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Conserved domains on  [gi|9629499|ref|NP_056907|]
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gag-pro-pol polyprotein [Simian T-lymphotropic virus 2]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
595-809 9.02e-66

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01645:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 213  Bit Score: 221.77  E-value: 9.02e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   595 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSL 674
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   675 STALPyLQTIDLTDAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFPMST 754
Cdd:cd01645   81 PKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIV 159
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 9629499   755 IIQYMDDILLASPTQEELQQLSKMTLQALVTHGLPVSQEKTQQTPGqIRFLGQVI 809
Cdd:cd01645  160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
Gag_p19 super family cl03491
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
1-91 5.91e-45

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


The actual alignment was detected with superfamily member pfam02228:

Pssm-ID: 460500  Cd Length: 92  Bit Score: 157.43  E-value: 5.91e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499       1 MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRT 80
Cdd:pfam02228    1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80
                           90
                   ....*....|.
gi 9629499      81 IEIINVLIKNQ 91
Cdd:pfam02228   81 NEILHILIQTQ 91
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
263-336 1.08e-29

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


The actual alignment was detected with superfamily member pfam19317:

Pssm-ID: 466038  Cd Length: 74  Bit Score: 112.96  E-value: 1.08e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9629499     263 TRDPSWAAILQGLEEPYCAFVERLNVALDNGLPEGTPKEPILRSLAYSNANKDCQKLLQARGHTnSPLGDMLRA 336
Cdd:pfam19317    2 YKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1229-1322 1.90e-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: 101.62  E-value: 1.90e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499    1229 PNHIWQGDVTHYKYKRN--RYCLHVWVDTFSNAVSITCKTKETSSETVSALLH-AITILGK-PLSINTDNGSAFLSQEFQ 1304
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALErAIAFRGGvPLIIHSDNGSEYTSKAFR 80
                           90
                   ....*....|....*...
gi 9629499    1305 AFCASWHIKHSTHVPYNS 1322
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
449-556 2.64e-16

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member pfam00077:

Pssm-ID: 472175  Cd Length: 101  Bit Score: 75.87  E-value: 2.64e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     449 QQHQPLLDVQVSIagappRPTQALLDTGADLTVLPQALAPESVSVS--DTTVLGAGGQTSSQFKLLQSPLCVYLPFR--R 524
Cdd:pfam00077    1 AEQRPLLTVKIGG-----KYFTALLDTGADDTVISQNDWPTNWPKQkaTTNIQGIGGGINVRQSDQILILIGEDKFRgtV 75
                           90       100       110
                   ....*....|....*....|....*....|..
gi 9629499     525 APVTLPSCLVDtnskwaIIGRDILQKCQSVLY 556
Cdd:pfam00077   76 SPLILPTCPVN------IIGRDLLQQLGGRLT 101
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
1042-1163 6.18e-15

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: 72.76  E-value: 6.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1042 LFSDGSSQKAAYVLWDQTiLHHDSVTLPPhgSNSAQKGELLALlsgIRAAKSWP--SLNIFLDSKYLIKYLHSL-AIGAF 1118
Cdd:cd09273    2 VFTDGSSFKAGYAIVSGT-EIVEAQPLPP--GTSAQRAELIAL---IQALELAKgkPVNIYTDSAYAVHALHLLeTIGIE 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 9629499  1119 LGTSTHQSLYAHLPTLLH----NKVIYLHHIRSHTNLPDPISTLNEYTD 1163
Cdd:cd09273   76 RGFLKSIKNLSLFLQLLEavqrPKPVAIIHIRAHSKLPGPLAEGNAQAD 124
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
146-263 5.41e-14

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: 70.00  E-value: 5.41e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     146 AHSPWQMKDLQAIKQEVSTSAPGSPQFMQTVRLAIQQFDPTAKDLQDLL-------QYLcssLVVSLHHQQFHTLITEAE 218
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAkavlspgQYL---LWKAEWQELAQEQARRNQ 77
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 9629499     219 TRG---------MTGYNPMAGPlRMQANNPaqQGLRREYQNLWLAAFSALPGNT 263
Cdd:pfam00607   78 RAGpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
1403-1445 3.05e-12

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


The actual alignment was detected with superfamily member pfam00552:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 62.42  E-value: 3.05e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 9629499    1403 YKLPGLTNQRWKGPLQSLQEAAGAALLSIDGS-PQWIPWRLLKK 1445
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQDASdPQWVPERLLKR 44
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
1177-1210 5.11e-07

