALQ 1165
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 757-842 8.98e-31

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: 116.60  E-value: 8.98e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   757 LHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVIPtLPFT 835
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVlLLEIDGEGHLGTILVYVLS-LPVN 79


                 ....*..
gi 9626967   836 LWGRDIM 842
Cdd:cd05482   80 LWGRDIL 86
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1312-1433 3.78e-29

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: 113.97  E-value: 3.78e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1312 VIFTDGSANGRSVTYIQGREPIIKENTQ--NTAQQAEIVAVITAFEE-VSQPFNLYTDSKYVTGLFPEIETA----TLSP 1384
Cdd:cd09273    1 TVFTDGSSFKAGYAIVSGTEIVEAQPLPpgTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLLETIgierGFLK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 9626967  1385 RTKIYTELKHLQRLIhKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTR 1433
Cdd:cd09273   81 SIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAK 128
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1494-1587 7.69e-25

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 100.08  E-value: 7.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    1494 PRVLWQMDVTHVSEFGK--LKYVHVTVDTYSHFTFATARTGE-ATKDVLQHLAQSFAYMGI-PQKIKTDNAPAYVSRSIQ 1569
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 9626967    1570 EFLARWKISHVTGIPYNP 1587
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 611-741 1.01e-22

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


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 95.76  E-value: 1.01e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     611 LNPEAPpftihdLP-RGTPGSAGLDLSSQKDLILsLEDGVSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGVI 686
Cdd:TIGR00576    7 LSPNAP------LPtYATEGAAGYDLRAAEDVTI-PPGERALVPTGIAIELPDGYYGRVAPRSGLaLKHGVTIDnsPGVI 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9626967     687 DSDFQGEIKV-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKEE-----RGSEGFGST 741
Cdd:TIGR00576   80 DADYRGEIKViLINLGKEDFTVKKGDRIAQLVVEKIVTEVEFEEVEEldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 611-741 2.20e-22

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: 94.70  E-value: 2.20e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   611 LNPEAPpftihdLPR-GTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGV 685
Cdd:COG0756    7 LDEDAP------LPAyATPGSAGLDLRAALDEPVTLKPGeRALVPTGLAIALPPGYEAQVRPRSGLaLKHGITLLnsPGT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9626967   686 IDSDFQGEIKV-MVKAAKNAVIIHKGERIAQllllpylklpnPVIKE---------------ERGSEGFGST 741
Cdd:COG0756   81 IDSDYRGEIKViLINLGDEPFTIERGDRIAQ-----------LVIAPvvqaefeeveeldetERGAGGFGST 141
dut PRK00601
dUTP diphosphatase;
621-741 5.46e-20

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 88.30  E-value: 5.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    621 HDLP-RGTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVL--PGVIDSDFQGEIK 695
Cdd:PRK00601   17 FPLPaYATEGSAGLDLRACLDEPVTLAPGeRALVPTGLAIHIPDGYEAQILPRSGlAHKHGIVLGnlPGTIDSDYRGELK 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 9626967    696 V-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PRK00601   97 VsLWNRGQEPFTIEPGERIAQLVIVPVVQAEFEEVEEfdetERGAGGFGST 147
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 631-715 2.07e-18

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: 81.77  E-value: 2.07e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   631 AGLDL-SSQKDLILSLE-DGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVL-PGVIDSDFQGEIKVMVKAAKNA-VI 706
Cdd:cd07557    1 AGYDLrLGEDFEGIVLPpGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpVV 80


                 ....*....
gi 9626967   707 IHKGERIAQ 715
Cdd:cd07557   81 IKKGDRIAQ 89
transpos_IS481 NF033577
IS481 family transposase; null
 1497-1624 7.62e-18

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 85.72  E-value: 7.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   1497 LWQMDVTHVSEF---GKLkYVHVTVDTYSHFTFA---TARTGEATKDVLQHLaqsFAYMGIP-QKIKTDNAPAYVSRSI- 1568
Cdd:NF033577  130 LWHIDIKKLGRIpdvGRL-YLHTAIDDHSRFAYAelyPDETAETAADFLRRA---FAEHGIPiRRVLTDNGSEFRSRAHg 205

