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Conserved domains on  [gi|392051002|gb|AFM52262|]
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Pol, partial [Rousettus leschenaultii retrovirus]

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 ...
 173-325 2.62e-82

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 cd03715:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 210  Bit Score: 253.04  E-value: 2.62e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 173 PVAIRQYPMTKEAREGIRPHIQRLLQQGILVRCQSPWNTPLLPVKKPGTGDYHPVQDLREVNKRVQDIHPTVPNPYNLLS 252
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392051002 253 SLPPDHVWYTVLDLKDTFFCLRLHPSSRNIFAFEWRDpdsgttGQLTWTRLPKGFKNSPTLFDEALHQDLAHF 325
Cdd:cd03715   81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPF 147
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 13-94 2.07e-27

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: 104.72  E-value: 2.07e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  13 VTLEVEWRPVEFLVDTGAQHSVLLEPAGPV---SHKKSWVIGATGHQQYSWTTRRT-VDLGKGRVTHSFLVIPKCPAPLL 88
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKqelSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                 ....*.
gi 392051002  89 GRDLLT 94
Cdd:cd06095   81 GRDLLS 86
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 365-460 5.43e-22

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: 90.07  E-value: 5.43e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  365 PGSYWEVDFTEVK-PARYGYRYLLVFVDTFSGWVKAFPTKKE-TAQMVAKKILEDIFPRFGVPKVIGSDNGPAFVAQVSQ 442
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 392051002  443 GLAKILGLDWKLHCAYRP 460
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 173-325 2.62e-82

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: 253.04  E-value: 2.62e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 173 PVAIRQYPMTKEAREGIRPHIQRLLQQGILVRCQSPWNTPLLPVKKPGTGDYHPVQDLREVNKRVQDIHPTVPNPYNLLS 252
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392051002 253 SLPPDHVWYTVLDLKDTFFCLRLHPSSRNIFAFEWRDpdsgttGQLTWTRLPKGFKNSPTLFDEALHQDLAHF 325
Cdd:cd03715   81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPF 147
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 13-94 2.07e-27

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: 104.72  E-value: 2.07e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  13 VTLEVEWRPVEFLVDTGAQHSVLLEPAGPV---SHKKSWVIGATGHQQYSWTTRRT-VDLGKGRVTHSFLVIPKCPAPLL 88
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKqelSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                 ....*.
gi 392051002  89 GRDLLT 94
Cdd:cd06095   81 GRDLLS 86
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 365-460 5.43e-22

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: 90.07  E-value: 5.43e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  365 PGSYWEVDFTEVK-PARYGYRYLLVFVDTFSGWVKAFPTKKE-TAQMVAKKILEDIFPRFGVPKVIGSDNGPAFVAQVSQ 442
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 392051002  443 GLAKILGLDWKLHCAYRP 460
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 9-100 6.28e-18

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: 78.95  E-value: 6.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002    9 PEPRVTLEVEWRPVEFLVDTGAQHSVLLEPAGP----VSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH--SFLVIPK 82
Cdd:pfam00077   3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPtnwpKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                          90
                  ....*....|....*...
gi 392051002   83 CPAPLLGRDLLTKMGAQI 100
Cdd:pfam00077  83 CPVNIIGRDLLQQLGGRL 100
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 216-320 4.99e-13

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: 67.33  E-value: 4.99e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  216 VKKPGTGDYHPV----QDLREVNKRVQD-IHPTVPNPYNLLSSLPPDH-----VWYTVLDLKDTFFCLRLHPSSRNIFAF 285
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQPGFRPGLAklkkaKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 392051002  286 ----EWRDPDSGTTGQL-TWTRLPKGFKNSPTLFDEALHQ 320
Cdd:pfam00078  81 ttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNE 120
transpos_IS481 NF033577
IS481 family transposase; null
 355-469 2.53e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 67.23  E-value: 2.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 355 AQGKRLRGDR--PGSYWEVDFTEVKPARY-GYRYLLVFVDTFSGWVKAFPTKKETAQMVAKkILEDIFPRFGVP-KVIGS 430
Cdd:NF033577 115 KTGKVKRYERahPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAYAELYPDETAETAAD-FLRRAFAEHGIPiRRVLT 193

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 392051002 431 DNGPAFVA---QVSQGLAKiLGLDWKLHCAYRPQSSGQVERM 469
Cdd:NF033577 194 DNGSEFRSrahGFELALAE-LGIEHRRTRPYHPQTNGKVERF 234
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
11-102 6.56e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 37.23  E-value: 6.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  11 PRVTLEVEWRPVEFLVDTGAQHSVL----LEPAG---PVSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH-SFLVIP- 81
Cdd:COG3577   42 FVVEGTINGQPVRFLVDTGASTVVLsesdARRLGldpEDLGRPVRVQTANGVVRAARVRLDSVRIGGITLRNvRAVVLPg 121