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: 47.37  E-value: 5.11e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9629499    1177 DLHKLTHCNSRALVSS-GATPQQAKSLLQTCYTCN 1210
Cdd:pfam02022    1 ELHSLHHVNAKALRKKfGITRKQARDIVQSCPTCQ 35
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
353-407 1.31e-06

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.42  E-value: 1.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9629499    353 PRKPPPT----QPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCPQfKPPPTE 407
Cdd:PTZ00368   17 PNSAPAGaakaRPCYKCGEPGHLSRECPSAPGGRGERSCYNcgKTGHLSRECPE-APPGSG 76
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
595-809 9.02e-66

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: 221.77  E-value: 9.02e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   595 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSL 674
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   675 STALPyLQTIDLTDAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFPMST 754
Cdd:cd01645   81 PKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIV 159
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 9629499   755 IIQYMDDILLASPTQEELQQLSKMTLQALVTHGLPVSQEKTQQTPGqIRFLGQVI 809
Cdd:cd01645  160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
1-91 5.91e-45

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


Pssm-ID: 460500  Cd Length: 92  Bit Score: 157.43  E-value: 5.91e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499       1 MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRT 80
Cdd:pfam02228    1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80
                           90
                   ....*....|.
gi 9629499      81 IEIINVLIKNQ 91
Cdd:pfam02228   81 NEILHILIQTQ 91
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
639-809 4.13e-44

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: 158.62  E-value: 4.13e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     639 KKPNGKWRFI----HDLRATNAIT-------TTLASPSPGPPDLTSLSTALPYLQTIDLTDAFFQIPLPKQFQPYFAFTI 707
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTT 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     708 PQPCN----YGPGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFpMSTIIQYMDDILLASPTQEELQQLSKMTLQAL 783
Cdd:pfam00078   83 PPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161
                          170       180
                   ....*....|....*....|....*...
gi 9629499     784 VTHGLPVSQEKTQQTPGQ--IRFLGQVI 809
Cdd:pfam00078  162 KESGLKINPEKTQFFLKSkeVKYLGVTL 189
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
263-336 1.08e-29

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: 112.96  E-value: 1.08e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9629499     263 TRDPSWAAILQGLEEPYCAFVERLNVALDNGLPEGTPKEPILRSLAYSNANKDCQKLLQARGHTnSPLGDMLRA 336
Cdd:pfam19317    2 YKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1229-1322 1.90e-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: 101.62  E-value: 1.90e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499    1229 PNHIWQGDVTHYKYKRN--RYCLHVWVDTFSNAVSITCKTKETSSETVSALLH-AITILGK-PLSINTDNGSAFLSQEFQ 1304
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALErAIAFRGGvPLIIHSDNGSEYTSKAFR 80
                           90
                   ....*....|....*...
gi 9629499    1305 AFCASWHIKHSTHVPYNS 1322
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1229-1346 8.68e-18

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 85.98  E-value: 8.68e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1229 PNHIWQGDVTHYKYKRNRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILG--KPLSINTDNGSAFLSQEFQA 1305
Cdd:COG2801  148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSReIVGWSVSDSMDAELVVDALEMAIERRGppKPLILHSDNGSQYTSKAYQE 227
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 9629499  1306 FCASWHIKHSTHVPYNSTSSGLVERTNGIVKA-LLNKYLLDS 1346
Cdd:COG2801  228 LLKKLGITQSMSRPGNPQDNAFIESFFGTLKYeLLYRRRFES 269
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
449-556 2.64e-16

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: 75.87  E-value: 2.64e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     449 QQHQPLLDVQVSIagappRPTQALLDTGADLTVLPQALAPESVSVS--DTTVLGAGGQTSSQFKLLQSPLCVYLPFR--R 524
Cdd:pfam00077    1 AEQRPLLTVKIGG-----KYFTALLDTGADDTVISQNDWPTNWPKQkaTTNIQGIGGGINVRQSDQILILIGEDKFRgtV 75
                           90       100       110
                   ....*....|....*....|....*....|..
gi 9629499     525 APVTLPSCLVDtnskwaIIGRDILQKCQSVLY 556
Cdd:pfam00077   76 SPLILPTCPVN------IIGRDLLQQLGGRLT 101
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
1042-1163 6.18e-15

