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Conserved domains on  [gi|1043372833|ref|YP_009259698|]
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polyprotein [Canna yellow mottle associated virus]

Protein Classification

reverse transcriptase family protein( domain architecture ID 10443361)

reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1160-1343 4.67e-61

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: 206.68  E-value: 4.67e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1160 GVIRPSNSKHRTTAMLVesgtevdPKtgeeKRGKQRLVFNYKRLNDNTEKDQYSLPGINTIIQRIGRSRVYSKFDLKSGF 1239
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-------KK----KDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1240 HQVAMEEESIPWTAFWAIDGLYEWLVMPFGLKNAPACFQRKMDNCFRG-KEHFIAVYIDDILIFSENKEQHVQHLKEFLR 1318
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDlLGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*
gi 1043372833 1319 IVKKEGLVLSPTKMKIGVPKVDFLG 1343
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1442-1569 3.79e-20

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 cd09274:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 121  Bit Score: 87.55  E-value: 3.79e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1442 TLETDGCMDGWGGVckwKMPGEPKSAEKICAYASGKF-PAIK--STIDAEIQAVINSLDKFKiYYLDKKEILIRTDCQAI 1518
Cdd:cd09274      1 ILETDASDYGIGAV---LSQEDDDGKERPIAFFSRKLtPAERnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKAL 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1043372833 1519 VafYAKTSQNKPSRV-RWLTF-SDYItglgmiVKFEHIDGKDNTIADTLSRMV 1569
Cdd:cd09274     77 K--YLLTQKDLNGRLaRWLLLlSEFD------FEIEYRPGKENVVADALSRLP 121
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 929-1038 7.63e-10

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: 57.76  E-value: 7.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833  929 YNGLYNIKVklevDGREIslNAILDTGATICVVRMEKLTEDWlEDAAMDYTIRGVNSVTKAnKVLKKGKLWIGEQFFRIP 1008
Cdd:pfam00077    3 QRPLLTVKI----GGKYF--TALLDTGADDTVISQNDWPTNW-PKQKATTNIQGIGGGINV-RQSDQILILIGEDKFRGT 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 1043372833 1009 RTMAVDMTLSAgidMILGCNFIRSMEGGLR 1038
Cdd:pfam00077   75 VSPLILPTCPV---NIIGRDLLQQLGGRLT 101
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 740-757 2.00e-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: 42.51  E-value: 2.00e-05
                           10
                   ....*....|....*...
gi 1043372833  740 CKCYACGEEGHFAKDCTN 757
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1160-1343 4.67e-61

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: 206.68  E-value: 4.67e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1160 GVIRPSNSKHRTTAMLVesgtevdPKtgeeKRGKQRLVFNYKRLNDNTEKDQYSLPGINTIIQRIGRSRVYSKFDLKSGF 1239
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-------KK----KDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1240 HQVAMEEESIPWTAFWAIDGLYEWLVMPFGLKNAPACFQRKMDNCFRG-KEHFIAVYIDDILIFSENKEQHVQHLKEFLR 1318
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDlLGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*
gi 1043372833 1319 IVKKEGLVLSPTKMKIGVPKVDFLG 1343
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1184-1346 1.88e-35

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: 133.97  E-value: 1.88e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1184 PKTGEekrGKQRLV----FNYKRLNDNTEK-------DQYSLPGINTIIQRIGRSRVYSKFDLKSGFHQVAMEEESIPWT 1252
Cdd:pfam00078    2 PKKGK---GKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1253 AF-----------WAIDGLYEWLVMPFGLKNAPACFQRKMDNCFRG----KEHFIAVYIDDILIFSENKEQHVQHLKEFL 1317
Cdd:pfam00078   79 AFttppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1043372833 1318 RIVKKEGLVLSPTKMKI--GVPKVDFLGATI 1346
Cdd:pfam00078  159 EWLKESGLKINPEKTQFflKSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1442-1569 3.79e-20