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9626967   1569 -QEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKlqkaGKYYTPHHLLAHAL 1624
Cdd:NF033577  206 fELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAY----ARPYESLAELQAAL 258
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1308-1433 9.54e-18

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: 81.65  E-value: 9.54e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    1308 EKGIVIFTDGSANGRS-------VTYiQGREPIIK-ENTQNTAQQAEIVAVITAFE--EVSQPFNLYTDSKYVTGLFPE- 1376
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPgpggagaVLY-RGHENISApLPGRTTNNRAELQAVIEALKalKSPSKVNIYTDSQYVIGGITQw 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9626967    1377 IETA-------TLSPRTKIYTELkhLQRLI-HKRQEKFYIGHIRGHTGLPgplaqGNAYADSLTR 1433
Cdd:pfam00075   80 VHGWkkngwptTSEGKPVKNKDL--WQLLKaLCKKHQVYWQWVKGHAGNP-----GNEMADRLAK 137
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1655-1700 4.33e-17

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: 76.28  E-value: 4.33e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 9626967    1655 VMWKDLLTGSWKGPDVLITAGRGYACVfPQDAETPIWVPDRFIRPF 1700
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCV-PQDASDPQWVPERLLKRI 45
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
550-584 1.59e-16

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 74.51  E-value: 1.59e-16
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9626967     550 PPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETN 584
Cdd:pfam14787    1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGN 35
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1443-1478 1.44e-15

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: 71.63  E-value: 1.44e-15
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 9626967    1443 ESHALHHQNAAALRFQFHITREQAREIVKLCPNCPD 1478
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1493-1604 2.68e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 57.47  E-value: 2.68e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1493 KPRVLWQMDVTHVS-EFGKLkYVHVTVDTYS----HFTFATARTGEatkDVLQHLAQSFAYMGIPQK--IKTDNAPAYVS 1565
Cdd:COG2801  147 APNQVWVTDITYIPtAEGWL-YLAAVIDLFSreivGWSVSDSMDAE---LVVDALEMAIERRGPPKPliLHSDNGSQYTS 222

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 9626967  1566 RSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQL 1604
Cdd:COG2801  223 KAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1311-1433 2.19e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 51.77  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1311 IVIFTDGSANGRS-------VTYIQGREPIIKE-NTQNTAQQAEIVAVITAFEEV----SQPFNLYTDSKYVTGLfpeIE 1378
Cdd:COG0328    3 IEIYTDGACRGNPgpggwgaVIRYGGEEKELSGgLGDTTNNRAELTALIAALEALkelgPCEVEIYTDSQYVVNQ---IT 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 9626967  1379 TATLSPRTKIYTELKH---LQRLIHK-RQEKFYIGHIRGHTGLPgplaqGNAYADSLTR 1433
Cdd:COG0328   80 GWIHGWKKNGWKPVKNpdlWQRLDELlARHKVTFEWVKGHAGHP-----GNERADALAN 133
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 525-567 4.14e-05

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: 46.38  E-value: 4.14e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 9626967   525 PVCFSCGKTGHIRKDCkdekgskraPPGLCPRCKKGYHWKSEC 567
Cdd:COG5082   61 PVCFNCGQNGHLRRDC---------PHSICYNCSWDGHRSNHC 94
transpos_IS21 NF033546
IS21 family transposase;
1499-1598 5.09e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 44.12  E-value: 5.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   1499 QMDVTHVSEF---GKLKYVHVTVDT--YSHFTFATARTGEATKDVLQHLAQSFAYM-GIPQKIKTDNAPAYVS------- 1565
Cdd:NF033546  120 QVDFGEATVVvtgGTGKILHVFVAVlgYSRYTYVEATPSESQEDLLDGHQRAFEFFgGVPREIVYDNLKTAVDkrdryee 199