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: 72.76  E-value: 6.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1042 LFSDGSSQKAAYVLWDQTiLHHDSVTLPPhgSNSAQKGELLALlsgIRAAKSWP--SLNIFLDSKYLIKYLHSL-AIGAF 1118
Cdd:cd09273    2 VFTDGSSFKAGYAIVSGT-EIVEAQPLPP--GTSAQRAELIAL---IQALELAKgkPVNIYTDSAYAVHALHLLeTIGIE 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 9629499  1119 LGTSTHQSLYAHLPTLLH----NKVIYLHHIRSHTNLPDPISTLNEYTD 1163
Cdd:cd09273   76 RGFLKSIKNLSLFLQLLEavqrPKPVAIIHIRAHSKLPGPLAEGNAQAD 124
transpos_IS3 NF033516
IS3 family transposase;
1229-1346 1.13e-14

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 77.61  E-value: 1.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   1229 PNHIWQGDVTHYKYKRNRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 1305
Cdd:NF033516  215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSReIVGWSVSTSMSAELVLDALEMAIEWRGKPegLILHSDNGSQYTSKAYRE 294
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 9629499   1306 FCASWHIKHSTHVPYNSTSSGLVERTNGIVKA-LLNKYLLDS 1346
Cdd:NF033516  295 WLKEHGITQSMSRPGNCWDNAVAESFFGTLKReCLYRRRFRT 336
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
146-263 5.41e-14

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: 70.00  E-value: 5.41e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     146 AHSPWQMKDLQAIKQEVSTSAPGSPQFMQTVRLAIQQFDPTAKDLQDLL-------QYLcssLVVSLHHQQFHTLITEAE 218
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAkavlspgQYL---LWKAEWQELAQEQARRNQ 77
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 9629499     219 TRG---------MTGYNPMAGPlRMQANNPaqQGLRREYQNLWLAAFSALPGNT 263
Cdd:pfam00607   78 RAGpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
transpos_IS481 NF033577
IS481 family transposase; null
1229-1337 3.01e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 68.77  E-value: 3.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   1229 PNHIWQGDVTHY---KYKRNRYcLHVWVDTFSNAVSITCKTKETSSETVSALLHAITILGKPL-SINTDNGSAFLS--QE 1302
Cdd:NF033577  127 PGELWHIDIKKLgriPDVGRLY-LHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrRVLTDNGSEFRSraHG 205
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 9629499   1303 FQAFCASWHIKHSTHVPYNSTSSGLVERTNGIVKA 1337
Cdd:NF033577  206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
1403-1445 3.05e-12

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: 62.42  E-value: 3.05e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 9629499    1403 YKLPGLTNQRWKGPLQSLQEAAGAALLSIDGS-PQWIPWRLLKK 1445
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQDASdPQWVPERLLKR 44
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
1042-1165 3.48e-11

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: 62.39  E-value: 3.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499    1042 LFSDGSSQ------KAAYVLW--DQTIlhhdSVTLPPHGSNsaQKGELLALLSGIRAAKSWPSLNIFLDSKYLIK----Y 1109
Cdd:pfam00075    6 VYTDGSCLgnpgpgGAGAVLYrgHENI----SAPLPGRTTN--NRAELQAVIEALKALKSPSKVNIYTDSQYVIGgitqW 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9629499    1110 LHSLAIGAFLGTST-----HQSLYAHLPTLLHNKVIYLHHIRSHTNLPDpistlNEYTDSL 1165
Cdd:pfam00075   80 VHGWKKNGWPTTSEgkpvkNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRL 135
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
1177-1210 5.11e-07

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: 47.37  E-value: 5.11e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9629499    1177 DLHKLTHCNSRALVSS-GATPQQAKSLLQTCYTCN 1210
Cdd:pfam02022    1 ELHSLHHVNAKALRKKfGITRKQARDIVQSCPTCQ 35
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
353-407 1.31e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.42  E-value: 1.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9629499    353 PRKPPPT----QPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCPQfKPPPTE 407
Cdd:PTZ00368   17 PNSAPAGaakaRPCYKCGEPGHLSRECPSAPGGRGERSCYNcgKTGHLSRECPE-APPGSG 76
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
468-549 2.09e-06

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133159  Cd Length: 86  Bit Score: 47.33  E-value: 2.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   468 PTQALLDTGADLTVLPQALAPESVSVSDTTVL-GAGGQTSSQFKLLQSPLCVylpfrrAPVTLP-SCLVDTNSKWAIIGR 545
Cdd:cd06095    9 PIVFLVDTGATHSVLKSDLGPKQELSTTSVLIrGVSGQSQQPVTTYRTLVDL------GGHTVShSFLVVPNCPDPLLGR 82