                         90       100
                 ....*....|....*....|..
gi 392051002  82 -KCPAPLLGRDLLTKMGAQISF 102
Cdd:COG3577  122 gELDDGLLGMSFLGRLDFEIDG 143
 
Name Accession Description Interval E-value
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 173-325 2.62e-82

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: 253.04  E-value: 2.62e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 173 PVAIRQYPMTKEAREGIRPHIQRLLQQGILVRCQSPWNTPLLPVKKPGTGDYHPVQDLREVNKRVQDIHPTVPNPYNLLS 252
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392051002 253 SLPPDHVWYTVLDLKDTFFCLRLHPSSRNIFAFEWRDpdsgttGQLTWTRLPKGFKNSPTLFDEALHQDLAHF 325
Cdd:cd03715   81 LLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG------QQYTFTRLPQGFKNSPTLFHEALARDLAPF 147
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 173-331 1.72e-27

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: 109.29  E-value: 1.72e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 173 PVAIRQYPMTKEAREGIRPHIQRLLQQGILVRCQSPWNTPLLPVKKPgTGDYHPVQDLREVNKRVQD---IHPTVPNPyn 249
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKK-SGKWRLLHDLRAVNAQTQDmgaLQPGLPHP-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 250 llSSLPPDhvWY-TVLDLKDTFFCLRLHPSSRNIFAFEWRDPDSGTTGQ-LTWTRLPKGFKNSPTLFDEALHQDLAHFCA 327
Cdd:cd01645   78 --AALPKG--WPlIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKrYQWKVLPQGMKNSPTICQSFVAQALEPFRK 153


                 ....
gi 392051002 328 SHPQ 331
Cdd:cd01645  154 QYPD 157
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 13-94 2.07e-27

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: 104.72  E-value: 2.07e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  13 VTLEVEWRPVEFLVDTGAQHSVLLEPAGPV---SHKKSWVIGATGHQQYSWTTRRT-VDLGKGRVTHSFLVIPKCPAPLL 88
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKqelSTTSVLIRGVSGQSQQPVTTYRTlVDLGGHTVSHSFLVVPNCPDPLL 80


                 ....*.
gi 392051002  89 GRDLLT 94
Cdd:cd06095   81 GRDLLS 86
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 200-326 5.57e-23

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: 95.35  E-value: 5.57e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 200 GILVRCQSPWNTPLLPVKKPGtGDYHPVQDLREVNKR-VQDIHPtVPNPYNLLSSLPpDHVWYTVLDLKDTFFCLRLHPS 278
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKD-GKLRLCVDYRKLNKVtIKDRYP-LPTIDELLEELA-GAKVFSKLDLRSGYHQIPLAEE 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392051002 279 SRNIFAFewrdpdsgTT--GQLTWTRLPKGFKNSPTLF----DEALHQDLAHFC 326
Cdd:cd01647   78 SRPKTAF--------RTpfGLYEYTRMPFGLKNAPATFqrlmNKILGDLLGDFV 123
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 365-460 5.43e-22

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: 90.07  E-value: 5.43e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  365 PGSYWEVDFTEVK-PARYGYRYLLVFVDTFSGWVKAFPTKKE-TAQMVAKKILEDIFPRFGVPKVIGSDNGPAFVAQVSQ 442
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 392051002  443 GLAKILGLDWKLHCAYRP 460
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 9-100 6.28e-18

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: 78.95  E-value: 6.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002    9 PEPRVTLEVEWRPVEFLVDTGAQHSVLLEPAGP----VSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH--SFLVIPK 82
Cdd:pfam00077   3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPtnwpKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGtvSPLILPT 82

                          90
                  ....*....|....*...
gi 392051002   83 CPAPLLGRDLLTKMGAQI 100
Cdd:pfam00077  83 CPVNIIGRDLLQQLGGRL 100
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 216-320 4.99e-13

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: 67.33  E-value: 4.99e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  216 VKKPGTGDYHPV----QDLREVNKRVQD-IHPTVPNPYNLLSSLPPDH-----VWYTVLDLKDTFFCLRLHPSSRNIFAF 285
Cdd:pfam00078   1 IPKKGKGKYRPIsllsIDYKALNKIIVKrLKPENLDSPPQPGFRPGLAklkkaKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 392051002  286 ----EWRDPDSGTTGQL-TWTRLPKGFKNSPTLFDEALHQ 320
Cdd:pfam00078  81 ttppININWNGELSGGRyEWKGLPQGLVLSPALFQLFMNE 120
transpos_IS481 NF033577
IS481 family transposase; null
 355-469 2.53e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 67.23  E-value: 2.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002 355 AQGKRLRGDR--PGSYWEVDFTEVKPARY-GYRYLLVFVDTFSGWVKAFPTKKETAQMVAKkILEDIFPRFGVP-KVIGS 430
Cdd:NF033577 115 KTGKVKRYERahPGELWHIDIKKLGRIPDvGRLYLHTAIDDHSRFAYAELYPDETAETAAD-FLRRAFAEHGIPiRRVLT 193