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 9626967   1566 ----RSIQEFLARWKISHVTGIPYNPQGQAIVERTHQ 1598
Cdd:NF033546  200 prlnPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVG 236
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1493-1604 8.10e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 43.31  E-value: 8.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   1493 KPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKD-VLQHLAQSFAYMGIPQK--IKTDNAPAYVSRSIQ 1569
Cdd:PHA02517  108 RPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGWRVSSSMDTDfVLDALEQALWARGRPGGliHHSDKGSQYVSLAYT 187

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 9626967   1570 EFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQL 1604
Cdd:PHA02517  188 QRLKEAGIRASTGSRGDSYDNAPAESINGLYKAEV 222
ZnF_C2HC smart00343
zinc finger;
526-541 1.15e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 1.15e-03
                            10
                    ....*....|....*.
gi 9626967      526 VCFSCGKTGHIRKDCK 541
Cdd:smart00343    1 KCYNCGKEGHIARDCP 16
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 527-570 1.48e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 9626967    527 CFSCGKTGHIRKDCKDEKGSKRAPPgLCPRCKKGYHWKSECKSK 570
Cdd:PTZ00368  106 CYNCGGEGHISRDCPNAGKRPGGDK-TCYNCGQTGHLSRDCPDK 148
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 525-541 3.03e-03

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 36.74  E-value: 3.03e-03
                           10
                   ....*....|....*..
gi 9626967     525 PVCFSCGKTGHIRKDCK 541
Cdd:pfam00098    1 GKCYNCGEPGHIARDCP 17
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 881-1093 8.56e-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: 406.28  E-value: 8.56e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   881 PVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNATMHDMGALQPGLPSPVAV 960
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   961 PKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYI 1040
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9626967  1041 VHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHI 1093
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 284-409 8.19e-44

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: 155.52  E-value: 8.19e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     284 VWEPLPLKTLKELQSAVRTMGPSAPYTLQVVD-MVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQK--AAG 360
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEaLASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRnqRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 9626967     361 KRKGkVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPG 409
Cdd:pfam00607   81 PDRG-ITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 924-1093 1.24e-43

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: 157.46  E-value: 1.24e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     924 IKKKS-GKWRLL----QDLRAVNATMHD-------MGALQPGLPSPVAVPKG-WEIIIIDLQDCFFNIKLHPEDCKRFAF 990
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKaKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     991 SVPSPNFK----RPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYqDSYIVHYMDDILLAHPSRSIVDEILTSMIQ 1066
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 9626967    1067 ALNKHGLVVSTEKIQ---KYDNLKYLGTHI 1093
Cdd:pfam00078  160 WLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 751-849 1.71e-38

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: 139.42  E-value: 1.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     751 SDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVI 829
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQiLILIGEDKFRGTVSPLIL 80

                           90       100
                   ....*....|....*....|
gi 9626967     830 PTLPFTLWGRDIMKDIKVRL 849
Cdd:pfam00077   81 PTCPVNIIGRDLLQQLGGRL 100
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-92 6.24e-38

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: 137.09  E-value: 6.24e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967       8 GQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQL 87
Cdd:pfam02337    1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                   ....*
gi 9626967      88 REILT 92
Cdd:pfam02337   81 RAVLD 85
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 881-1090 5.13e-37

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: 139.41  E-value: 5.13e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   881 PVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSG-KWRLLQDLRAVNATMHDmgaLQPGLPSPVA 959
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLP---IHPAVPNPYT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   960 V-----PKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSpnfkrpyQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDK 1034
Cdd:cd03715   78 LlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG-------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLE 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9626967  1035 YQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDN-LKYLG 1090
Cdd:cd03715  151 HEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAeVKFLG 207
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 619-741 1.92e-35

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 131.64  E-value: 1.92e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     619 TIHDLPRGTPGSAGLDLSSQKDLILSLeDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMV 698
Cdd:pfam00692    2 EAEIPTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 9626967     699 KAAKNA-VIIHKGERIAQ----LLLLPYLKLPNPVIKEERGSEGFGST 741
Cdd:pfam00692   81 FNLGKSdFTIKKGDRIAQlifePILHPELEPVETLDNTDRGDGGFGSS 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 409-482 2.46e-34