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 87.55  E-value: 3.79e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1442 TLETDGCMDGWGGVckwKMPGEPKSAEKICAYASGKF-PAIK--STIDAEIQAVINSLDKFKiYYLDKKEILIRTDCQAI 1518
Cdd:cd09274      1 ILETDASDYGIGAV---LSQEDDDGKERPIAFFSRKLtPAERnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKAL 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1043372833 1519 VafYAKTSQNKPSRV-RWLTF-SDYItglgmiVKFEHIDGKDNTIADTLSRMV 1569
Cdd:cd09274     77 K--YLLTQKDLNGRLaRWLLLlSEFD------FEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1431-1536 7.98e-12

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 63.30  E-value: 7.98e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1431 DMELPpdnavITLETDGCMDGWGGVCKWKMPGEPksaEKICAYASGKF-PAIK--STIDAEIQAVINSLDKFKiYYLDKK 1507
Cdd:pfam17917    1 DPSKP-----FILETDASDYGIGAVLSQKDEDGK---ERPIAYASRKLtPAERnySTTEKELLAIVWALKKFR-HYLLGR 71

                           90       100       110
                   ....*....|....*....|....*....|
gi 1043372833 1508 EILIRTDCQAIVafYAKTSQNKPSRV-RWL 1536
Cdd:pfam17917   72 KFTVYTDHKPLK--YLFTPKELNGRLaRWA 99
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 929-1038 7.63e-10

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: 57.76  E-value: 7.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833  929 YNGLYNIKVklevDGREIslNAILDTGATICVVRMEKLTEDWlEDAAMDYTIRGVNSVTKAnKVLKKGKLWIGEQFFRIP 1008
Cdd:pfam00077    3 QRPLLTVKI----GGKYF--TALLDTGADDTVISQNDWPTNW-PKQKATTNIQGIGGGINV-RQSDQILILIGEDKFRGT 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 1043372833 1009 RTMAVDMTLSAgidMILGCNFIRSMEGGLR 1038
Cdd:pfam00077   75 VSPLILPTCPV---NIIGRDLLQQLGGRLT 101
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 740-757 2.00e-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: 42.51  E-value: 2.00e-05
                           10
                   ....*....|....*...
gi 1043372833  740 CKCYACGEEGHFAKDCTN 757
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
741-757 1.62e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.12  E-value: 1.62e-04
                            10
                    ....*....|....*..
gi 1043372833   741 KCYACGEEGHFAKDCTN 757
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 741-760 1.18e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 1.18e-03
                           10        20
                   ....*....|....*....|
gi 1043372833  741 KCYACGEEGHFAKDCTNPRK 760
Cdd:PTZ00368    79 SCYNCGQTGHISRECPNRAK 98
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 937-1031 3.67e-03

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: 38.47  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833  937 VKLEVDGREISlnAILDTGATICVVR---MEKLTEDWLEDAAmDYTIRGVN-SVTKANKVLKKGKLWIGEQFFRIPrtma 1012
Cdd:cd00303      1 LKGKINGVPVR--ALVDSGASVNFISeslAKKLGLPPRLLPT-PLKVKGANgSSVKTLGVILPVTIGIGGKTFTVD---- 73

                           90
                   ....*....|....*....
gi 1043372833 1013 VDMTLSAGIDMILGCNFIR 1031
Cdd:cd00303     74 FYVLDLLSYDVILGRPWLE 92
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1160-1343 4.67e-61

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: 206.68  E-value: 4.67e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1160 GVIRPSNSKHRTTAMLVesgtevdPKtgeeKRGKQRLVFNYKRLNDNTEKDQYSLPGINTIIQRIGRSRVYSKFDLKSGF 1239
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-------KK----KDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1240 HQVAMEEESIPWTAFWAIDGLYEWLVMPFGLKNAPACFQRKMDNCFRG-KEHFIAVYIDDILIFSENKEQHVQHLKEFLR 1318
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDlLGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*
gi 1043372833 1319 IVKKEGLVLSPTKMKIGVPKVDFLG 1343
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1184-1346 1.88e-35