                 ....
gi 9629499   546 DILQ 549
Cdd:cd06095   83 DLLS 86
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1042-1165 1.49e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 45.99  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1042 LFSDGSSQK------AAYVLWDQTILHHDSVTLPpHGSNsaQKGELLALLSGIRAAKSWP--SLNIFLDSKYLI----KY 1109
Cdd:COG0328    5 IYTDGACRGnpgpggWGAVIRYGGEEKELSGGLG-DTTN--NRAELTALIAALEALKELGpcEVEIYTDSQYVVnqitGW 81
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 9629499  1110 LHSLAIGAFLGTStHQSLYAHLPTLLHNKVIYLHHIRSHTNLPdpistLNEYTDSL 1165
Cdd:COG0328   82 IHGWKKNGWKPVK-NPDLWQRLDELLARHKVTFEWVKGHAGHP-----GNERADAL 131
ZnF_C2HC smart00343
zinc finger;
362-376 4.26e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 4.26e-05
                            10
                    ....*....|....*
gi 9629499      362 CFRCGKTGHWSRDCT 376
Cdd:smart00343    2 CYNCGKEGHIARDCP 16
PHA02517 PHA02517
putative transposase OrfB; Reviewed
1229-1337 5.26e-05

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 46.78  E-value: 5.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   1229 PNHIWQGDVTHYKYKRNRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 1305
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARrIVGWRVSSSMDTDFVLDALEQALWARGRPggLIHHSDKGSQYVSLAYTQ 188
                          90       100       110
                  ....*....|....*....|....*....|..
gi 9629499   1306 FCASWHIKHSTHVPYNSTSSGLVERTNGIVKA 1337
Cdd:PHA02517  189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA 220
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
360-376 8.58e-05

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.59  E-value: 8.58e-05
                           10
                   ....*....|....*..
gi 9629499     360 QPCFRCGKTGHWSRDCT 376
Cdd:pfam00098    1 GKCYNCGEPGHIARDCP 17
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
457-505 2.70e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 39.93  E-value: 2.70e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9629499   457 VQVSIAGappRPTQALLDTGADLTVLPQALA-----PESVSVSDTTVLGAGGQT 505
Cdd:COG3577   44 VEGTING---QPVRFLVDTGASTVVLSESDArrlglDPEDLGRPVRVQTANGVV 94
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
595-809 9.02e-66

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: 221.77  E-value: 9.02e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   595 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSL 674
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   675 STALPyLQTIDLTDAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFPMST 754
Cdd:cd01645   81 PKGWP-LIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIV 159
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 9629499   755 IIQYMDDILLASPTQEELQQLSKMTLQALVTHGLPVSQEKTQQTPGqIRFLGQVI 809
Cdd:cd01645  160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
595-809 6.01e-55

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: 190.64  E-value: 6.01e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   595 PPQIDQFPFKPERLQALTDLVSKALEASYIEPYSGPGNNPVFPVKKPNG-KWRFIHDLRATNAITTTLASPSPGPPDLTS 673
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   674 -LSTALPYLQTIDLTDAFFQIPLPKQFQPYFAFTIPqpcnygpGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFPM 752
Cdd:cd03715   81 lLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEG 153
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9629499   753 STIIQYMDDILLASPTQEELQQLSKMTLQALVTHGLPVSQEKTQQTPGQIRFLGQVI 809
Cdd:cd03715  154 TILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
1-91 5.91e-45

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


Pssm-ID: 460500  Cd Length: 92  Bit Score: 157.43  E-value: 5.91e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499       1 MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRT 80
Cdd:pfam02228    1 MGKIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFLKIALETPVWICPINYSLLASLLPKGYPGRV 80
                           90
                   ....*....|.
gi 9629499      81 IEIINVLIKNQ 91
Cdd:pfam02228   81 NEILHILIQTQ 91
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
639-809 4.13e-44

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: 158.62  E-value: 4.13e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     639 KKPNGKWRFI----HDLRATNAIT-------TTLASPSPGPPDLTSLSTALPYLQTIDLTDAFFQIPLPKQFQPYFAFTI 707
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTT 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     708 PQPCN----YGPGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFpMSTIIQYMDDILLASPTQEELQQLSKMTLQAL 783
Cdd:pfam00078   83 PPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLEWL 161
                          170       180
                   ....*....|....*....|....*...
gi 9629499     784 VTHGLPVSQEKTQQTPGQ--IRFLGQVI 809
Cdd:pfam00078  162 KESGLKINPEKTQFFLKSkeVKYLGVTL 189
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
623-809 4.74e-36