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: 126.44  E-value: 2.46e-34
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9626967     409 GVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRA 482
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 1100-1165 5.67e-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: 122.43  E-value: 5.67e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9626967    1100 YQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEILNGDSNPISTRKLTPEACKALQ 1165
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 757-842 8.98e-31

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: 116.60  E-value: 8.98e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   757 LHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVIPtLPFT 835
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVlLLEIDGEGHLGTILVYVLS-LPVN 79


                 ....*..
gi 9626967   836 LWGRDIM 842
Cdd:cd05482   80 LWGRDIL 86
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 908-1093 4.49e-30

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 118.08  E-value: 4.49e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   908 GHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNATMHDMGALQPGLPSPVAVPKGWEII-IIDLQDCFFNIKLHPEDCK 986
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFsKLDLRSGYHQIPLAEESRP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   987 RFAFSVpspnfkrPYQRFQWKVLPQGMKNSPTLCQKFVDKAIltvrDKYQDSYIVHYMDDILLAhpSRSIVD--EILTSM 1064
Cdd:cd01647   81 KTAFRT-------PFGLYEYTRMPFGLKNAPATFQRLMNKIL----GDLLGDFVEVYLDDILVY--SKTEEEhlEHLREV 147

                        170       180       190
                 ....*....|....*....|....*....|
gi 9626967  1065 IQALNKHGLVVSTEKIQ-KYDNLKYLGTHI 1093
Cdd:cd01647  148 LERLREAGLKLNPEKCEfGVPEVEFLGHIV 177
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1312-1433 3.78e-29

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: 113.97  E-value: 3.78e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1312 VIFTDGSANGRSVTYIQGREPIIKENTQ--NTAQQAEIVAVITAFEE-VSQPFNLYTDSKYVTGLFPEIETA----TLSP 1384
Cdd:cd09273    1 TVFTDGSSFKAGYAIVSGTEIVEAQPLPpgTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLLETIgierGFLK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 9626967  1385 RTKIYTELKHLQRLIhKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTR 1433
Cdd:cd09273   81 SIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAK 128
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1494-1587 7.69e-25

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 100.08  E-value: 7.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    1494 PRVLWQMDVTHVSEFGK--LKYVHVTVDTYSHFTFATARTGE-ATKDVLQHLAQSFAYMGI-PQKIKTDNAPAYVSRSIQ 1569
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGvPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 9626967    1570 EFLARWKISHVTGIPYNP 1587
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 611-741 1.01e-22

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


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 95.76  E-value: 1.01e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967     611 LNPEAPpftihdLP-RGTPGSAGLDLSSQKDLILsLEDGVSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGVI 686
Cdd:TIGR00576    7 LSPNAP------LPtYATEGAAGYDLRAAEDVTI-PPGERALVPTGIAIELPDGYYGRVAPRSGLaLKHGVTIDnsPGVI 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9626967     687 DSDFQGEIKV-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKEE-----RGSEGFGST 741
Cdd:TIGR00576   80 DADYRGEIKViLINLGKEDFTVKKGDRIAQLVVEKIVTEVEFEEVEEldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 611-741 2.20e-22

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: 94.70  E-value: 2.20e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   611 LNPEAPpftihdLPR-GTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGV 685
Cdd:COG0756    7 LDEDAP------LPAyATPGSAGLDLRAALDEPVTLKPGeRALVPTGLAIALPPGYEAQVRPRSGLaLKHGITLLnsPGT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9626967   686 IDSDFQGEIKV-MVKAAKNAVIIHKGERIAQllllpylklpnPVIKE---------------ERGSEGFGST 741
Cdd:COG0756   81 IDSDYRGEIKViLINLGDEPFTIERGDRIAQ-----------LVIAPvvqaefeeveeldetERGAGGFGST 141
dut PRK00601
dUTP diphosphatase;
621-741 5.46e-20

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 88.30  E-value: 5.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    621 HDLP-RGTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVL--PGVIDSDFQGEIK 695
Cdd:PRK00601   17 FPLPaYATEGSAGLDLRACLDEPVTLAPGeRALVPTGLAIHIPDGYEAQILPRSGlAHKHGIVLGnlPGTIDSDYRGELK 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 9626967    696 V-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PRK00601   97 VsLWNRGQEPFTIEPGERIAQLVIVPVVQAEFEEVEEfdetERGAGGFGST 147
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 631-715 2.07e-18