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: 133.97  E-value: 1.88e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1184 PKTGEekrGKQRLV----FNYKRLNDNTEK-------DQYSLPGINTIIQRIGRSRVYSKFDLKSGFHQVAMEEESIPWT 1252
Cdd:pfam00078    2 PKKGK---GKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1253 AF-----------WAIDGLYEWLVMPFGLKNAPACFQRKMDNCFRG----KEHFIAVYIDDILIFSENKEQHVQHLKEFL 1317
Cdd:pfam00078   79 AFttppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1043372833 1318 RIVKKEGLVLSPTKMKI--GVPKVDFLGATI 1346
Cdd:pfam00078  159 EWLKESGLKINPEKTQFflKSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1442-1569 3.79e-20

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 87.55  E-value: 3.79e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1442 TLETDGCMDGWGGVckwKMPGEPKSAEKICAYASGKF-PAIK--STIDAEIQAVINSLDKFKiYYLDKKEILIRTDCQAI 1518
Cdd:cd09274      1 ILETDASDYGIGAV---LSQEDDDGKERPIAFFSRKLtPAERnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKAL 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1043372833 1519 VafYAKTSQNKPSRV-RWLTF-SDYItglgmiVKFEHIDGKDNTIADTLSRMV 1569
Cdd:cd09274     77 K--YLLTQKDLNGRLaRWLLLlSEFD------FEIEYRPGKENVVADALSRLP 121
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1151-1343 1.02e-19

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: 89.33  E-value: 1.02e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1151 KHVNQLLKLGVIRPSNSKHRTTAMLVesgtevdPKTGEEKrgkQRLVFNYKRLNDNTEKDQYSLPGINTIIQRIGR-SRV 1229
Cdd:cd03715     19 PHIQELLEAGILVPCQSPWNTPILPV-------KKPGGND---YRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPPkHQW 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1230 YSKFDLKSGFHQVAMEEESIPWTAFWAIDGLYEWLVMPFGLKNAPACF----QRKMDNCFRGKEHFIAV-YIDDILIFSE 1304
Cdd:cd03715     89 YTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILLqYVDDLLLAAD 168

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1043372833 1305 NKEQHVQHLKEFLRIVKKEGLVLSPTKMKIGVPKVDFLG 1343
Cdd:cd03715    169 SEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLG 207
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1133-1346 6.96e-14

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: 72.32  E-value: 6.96e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1133 IEDRPLkhvtPKMKEDMAKH-VNQLLKLGVIRPSNSKHRTTAMLVEsgtevdpktgeEKRGKQRLVFNYKRLNDNTEKD- 1210
Cdd:cd01645      4 IKQWPL----TEEKLEALTElVTEQLKEGHIEPSTSPWNTPVFVIK-----------KKSGKWRLLHDLRAVNAQTQDMg 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1211 --QYSLPGINTIIQRigrsrvYSK--FDLKSGFHQVAMEEESIPWTAFW--AIDGL-----YEWLVMPFGLKNAPACFQR 1279
Cdd:cd01645     69 alQPGLPHPAALPKG------WPLivLDLKDCFFSIPLHPDDRERFAFTvpSINNKgpakrYQWKVLPQGMKNSPTICQS 142

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1043372833 1280 KMDNC---FRGK--EHFIAVYIDDILIFSENKEQHVQHLKEFLRIVKKEGLVLSPTKMKIGVPkVDFLGATI 1346
Cdd:cd01645    143 FVAQAlepFRKQypDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLGYEL 213
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1431-1536 7.98e-12

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 63.30  E-value: 7.98e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1431 DMELPpdnavITLETDGCMDGWGGVCKWKMPGEPksaEKICAYASGKF-PAIK--STIDAEIQAVINSLDKFKiYYLDKK 1507
Cdd:pfam17917    1 DPSKP-----FILETDASDYGIGAVLSQKDEDGK---ERPIAYASRKLtPAERnySTTEKELLAIVWALKKFR-HYLLGR 71