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: 135.03  E-value: 4.74e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   623 YIEPYSGPGNNPVFPVKKPNGKWRFIHDLRATNAITTTLASPSPGPPDLTSLSTALPYLQTIDLTDAFFQIPLPKQFQPY 702
Cdd:cd01647    2 IIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRPK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   703 FAFTIpqpcnygPGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTFpmstIIQYMDDILLASPTQEELQQLSKMTLQA 782
Cdd:cd01647   82 TAFRT-------PFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF----VEVYLDDILVYSKTEEEHLEHLREVLER 150
                        170       180
                 ....*....|....*....|....*..
gi 9629499   783 LVTHGLPVSQEKTQQTPGQIRFLGQVI 809
Cdd:cd01647  151 LREAGLKLNPEKCEFGVPEVEFLGHIV 177
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
263-336 1.08e-29

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: 112.96  E-value: 1.08e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9629499     263 TRDPSWAAILQGLEEPYCAFVERLNVALDNGLPEGTPKEPILRSLAYSNANKDCQKLLQARGHTnSPLGDMLRA 336
Cdd:pfam19317    2 YKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKT-GTLSDMIRA 74
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
1229-1322 1.90e-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: 101.62  E-value: 1.90e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499    1229 PNHIWQGDVTHYKYKRN--RYCLHVWVDTFSNAVSITCKTKETSSETVSALLH-AITILGK-PLSINTDNGSAFLSQEFQ 1304
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGGggKLYLLVIVDDFSREILAWALSSEMDAELVLDALErAIAFRGGvPLIIHSDNGSEYTSKAFR 80
                           90
                   ....*....|....*...
gi 9629499    1305 AFCASWHIKHSTHVPYNS 1322
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1229-1346 8.68e-18

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 85.98  E-value: 8.68e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1229 PNHIWQGDVTHYKYKRNRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILG--KPLSINTDNGSAFLSQEFQA 1305
Cdd:COG2801  148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSReIVGWSVSDSMDAELVVDALEMAIERRGppKPLILHSDNGSQYTSKAYQE 227
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 9629499  1306 FCASWHIKHSTHVPYNSTSSGLVERTNGIVKA-LLNKYLLDS 1346
Cdd:COG2801  228 LLKKLGITQSMSRPGNPQDNAFIESFFGTLKYeLLYRRRFES 269
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
449-556 2.64e-16

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: 75.87  E-value: 2.64e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     449 QQHQPLLDVQVSIagappRPTQALLDTGADLTVLPQALAPESVSVS--DTTVLGAGGQTSSQFKLLQSPLCVYLPFR--R 524
Cdd:pfam00077    1 AEQRPLLTVKIGG-----KYFTALLDTGADDTVISQNDWPTNWPKQkaTTNIQGIGGGINVRQSDQILILIGEDKFRgtV 75
                           90       100       110
                   ....*....|....*....|....*....|..
gi 9629499     525 APVTLPSCLVDtnskwaIIGRDILQKCQSVLY 556
Cdd:pfam00077   76 SPLILPTCPVN------IIGRDLLQQLGGRLT 101
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
1042-1163 6.18e-15

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: 72.76  E-value: 6.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1042 LFSDGSSQKAAYVLWDQTiLHHDSVTLPPhgSNSAQKGELLALlsgIRAAKSWP--SLNIFLDSKYLIKYLHSL-AIGAF 1118
Cdd:cd09273    2 VFTDGSSFKAGYAIVSGT-EIVEAQPLPP--GTSAQRAELIAL---IQALELAKgkPVNIYTDSAYAVHALHLLeTIGIE 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 9629499  1119 LGTSTHQSLYAHLPTLLH----NKVIYLHHIRSHTNLPDPISTLNEYTD 1163
Cdd:cd09273   76 RGFLKSIKNLSLFLQLLEavqrPKPVAIIHIRAHSKLPGPLAEGNAQAD 124
transpos_IS3 NF033516
IS3 family transposase;
1229-1346 1.13e-14

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 77.61  E-value: 1.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   1229 PNHIWQGDVTHYKYKRNRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 1305
Cdd:NF033516  215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSReIVGWSVSTSMSAELVLDALEMAIEWRGKPegLILHSDNGSQYTSKAYRE 294
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 9629499   1306 FCASWHIKHSTHVPYNSTSSGLVERTNGIVKA-LLNKYLLDS 1346
Cdd:NF033516  295 WLKEHGITQSMSRPGNCWDNAVAESFFGTLKReCLYRRRFRT 336
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
684-806 1.47e-14