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: 81.77  E-value: 2.07e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   631 AGLDL-SSQKDLILSLE-DGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVL-PGVIDSDFQGEIKVMVKAAKNA-VI 706
Cdd:cd07557    1 AGYDLrLGEDFEGIVLPpGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpVV 80


                 ....*....
gi 9626967   707 IHKGERIAQ 715
Cdd:cd07557   81 IKKGDRIAQ 89
transpos_IS481 NF033577
IS481 family transposase; null
 1497-1624 7.62e-18

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 85.72  E-value: 7.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   1497 LWQMDVTHVSEF---GKLkYVHVTVDTYSHFTFA---TARTGEATKDVLQHLaqsFAYMGIP-QKIKTDNAPAYVSRSI- 1568
Cdd:NF033577  130 LWHIDIKKLGRIpdvGRL-YLHTAIDDHSRFAYAelyPDETAETAADFLRRA---FAEHGIPiRRVLTDNGSEFRSRAHg 205

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9626967   1569 -QEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKlqkaGKYYTPHHLLAHAL 1624
Cdd:NF033577  206 fELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAY----ARPYESLAELQAAL 258
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1308-1433 9.54e-18

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: 81.65  E-value: 9.54e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    1308 EKGIVIFTDGSANGRS-------VTYiQGREPIIK-ENTQNTAQQAEIVAVITAFE--EVSQPFNLYTDSKYVTGLFPE- 1376
Cdd:pfam00075    1 PKAVTVYTDGSCLGNPgpggagaVLY-RGHENISApLPGRTTNNRAELQAVIEALKalKSPSKVNIYTDSQYVIGGITQw 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9626967    1377 IETA-------TLSPRTKIYTELkhLQRLI-HKRQEKFYIGHIRGHTGLPgplaqGNAYADSLTR 1433
Cdd:pfam00075   80 VHGWkkngwptTSEGKPVKNKDL--WQLLKaLCKKHQVYWQWVKGHAGNP-----GNEMADRLAK 137
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1655-1700 4.33e-17

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: 76.28  E-value: 4.33e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 9626967    1655 VMWKDLLTGSWKGPDVLITAGRGYACVfPQDAETPIWVPDRFIRPF 1700
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCV-PQDASDPQWVPERLLKRI 45
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
550-584 1.59e-16

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 74.51  E-value: 1.59e-16
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9626967     550 PPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETN 584
Cdd:pfam14787    1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGN 35
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1443-1478 1.44e-15

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: 71.63  E-value: 1.44e-15
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 9626967    1443 ESHALHHQNAAALRFQFHITREQAREIVKLCPNCPD 1478
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
PLN02547 PLN02547
dUTP pyrophosphatase
 623-741 4.36e-14

dUTP pyrophosphatase


Pssm-ID: 215302  Cd Length: 157  Bit Score: 71.75  E-value: 4.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    623 LP-RGTPGSAGLDLSSQKDLILSLEdGVSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVLPGVIDSDFQGEIKVMV-K 699
Cdd:PLN02547   28 LPsRGSALAAGYDLSSAYDTVVPAR-GKALVPTDLSIAIPEGTYARIAPRSGlAWKHSIDVGAGVIDADYRGPVGVILfN 106

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 9626967    700 AAKNAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PLN02547  107 HSDVDFEVKVGDRIAQLILEKIVTPEVVEVEDldatVRGAGGFGST 152
PHA03094 PHA03094
dUTPase; Provisional
 625-741 1.37e-10

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 60.93  E-value: 1.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    625 RGTPGSAGLDLSSQKDLILSLEDGVsLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVLPGVIDSDFQGEIKVM-VKAAK 702
Cdd:PHA03094   20 RSSPKSAGYDLYSAYDYTVPPKERI-LVKTDISLSIPKFCYGRIAPRSGlSLNYGIDIGGGVIDEDYRGNIGVIfINNGK 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 9626967    703 NAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PHA03094   99 CTFNIKTGDRIAQIIFERIEYPELKEVQSldstDRGDQGFGSS 141
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 625-741 7.60e-10

