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Conserved domains on  [gi|2254927262|gb|USH10133|]
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ORF3 [Gulupa bacilliform virus A]

Protein Classification

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 ...
 1280-1466 1.41e-67

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: 225.55  E-value: 1.41e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1280 GVIRPSKSRHRTMAIIVysgttvdaetrR*TKGKERMVCNYRTLNDNTYKDQYSLPGINTIIZKVGNSTIFSKFDLKSGF 1359
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1360 HQVAMAEESIPWTAFITPGGLYEWLVMPFGLKNAPAIFQRKMDECFKD-CQDFIAVYIDDILVFSRNEKEHAEHL*KMLK 1438
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDlLGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*...
gi 2254927262 1439 ICEKEGLILSPTKMKIAVEEIEFLGAII 1466
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1562-1689 3.34e-17

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: 79.46  E-value: 3.34e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1562 IIE*DGCMDGWGAVckwkHKRMDPRSKEKICAYASGKF---QQ*KSTIDAEIHAVMEA*QSFKiYYLDKEEVTIRTDCQA 1638
Cdd:cd09274      1 ILETDASDYGIGAV----LSQEDDDGKERPIAFFSRKLtpaERNYSTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2254927262 1639 IIGFYNKsnQHKPSRV-RWIgf*DFIngSGJT*HFEHIEGKNNTLADTLSRL 1689
Cdd:cd09274     76 LKYLLTQ--KDLNGRLaRWL---LLL--SEFDFEIEYRPGKENVVADALSRL 120
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 809-826 4.80e-05

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


:

Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 41.74  E-value: 4.80e-05
                           10
                   ....*....|....*...
gi 2254927262  809 CKCYICGK*GHFARDCTS 826
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
Peptidase_A3 super family cl23521
Cauliflower mosaic virus peptidase (A3);
1057-1148 9.26e-03

Cauliflower mosaic virus peptidase (A3);


The actual alignment was detected with superfamily member pfam02160:

Pssm-ID: 280345  Cd Length: 208  Bit Score: 39.70  E-value: 9.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1057 GVKEFKVQAIMDTG*TTCC*NIGSVPEEALEDSPIPTRFT-GINSRDLATKKLKGGQMRIEGNKFRIPFVYafsMMTDGI 1135
Cdd:pfam02160   15 GFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIiADGSKHTIREACKDIDLIIAGEEFLIPIIY---LHDSGI 91

                           90
                   ....*....|...
gi 2254927262 1136 EMLIGCNFIRAMQ 1148
Cdd:pfam02160   92 DFIIGNNFCKLYE 104
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1280-1466 1.41e-67

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: 225.55  E-value: 1.41e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1280 GVIRPSKSRHRTMAIIVysgttvdaetrR*TKGKERMVCNYRTLNDNTYKDQYSLPGINTIIZKVGNSTIFSKFDLKSGF 1359
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1360 HQVAMAEESIPWTAFITPGGLYEWLVMPFGLKNAPAIFQRKMDECFKD-CQDFIAVYIDDILVFSRNEKEHAEHL*KMLK 1438
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDlLGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*...
gi 2254927262 1439 ICEKEGLILSPTKMKIAVEEIEFLGAII 1466
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1310-1466 5.82e-39

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: 144.37  E-value: 5.82e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1310 TKGKERMV----CNYRTLNDNTYK-------DQYSLPGINTIIZKVGNSTIFSKFDLKSGFHQVAMAEESIPWTAFITP- 1377
Cdd:pfam00078    5 GKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPp 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1378 ----------GGLYEWLVMPFGLKNAPAIFQRKMDECFKD----CQDFIAVYIDDILVFSRNEKEHAEHL*KMLKICEKE 1443
Cdd:pfam00078   85 ininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKES 164

                          170       180
                   ....*....|....*....|....*
gi 2254927262 1444 GLILSPTKMKIA--VEEIEFLGAII 1466
Cdd:pfam00078  165 GLKINPEKTQFFlkSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1562-1689 3.34e-17

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: 79.46  E-value: 3.34e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1562 IIE*DGCMDGWGAVckwkHKRMDPRSKEKICAYASGKF---QQ*KSTIDAEIHAVMEA*QSFKiYYLDKEEVTIRTDCQA 1638
Cdd:cd09274      1 ILETDASDYGIGAV----LSQEDDDGKERPIAFFSRKLtpaERNYSTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2254927262 1639 IIGFYNKsnQHKPSRV-RWIgf*DFIngSGJT*HFEHIEGKNNTLADTLSRL 1689
Cdd:cd09274     76 LKYLLTQ--KDLNGRLaRWL---LLL--SEFDFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1561-1656 8.65e-10