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 392051002 431 DNGPAFVA---QVSQGLAKiLGLDWKLHCAYRPQSSGQVERM 469
Cdd:NF033577 194 DNGSEFRSrahGFELALAE-LGIEHRRTRPYHPQTNGKVERF 234
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 13-93 2.58e-07

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: 48.34  E-value: 2.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002   13 VTLEVEWRPVEFLVDTGAQHSVL---------LEPAgpVSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH-SFLVIP- 81
Cdd:pfam13975   1 VDVTINGRPVRFLVDTGASVTVIsealaerlgLDRL--VDAYPVTVRTANGTVRAARVRLDSVKIGGIELRNvPAVVLPg 78

                          90
                  ....*....|..
gi 392051002   82 KCPAPLLGRDLL 93
Cdd:pfam13975  79 DLDDVLLGMDFL 90
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 13-94 3.25e-07

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


Pssm-ID: 133136  Cd Length: 92  Bit Score: 48.10  E-value: 3.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  13 VTLEVEWRPVEFLVDTGAQHSVLLEPA------GPVSHKKSWVI-GATGHQQYSWTTRRTVDLGKG--RVTHSFLVIPKC 83
Cdd:cd00303    1 LKGKINGVPVRALVDSGASVNFISESLakklglPPRLLPTPLKVkGANGSSVKTLGVILPVTIGIGgkTFTVDFYVLDLL 80

                         90
                 ....*....|..
gi 392051002  84 PAP-LLGRDLLT 94
Cdd:cd00303   81 SYDvILGRPWLE 92
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 264-315 3.13e-04

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: 40.40  E-value: 3.13e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 392051002 264 LDLKDTFFCLRLHPSSRNIFAFEWRDPdsgttgQLTWTRLPKGFKNSPTLFD 315
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQGE------TYQFKALPFGLSLAPRVFT 46
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 11-93 1.33e-03

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: 37.99  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  11 PRVTLEVEWRPVEFLVDTGAQHSVLLEPA------GPVSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH-SFLVIPKC 83
Cdd:cd05483    3 FVVPVTINGQPVRFLLDTGASTTVISEELaerlglPLTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNvPAVVLPGD 82

                         90
                 ....*....|...
gi 392051002  84 PAP---LLGRDLL 93
Cdd:cd05483   83 ALGvdgLLGMDFL 95
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 13-92 1.58e-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: 37.65  E-value: 1.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002   13 VTLEVEWRPVEFLVDTGAQHSVL-------LEPAGPVSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH-SFLVIPK-- 82
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVIspslaerLGLKVRGLAYTVRVSTAGGRVSAARVRLDSLRLGGLTLENvPALVLDLgd 80

                          90
                  ....*....|
gi 392051002   83 CPAPLLGRDL 92
Cdd:pfam13650  81 LIDGLLGMDF 90
RP_Saci_like cd06094
RP_Saci_like, retropepsin family; Retropepsin on retrotransposons with long terminal repeats ...
 24-93 1.81e-03

RP_Saci_like, retropepsin family; Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. 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: 133158  Cd Length: 89  Bit Score: 37.60  E-value: 1.81e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392051002  24 FLVDTGAQHSVLlePAGPV---SHKKSWVIGA---TGHQQYSwTTRRTVDLGKGRVTHSFLVIPKCPAPLLGRDLL 93
Cdd:cd06094   12 FLVDTGAAVSVL--PASSTkksLKPSPLTLQAangTPIATYG-TRSLTLDLGLRRPFAWNFVVADVPHPILGADFL 84
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
11-102 6.56e-03

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 37.23  E-value: 6.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392051002  11 PRVTLEVEWRPVEFLVDTGAQHSVL----LEPAG---PVSHKKSWVIGATGHQQYSWTTRRTVDLGKGRVTH-SFLVIP- 81
Cdd:COG3577   42 FVVEGTINGQPVRFLVDTGASTVVLsesdARRLGldpEDLGRPVRVQTANGVVRAARVRLDSVRIGGITLRNvRAVVLPg 121

                         90       100
                 ....*....|....*....|..
gi 392051002  82 -KCPAPLLGRDLLTKMGAQISF 102
Cdd:COG3577  122 gELDDGLLGMSFLGRLDFEIDG 143
 
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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