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: 71.61  E-value: 1.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   684 IDLTDAFFQIPLPKQFQPYFAFtIPQpcnygpGARYAWTVLPQGFKNSPTLFEQQLAAVLSPIRKTfpMSTIIQYMDDIL 763
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLL--GVRIFSYLDDLL 71
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 9629499   764 LASPTQEE----LQQLSKMTLQALvthGLPVSQEKTQQTPGQ-IRFLG 806
Cdd:cd03714   72 IIASSIKTseavLRHLRATLLANL---GFTLNLEKSKLGPTQrITFLG 116
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
146-263 5.41e-14

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: 70.00  E-value: 5.41e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499     146 AHSPWQMKDLQAIKQEVSTSAPGSPQFMQTVRLAIQQFDPTAKDLQDLL-------QYLcssLVVSLHHQQFHTLITEAE 218
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAkavlspgQYL---LWKAEWQELAQEQARRNQ 77
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 9629499     219 TRG---------MTGYNPMAGPlRMQANNPaqQGLRREYQNLWLAAFSALPGNT 263
Cdd:pfam00607   78 RAGpdrgitldmLTGTGQYATP-QAQAQLP--PEVLEQIKALALRAWKKLPPPG 128
transpos_IS481 NF033577
IS481 family transposase; null
1229-1337 3.01e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 68.77  E-value: 3.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   1229 PNHIWQGDVTHY---KYKRNRYcLHVWVDTFSNAVSITCKTKETSSETVSALLHAITILGKPL-SINTDNGSAFLS--QE 1302
Cdd:NF033577  127 PGELWHIDIKKLgriPDVGRLY-LHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrRVLTDNGSEFRSraHG 205
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 9629499   1303 FQAFCASWHIKHSTHVPYNSTSSGLVERTNGIVKA 1337
Cdd:NF033577  206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
1403-1445 3.05e-12

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: 62.42  E-value: 3.05e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 9629499    1403 YKLPGLTNQRWKGPLQSLQEAAGAALLSIDGS-PQWIPWRLLKK 1445
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQDASdPQWVPERLLKR 44
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
1042-1165 3.48e-11

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: 62.39  E-value: 3.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499    1042 LFSDGSSQ------KAAYVLW--DQTIlhhdSVTLPPHGSNsaQKGELLALLSGIRAAKSWPSLNIFLDSKYLIK----Y 1109
Cdd:pfam00075    6 VYTDGSCLgnpgpgGAGAVLYrgHENI----SAPLPGRTTN--NRAELQAVIEALKALKSPSKVNIYTDSQYVIGgitqW 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9629499    1110 LHSLAIGAFLGTST-----HQSLYAHLPTLLHNKVIYLHHIRSHTNLPDpistlNEYTDSL 1165
Cdd:pfam00075   80 VHGWKKNGWPTTSEgkpvkNKDLWQLLKALCKKHQVYWQWVKGHAGNPG-----NEMADRL 135
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
684-809 6.60e-09

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: 54.66  E-value: 6.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   684 IDLTDAFFQIPLPkqfqpyfaftipqpcnygpgaryawtvlpQGFKNSPTLFEQQLAAVLSPIRKTFPMSTIIQYMDDIL 763
Cdd:cd00304    1 FDVKSFFTSIPLP-----------------------------QGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 9629499   764 LASPTQEELQQLSKMTlQALVTHGLPVSQEKTQQTP--GQIRFLGQVI 809
Cdd:cd00304   52 VIAKSEQQAVKKRELE-EFLARLGLNLSDEKTQFTEkeKKFKFLGILV 98
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
1177-1210 5.11e-07

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: 47.37  E-value: 5.11e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 9629499    1177 DLHKLTHCNSRALVSS-GATPQQAKSLLQTCYTCN 1210
Cdd:pfam02022    1 ELHSLHHVNAKALRKKfGITRKQARDIVQSCPTCQ 35
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
353-407 1.31e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.42  E-value: 1.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9629499    353 PRKPPPT----QPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCPQfKPPPTE 407
Cdd:PTZ00368   17 PNSAPAGaakaRPCYKCGEPGHLSRECPSAPGGRGERSCYNcgKTGHLSRECPE-APPGSG 76
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1233-1374 1.86e-06