                           90       100       110
                   ....*....|....*....|....*....|
gi 1043372833 1508 EILIRTDCQAIVafYAKTSQNKPSRV-RWL 1536
Cdd:pfam17917   72 KFTVYTDHKPLK--YLFTPKELNGRLaRWA 99
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1420-1511 1.36e-10

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 59.82  E-value: 1.36e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1420 NKIKQQVQNLPDMELPPDNAVITLETDGCMDGWGGVCKWKMPGEPksaEKICAYASGKFPAIK---STIDAEIQAVINSL 1496
Cdd:pfam17919   10 EKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGG---ERPIAYASRKLSPAErnySTTEKELLAIVFAL 86

                           90
                   ....*....|....*
gi 1043372833 1497 DKFKiYYLDKKEILI 1511
Cdd:pfam17919   87 KKFR-HYLLGRKFTV 100
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1233-1346 1.92e-10

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: 60.05  E-value: 1.92e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1233 FDLKSGFHQVAMEEESIPWTAFWAIDGLYEWLVMPFGLKNAPACFQRKMDNCF---RGKEHFIAVYIDDILIFSEN---K 1306
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLaplRLLGVRIFSYLDDLLIIASSiktS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1043372833 1307 EQHVQHLKEFLRIvkKEGLVLSPTKMKIG-VPKVDFLGATI 1346
Cdd:cd03714     81 EAVLRHLRATLLA--NLGFTLNLEKSKLGpTQRITFLGLEL 119
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 929-1038 7.63e-10

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: 57.76  E-value: 7.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833  929 YNGLYNIKVklevDGREIslNAILDTGATICVVRMEKLTEDWlEDAAMDYTIRGVNSVTKAnKVLKKGKLWIGEQFFRIP 1008
Cdd:pfam00077    3 QRPLLTVKI----GGKYF--TALLDTGADDTVISQNDWPTNW-PKQKATTNIQGIGGGINV-RQSDQILILIGEDKFRGT 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 1043372833 1009 RTMAVDMTLSAgidMILGCNFIRSMEGGLR 1038
Cdd:pfam00077   75 VSPLILPTCPV---NIIGRDLLQQLGGRLT 101
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1233-1346 5.43e-07

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 49.27  E-value: 5.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1233 FDLKSGFHQVAMeeesipwtafwaidglyewlvmPFGLKNAPACFQRKMDN-----CFRGKEHFIAVYIDDILIFSENkE 1307
Cdd:cd00304      1 FDVKSFFTSIPL----------------------PQGSPLSPALANLYMEKleapiLKQLLDITLIRYVDDLVVIAKS-E 57

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1043372833 1308 QHVQHLKEFLRIVKKEGLVLSPTKMKIGV--PKVDFLGATI 1346
Cdd:cd00304     58 QQAVKKRELEEFLARLGLNLSDEKTQFTEkeKKFKFLGILV 98
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 740-757 2.00e-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: 42.51  E-value: 2.00e-05
                           10
                   ....*....|....*...
gi 1043372833  740 CKCYACGEEGHFAKDCTN 757
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1442-1567 3.77e-05

DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 44.58  E-value: 3.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1442 TLETDGCMDGWGGVCKwkmpgepksaekiCAYASGKFPAIKST--IDA-EIQAVINSLDKFKiYYLDKKEILIRTDCQAI 1518
Cdd:cd09275      1 VLFTDASLSGWGAYLL-------------NSRAHGPWSADERNkhINLlELKAVLLALQHFA-AELKNRKILIRTDNTTA 66

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1043372833 1519 VAFYAKTSQNKPSRVR------WLTFSDYitglGMIVKFEHIDGKDNTIADTLSR 1567
Cdd:cd09275     67 VAYINKQGGTSSPPLLalarqiLLWCEQR----NIWLRASHIPGVLNTEADRLSR 117
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 1192-1329 1.54e-04