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 59.61  E-value: 7.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    625 RGTPGSAGLDLSSQKDLILSlEDGVSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVLPGVIDSDFQGEIKVMV-KAAK 702
Cdd:PHA02703   28 RGSPGAAGLDLCSACDCIVP-AGCRCVVFTDLLIKLPDGCYGRIAPRSGlAVKHFIDVGAGVIDADYRGNVGVVLfNFGH 106

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 9626967    703 NAVIIHKGERIAQLLLLPYLKLPNPVIK----EERGSEGFGST 741
Cdd:PHA02703  107 NDFEVKKGDRIAQLICERAAFPAVEEVAclddTDRGAGGFGST 149
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1493-1604 2.68e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 57.47  E-value: 2.68e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1493 KPRVLWQMDVTHVS-EFGKLkYVHVTVDTYS----HFTFATARTGEatkDVLQHLAQSFAYMGIPQK--IKTDNAPAYVS 1565
Cdd:COG2801  147 APNQVWVTDITYIPtAEGWL-YLAAVIDLFSreivGWSVSDSMDAE---LVVDALEMAIERRGPPKPliLHSDNGSQYTS 222

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 9626967  1566 RSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQL 1604
Cdd:COG2801  223 KAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 969-1090 7.80e-08

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: 52.35  E-value: 7.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   969 IDLQDCFFNIKLHPEDCK--RFAFSvpspnfkrpYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRdkYQDSYIVHYMDD 1046
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDllGFAWQ---------GETYQFKALPFGLSLAPRVFTKVVEALLAPLR--LLGVRIFSYLDD 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 9626967  1047 ILLAHPSRSIVDEILTSM-IQALNKHGLVVSTEKIQKY--DNLKYLG 1090
Cdd:cd03714   70 LLIIASSIKTSEAVLRHLrATLLANLGFTLNLEKSKLGptQRITFLG 116
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1311-1433 2.19e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 51.77  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1311 IVIFTDGSANGRS-------VTYIQGREPIIKE-NTQNTAQQAEIVAVITAFEEV----SQPFNLYTDSKYVTGLfpeIE 1378
Cdd:COG0328    3 IEIYTDGACRGNPgpggwgaVIRYGGEEKELSGgLGDTTNNRAELTALIAALEALkelgPCEVEIYTDSQYVVNQ---IT 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 9626967  1379 TATLSPRTKIYTELKH---LQRLIHK-RQEKFYIGHIRGHTGLPgplaqGNAYADSLTR 1433
Cdd:COG0328   80 GWIHGWKKNGWKPVKNpdlWQRLDELlARHKVTFEWVKGHAGHP-----GNERADALAN 133
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 964-1125 3.91e-07

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 52.69  E-value: 3.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   964 WEIIII-DLQDCFFNIKLHPEDCK--RFAFsVPSPNFKRPyQRFQWKVLPQGMKNSPTLCQKfvdkAILTVRDKYQDSYI 1040
Cdd:cd01644   58 GKIAVSaDIEKMFHQVKVRPEDRDvlRFLW-RKDGDEPKP-IEYRMTVVPFGAASAPFLANR----ALKQHAEDHPHEAA 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1041 V------HYMDDILLAHPSRSIVDEILTSMIQALNKHGLvvsteKIQKYD-NLKYLGTHIQGdsvsyqklqIRTDKLRTL 1113
Cdd:cd01644  132 AkiikrnFYVDDILVSTDTLNEAVNVAKRLIALLKKGGF-----NLRKWAsNSQEVLDDLPE---------ERVLLDRDS 197

                        170
                 ....*....|..
gi 9626967  1114 NDFQKLLGnINW 1125
Cdd:cd01644  198 DVTEKTLG-LRW 208
dut PRK13956
dUTP diphosphatase;
623-743 5.51e-07

dUTP diphosphatase;