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 51.81  E-value: 1.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1233 WQGDVTHYKykRNRYCLHVWVDTFSNAVsITCKTKETSSETVS-ALLHAITILGKPL--SINTDNGSAFLsqEFQAFCAS 1309
Cdd:COG2826  175 WEGDLIIGK--RGKSALLTLVERKSRFV-ILLKLPDKTAESVAdALIRLLRKLPAFLrkSITTDNGKEFA--DHKEIEAA 249
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9629499  1310 WHIKHS-THvPYNSTSSGLVERTNGivkaLLNKYLLDSPNLP--LDNAISKALWTLNQ-----LNvmssqWKT 1374
Cdd:COG2826  250 LGIKVYfAD-PYSPWQRGTNENTNG----LLRQYFPKGTDFStvTQEELDAIADRLNNrprkcLG-----YKT 312
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
468-549 2.09e-06

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133159  Cd Length: 86  Bit Score: 47.33  E-value: 2.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   468 PTQALLDTGADLTVLPQALAPESVSVSDTTVL-GAGGQTSSQFKLLQSPLCVylpfrrAPVTLP-SCLVDTNSKWAIIGR 545
Cdd:cd06095    9 PIVFLVDTGATHSVLKSDLGPKQELSTTSVLIrGVSGQSQQPVTTYRTLVDL------GGHTVShSFLVVPNCPDPLLGR 82

                 ....
gi 9629499   546 DILQ 549
Cdd:cd06095   83 DLLS 86
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1042-1165 1.49e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 45.99  E-value: 1.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499  1042 LFSDGSSQK------AAYVLWDQTILHHDSVTLPpHGSNsaQKGELLALLSGIRAAKSWP--SLNIFLDSKYLI----KY 1109
Cdd:COG0328    5 IYTDGACRGnpgpggWGAVIRYGGEEKELSGGLG-DTTN--NRAELTALIAALEALKELGpcEVEIYTDSQYVVnqitGW 81
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 9629499  1110 LHSLAIGAFLGTStHQSLYAHLPTLLHNKVIYLHHIRSHTNLPdpistLNEYTDSL 1165
Cdd:COG0328   82 IHGWKKNGWKPVK-NPDLWQRLDELLARHKVTFEWVKGHAGHP-----GNERADAL 131
ZnF_C2HC smart00343
zinc finger;
362-376 4.26e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 4.26e-05
                            10
                    ....*....|....*
gi 9629499      362 CFRCGKTGHWSRDCT 376
Cdd:smart00343    2 CYNCGKEGHIARDCP 16
PHA02517 PHA02517
putative transposase OrfB; Reviewed
1229-1337 5.26e-05

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 46.78  E-value: 5.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   1229 PNHIWQGDVTHYKYKRNRYCLHVWVDTFSN-AVSITCKTKETSSETVSALLHAITILGKP--LSINTDNGSAFLSQEFQA 1305
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARrIVGWRVSSSMDTDFVLDALEQALWARGRPggLIHHSDKGSQYVSLAYTQ 188
                          90       100       110
                  ....*....|....*....|....*....|..
gi 9629499   1306 FCASWHIKHSTHVPYNSTSSGLVERTNGIVKA 1337
Cdd:PHA02517  189 RLKEAGIRASTGSRGDSYDNAPAESINGLYKA 220
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
666-787 5.80e-05

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


Pssm-ID: 238822  Cd Length: 213  Bit Score: 45.76  E-value: 5.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   666 PGPPDLTSLSTAL------PYLQTIDLTDAFFQIPLPKQFQPYFAFTIPQPCNYGPGARYAWTVLPQGFKNSPTLfeqqL 739
Cdd:cd01644   40 KGPDLLNSLFGVLlrfrqgKIAVSADIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFL----A 115
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9629499   740 AAVLSPIRKTFP---MSTIIQ---YMDDILLASPTQEELQQLSKmTLQALVTHG 787
Cdd:cd01644  116 NRALKQHAEDHPheaAAKIIKrnfYVDDILVSTDTLNEAVNVAK-RLIALLKKG 168
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
353-399 7.16e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 44.41  E-value: 7.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 9629499    353 PRKPPPTQPCFRCGKTGHWSRDCTLPRPPPGPCPLCK--DPSHWKRDCP 399
Cdd:PTZ00368   46 APGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNcgQTGHISRECP 94
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
360-376 8.58e-05

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.59  E-value: 8.58e-05
                           10
                   ....*....|....*..
gi 9629499     360 QPCFRCGKTGHWSRDCT 376
Cdd:pfam00098    1 GKCYNCGEPGHIARDCP 17
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
457-505 1.12e-04