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: 44.99  E-value: 1.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1192 GKQRLVFN----YK--RLNDntekdqYSLPGINTIIQRIG---RSRVYsKF----DLKSGFHQVAMEEESIPWTAF-WAI 1257
Cdd:cd01644     17 TKLRVVFDasarYNgvSLND------MLLKGPDLLNSLFGvllRFRQG-KIavsaDIEKMFHQVKVRPEDRDVLRFlWRK 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833 1258 DG------LYEWLVMPFGLKNAPACFQRKM-----DNCFRGKEHFIA--VYIDDILIFSENKEQHVQHLKEFLRIVKKEG 1324
Cdd:cd01644     90 DGdepkpiEYRMTVVPFGAASAPFLANRALkqhaeDHPHEAAAKIIKrnFYVDDILVSTDTLNEAVNVAKRLIALLKKGG 169


                   ....*
gi 1043372833 1325 LVLSP 1329
Cdd:cd01644    170 FNLRK 174
ZnF_C2HC smart00343
zinc finger;
741-757 1.62e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.12  E-value: 1.62e-04
                            10
                    ....*....|....*..
gi 1043372833   741 KCYACGEEGHFAKDCTN 757
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 1277-1346 2.09e-04

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


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 43.47  E-value: 2.09e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1043372833 1277 FQRKMDNCFRGKEHFiaVYIDDILIFSENKEQHVQHLKEFLRIVKKEGLVLSPTKMKI-----GVPKVDFLGATI 1346
Cdd:cd01646     72 VDHELKSKLKGVDYV--RYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEIlplpeGTASKDFLGYRF 144
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 741-760 1.18e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 1.18e-03
                           10        20
                   ....*....|....*....|
gi 1043372833  741 KCYACGEEGHFAKDCTNPRK 760
Cdd:PTZ00368    79 SCYNCGQTGHISRECPNRAK 98
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 742-759 2.23e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.18  E-value: 2.23e-03
                           10
                   ....*....|....*...
gi 1043372833  742 CYACGEEGHFAKDCTNPR 759
Cdd:PTZ00368    30 CYKCGEPGHLSRECPSAP 47
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 937-1029 2.68e-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: 38.81  E-value: 2.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833  937 VKLEVDGREIslNAILDTGATICVVR---MEKLTEDwLEDAAMDYTIRGVNSVTKANKVlKKGKLWIGEQFFRIPRTMAV 1013
Cdd:pfam13650    1 VPVTINGKPV--RFLVDTGASGTVISpslAERLGLK-VRGLAYTVRVSTAGGRVSAARV-RLDSLRLGGLTLENVPALVL 76

                           90
                   ....*....|....*.
gi 1043372833 1014 DMtlSAGIDMILGCNF 1029
Cdd:pfam13650   77 DL--GDLIDGLLGMDF 90
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 937-1031 3.67e-03

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: 38.47  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043372833  937 VKLEVDGREISlnAILDTGATICVVR---MEKLTEDWLEDAAmDYTIRGVN-SVTKANKVLKKGKLWIGEQFFRIPrtma 1012
Cdd:cd00303      1 LKGKINGVPVR--ALVDSGASVNFISeslAKKLGLPPRLLPT-PLKVKGANgSSVKTLGVILPVTIGIGGKTFTVD---- 73

                           90
                   ....*....|....*....
gi 1043372833 1013 VDMTLSAGIDMILGCNFIR 1031
Cdd:cd00303     74 FYVLDLLSYDVILGRPWLE 92
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 741-760 4.37e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.40  E-value: 4.37e-03
                           10        20
                   ....*....|....*....|
gi 1043372833  741 KCYACGEEGHFAKDCTNPRK 760
Cdd:PTZ00368   105 ACYNCGGEGHISRDCPNAGK 124
 
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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