Pssm-ID: 184417 [Multi-domain]  Cd Length: 147  Bit Score: 50.95  E-value: 5.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    623 LP-RGTPGSAGLDLSSQKDLILSLEDgVSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVLP--GVIDSDF------QG 692
Cdd:PRK13956   18 LPkRETAHAAGYDLKVAERTVIAPGE-IKLVPTGVKAYMQPGEVLYLYDRSSNpRKKGLVLINsvGVIDGDYygnpanEG 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 9626967    693 EIKVMVKAAKN-AVIIHKGERIAQLLLLPYLKLPNPVIKEERgSEGFGSTSH 743
Cdd:PRK13956   97 HIFAQMKNITDqEVVLEVGERIVQGVFMPFLIADGDQADGER-TGGFGSTGK 147
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1312-1431 2.45e-06

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: 48.37  E-value: 2.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1312 VIFTDGSANGRSVTY----------IQGREPIikeNTQNTAQQAEIVAVITAFEEVS------QPFNLYTDSKYVTGLfp 1375
Cdd:cd09276    1 VIYTDGSKLEGSVGAgfviyrggevISRSYRL---GTHASVFDAELEAILEALELALatarraRKVTIFTDSQSALQA-- 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 9626967  1376 eIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPgplaqGNAYADSL 1431
Cdd:cd09276   76 -LRNPRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIE-----GNEAADRL 125
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1312-1434 3.97e-06

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: 48.33  E-value: 3.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1312 VIFTDGSA--NGRS-------VTY-----------IQGREPiikentqnTAQQAEIVAVITAFEEVSQ----PFNLYTDS 1367
Cdd:cd09280    1 VVYTDGSClnNGKPgaragigVYFgpgdprnvsepLPGRKQ--------TNNRAELLAVIHALEQAPEegirKLEIRTDS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1368 KYVtglfpeIETATL--------SPRTKIYTELKH------LQRLIHKRQEKFYIGHIRGHTGLPgplaqGNAYADSLTR 1433
Cdd:cd09280   73 KYA------INCITKwipkwkknGWKTSKGKPVKNqdlikeLDKLLRKRGIKVKFEHVKGHSGDP-----GNEEADRLAR 141


                 .
gi 9626967  1434 I 1434
Cdd:cd09280  142 E 142
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 970-1081 4.60e-06

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


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 48.48  E-value: 4.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   970 DLQDCFFNIKLH--PEDCKRFAFSVPS-----------PNFKRPYQRFQWKVLPQGmknsPTLCQKF-------VDKAIl 1029
Cdd:cd01646    2 DISNFYDSIYTHslPWALHGKIKAKQLlkllrllgnllDLLLLSSQYGQTNGLPIG----PLTSRFLaniylndVDHEL- 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9626967  1030 tvRDKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQ 1081
Cdd:cd01646   77 --KSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTE 126
PTZ00143 PTZ00143
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
 628-742 2.04e-05

deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional


Pssm-ID: 240288 [Multi-domain]  Cd Length: 155  Bit Score: 46.65  E-value: 2.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967    628 PGSAGLDLSSQKDLILSLED------GVSLVPTLVKGTLPEG--TTGLIIGRSSNYKKGLEVLP--GVIDSDFQGEIKVM 697
Cdd:PTZ00143   24 EGDSGLDLFIVKDQTIKPGEtafiklGIKAAAFQKDEDGSDGknVSWLLFPRSSISKTPLRLANsiGLIDAGYRGELIAA 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 9626967    698 VKAAKN-AVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGSTS 742
Cdd:PTZ00143  104 VDNIKDePYTIKKGDRLVQLVSFDGEPITFELVDEldetTRGEGGFGSTG 153
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 525-567 4.14e-05

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: 46.38  E-value: 4.14e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 9626967   525 PVCFSCGKTGHIRKDCkdekgskraPPGLCPRCKKGYHWKSEC 567
Cdd:COG5082   61 PVCFNCGQNGHLRRDC---------PHSICYNCSWDGHRSNHC 94
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1311-1370 5.22e-05