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 42.56  E-value: 1.12e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 9629499     457 VQVSIAGappRPTQALLDTGADLTVLPQALA-----PESVSVSDTTVLGAGGQT 505
Cdd:pfam13975    1 VDVTING---RPVRFLVDTGASVTVISEALAerlglDRLVDAYPVTVRTANGTV 51
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
457-514 1.63e-04

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 42.23  E-value: 1.63e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9629499   457 VQVSIAGappRPTQALLDTGADLTVLPQALAPE----SVSVSDTTVLGAGGQTSSQFKLLQS 514
Cdd:cd05483    5 VPVTING---QPVRFLLDTGASTTVISEELAERlglpLTLGGKVTVQTANGRVRAARVRLDS 63
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
1042-1112 2.01e-04

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 42.69  E-value: 2.01e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9629499  1042 LFSDGSSQK------AAYVLWDQTILHHDSVTLPPHGSnSAQKGELLALLSGIRAAKSWPSLNIFL--DSKYLIKYLHS 1112
Cdd:cd06222    1 INVDGSCRGnpgpagIGGVLRDHEGGWLGGFALKIGAP-TALEAELLALLLALELALDLGYLKVIIesDSKYVVDLINS 78
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
362-407 6.05e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 41.72  E-value: 6.05e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9629499    362 CFRCGKTGHWSRDCTLPRPPPGPCPLC----KDPSHWKRDCPQFKPPPTE 407
Cdd:PTZ00368    3 CYRCGGVGHQSRECPNSAPAGAAKARPcykcGEPGHLSRECPSAPGGRGE 52
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
457-509 1.08e-03

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 39.58  E-value: 1.08e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 9629499     457 VQVSIAGappRPTQALLDTGADLTVLPQALA-----PESVSVSDTTVLGAGGQTSSQF 509
Cdd:pfam13650    1 VPVTING---KPVRFLVDTGASGTVISPSLAerlglKVRGLAYTVRVSTAGGRVSAAR 55
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
353-408 1.19e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 1.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9629499    353 PRKPPPTQP--CFRCGKTGHWSRDCTLPRPPPGPCPL---CKDPSHWKRDCPQFKPPPTEE 408
Cdd:PTZ00368   69 PEAPPGSGPrsCYNCGQTGHISRECPNRAKGGAARRAcynCGGEGHISRDCPNAGKRPGGD 129
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
467-549 1.31e-03

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 39.17  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   467 RPTQALLDTGADLTVLPQALAPESVS--VSDTTVLGAGGQT----SSQFKLLQSPLCVYLPFRRAPVTLPSCLvdtnskw 540
Cdd:cd05482    8 KLFEGLLDTGADVSIIAENDWPKNWPiqPAPSNLTGIGGAItpsqSSVLLLEIDGEGHLGTILVYVLSLPVNL------- 80

                 ....*....
gi 9629499   541 aiIGRDILQ 549
Cdd:cd05482   81 --WGRDILS 87
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
457-505 2.70e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 39.93  E-value: 2.70e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9629499   457 VQVSIAGappRPTQALLDTGADLTVLPQALA-----PESVSVSDTTVLGAGGQT 505
Cdd:COG3577   44 VEGTING---QPVRFLVDTGASTVVLSESDArrlglDPEDLGRPVRVQTANGVV 94
RT_nLTR_like cd01650
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse ...
718-816 3.42e-03

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.


Pssm-ID: 238827 [Multi-domain]  Cd Length: 220  Bit Score: 40.74  E-value: 3.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9629499   718 RYAWTVL--PQGFKNSPTLFEQQLAAVLSPIRKTFPM------STIIQYMDDILLASPTQEELQQLSKMTLQ-ALVTHGL 788
Cdd:cd01650   99 EFLLKALgvRQGDPLSPLLFNLALDDLLRLLNKEEEIklggpgITHLAYADDIVLFSEGKSRKLQELLQRLQeWSKESGL 178
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 9629499   789 PVSQEKTQ--------QTPGQIRFLGQVISP-NHITY 816
Cdd:cd01650  179 KINPSKSKvmlignkkKRLKDITLNGTPIEAvETFKY 215
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
353-399 8.97e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 38.25  E-value: 8.97e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9629499    353 PRKPPPTQPCFRCGKTGHWSRDCTLPRPPPGPCPLCK---DPSHWKRDCP 399
Cdd:PTZ00368   97 AKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYncgQTGHLSRDCP 146
 
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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