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: 44.78  E-value: 5.22e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9626967  1311 IVIFTDGSANGRS-------VTYIQGREPIIK---ENTQNtaQQAEIVAVITAFEEVSQPFN--LYTDSKYV 1370
Cdd:cd09278    2 IVIYTDGACLGNPgpggwaaVIRYGDHEKELSggePGTTN--NRMELTAAIEALEALKEPCPvtIYTDSQYV 71
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1009-1091 1.52e-04

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: 42.34  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967  1009 LPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIVHYMDDILLAH--PSRSIVDEILTsmiQALNKHGLVVSTEKIQK-YDN 1085
Cdd:cd00304   12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAksEQQAVKKRELE---EFLARLGLNLSDEKTQFtEKE 88


                 ....*...
gi 9626967  1086 --LKYLGT 1091
Cdd:cd00304   89 kkFKFLGI 96
transpos_IS21 NF033546
IS21 family transposase;
1499-1598 5.09e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 44.12  E-value: 5.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   1499 QMDVTHVSEF---GKLKYVHVTVDT--YSHFTFATARTGEATKDVLQHLAQSFAYM-GIPQKIKTDNAPAYVS------- 1565
Cdd:NF033546  120 QVDFGEATVVvtgGTGKILHVFVAVlgYSRYTYVEATPSESQEDLLDGHQRAFEFFgGVPREIVYDNLKTAVDkrdryee 199

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 9626967   1566 ----RSIQEFLARWKISHVTGIPYNPQGQAIVERTHQ 1598
Cdd:NF033546  200 prlnPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVG 236
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1493-1604 8.10e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 43.31  E-value: 8.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626967   1493 KPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKD-VLQHLAQSFAYMGIPQK--IKTDNAPAYVSRSIQ 1569
Cdd:PHA02517  108 RPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGWRVSSSMDTDfVLDALEQALWARGRPGGliHHSDKGSQYVSLAYT 187

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 9626967   1570 EFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQL 1604
Cdd:PHA02517  188 QRLKEAGIRASTGSRGDSYDNAPAESINGLYKAEV 222
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 733-765 9.28e-04

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 40.52  E-value: 9.28e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 9626967   733 RGSEGFGSTSHVHWVQEISDSRPMLHIYLNGRR 765
Cdd:cd04984   21 TGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHR 53
ZnF_C2HC smart00343
zinc finger;
526-541 1.15e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 1.15e-03
                            10
                    ....*....|....*.
gi 9626967      526 VCFSCGKTGHIRKDCK 541
Cdd:smart00343    1 KCYNCGKEGHIARDCP 16
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 526-569 1.38e-03

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: 41.76  E-value: 1.38e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9626967   526 VCFSCGKTGHIRKDCkDEKGSKRAPpglCPRCKKGYHWKSECKS 569
Cdd:COG5082   99 KCYNCGETGHLSRDC-NPSKDQQKS---CFDCNSTRHSSEDCPS 138
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 527-570 1.48e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 9626967    527 CFSCGKTGHIRKDCKDEKGSKRAPPgLCPRCKKGYHWKSECKSK 570
Cdd:PTZ00368  106 CYNCGGEGHISRDCPNAGKRPGGDK-TCYNCGQTGHLSRDCPDK 148
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 525-541 3.03e-03

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 36.74  E-value: 3.03e-03
                           10
                   ....*....|....*..
gi 9626967     525 PVCFSCGKTGHIRKDCK 541
Cdd:pfam00098    1 GKCYNCGEPGHIARDCP 17
dCTP_deam TIGR02274
deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli ...
 651-715 3.25e-03

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


Pssm-ID: 274062  Cd Length: 179  Bit Score: 40.38  E-value: 3.25e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9626967     651 LVPTLVKGTLPEGTTGLIIGRSSNYKKGL--EVLPGVIDSDFQGEIKV-MVKAAKNAVIIHKGERIAQ 715
Cdd:TIGR02274   80 LATTLEYVKLPDDVVGFLEGRSSLARLGLfiHVTAGRIDPGFEGNITLeLFNAGKLPVKLRPGMRIAQ 147
 
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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