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: 57.52  E-value: 8.65e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1561 IIIE*DGCMDGWGAVCKwkhkRMDPRSKEKICAYASGKF---QQ*KSTIDAEIHAVMEA*QSFKiYYLDKEEVTIRTDCQ 1637
Cdd:pfam17917    6 FILETDASDYGIGAVLS----QKDEDGKERPIAYASRKLtpaERNYSTTEKELLAIVWALKKFR-HYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|
gi 2254927262 1638 AIIGFynKSNQHKPSRV-RW 1656
Cdd:pfam17917   81 PLKYL--FTPKELNGRLaRW 98
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 809-826 4.80e-05

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 41.74  E-value: 4.80e-05
                           10
                   ....*....|....*...
gi 2254927262  809 CKCYICGK*GHFARDCTS 826
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
810-826 5.98e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 5.98e-05
                            10
                    ....*....|....*..
gi 2254927262   810 KCYICGK*GHFARDCTS 826
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
Peptidase_A3 pfam02160
Cauliflower mosaic virus peptidase (A3);
1057-1148 9.26e-03

Cauliflower mosaic virus peptidase (A3);


Pssm-ID: 280345  Cd Length: 208  Bit Score: 39.70  E-value: 9.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1057 GVKEFKVQAIMDTG*TTCC*NIGSVPEEALEDSPIPTRFT-GINSRDLATKKLKGGQMRIEGNKFRIPFVYafsMMTDGI 1135
Cdd:pfam02160   15 GFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIiADGSKHTIREACKDIDLIIAGEEFLIPIIY---LHDSGI 91

                           90
                   ....*....|...
gi 2254927262 1136 EMLIGCNFIRAMQ 1148
Cdd:pfam02160   92 DFIIGNNFCKLYE 104
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1280-1466 1.41e-67

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: 225.55  E-value: 1.41e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1280 GVIRPSKSRHRTMAIIVysgttvdaetrR*TKGKERMVCNYRTLNDNTYKDQYSLPGINTIIZKVGNSTIFSKFDLKSGF 1359
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1360 HQVAMAEESIPWTAFITPGGLYEWLVMPFGLKNAPAIFQRKMDECFKD-CQDFIAVYIDDILVFSRNEKEHAEHL*KMLK 1438
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDlLGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*...
gi 2254927262 1439 ICEKEGLILSPTKMKIAVEEIEFLGAII 1466
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLGHIV 177
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1310-1466 5.82e-39

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: 144.37  E-value: 5.82e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1310 TKGKERMV----CNYRTLNDNTYK-------DQYSLPGINTIIZKVGNSTIFSKFDLKSGFHQVAMAEESIPWTAFITP- 1377
Cdd:pfam00078    5 GKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFTTPp 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1378 ----------GGLYEWLVMPFGLKNAPAIFQRKMDECFKD----CQDFIAVYIDDILVFSRNEKEHAEHL*KMLKICEKE 1443
Cdd:pfam00078   85 ininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLKES 164

                          170       180
                   ....*....|....*....|....*
gi 2254927262 1444 GLILSPTKMKIA--VEEIEFLGAII 1466
Cdd:pfam00078  165 GLKINPEKTQFFlkSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1272-1466 7.53e-24

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: 101.66  E-value: 7.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1272 HIDSLLELGVIRPSKSRHRTMAIIVysgttvdaetRR*TKGKERMVCNYRTLNDNTYKDQYSLPGINTIIZKV-GNSTIF 1350
Cdd:cd03715     20 HIQELLEAGILVPCQSPWNTPILPV----------KKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLpPKHQWY 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1351 SKFDLKSGFHQVAMAEESIPWTAFITPGGLYEWLVMPFGLKNAPAIF----QRKMDECFKDCQDFIAV-YIDDILVFSRN 1425
Cdd:cd03715     90 TVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILLqYVDDLLLAADS 169

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2254927262 1426 EKEHAEHL*KMLKICEKEGLILSPTKMKIAVEEIEFLGAII 1466
Cdd:cd03715    170 EEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1562-1689 3.34e-17

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: 79.46  E-value: 3.34e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1562 IIE*DGCMDGWGAVckwkHKRMDPRSKEKICAYASGKF---QQ*KSTIDAEIHAVMEA*QSFKiYYLDKEEVTIRTDCQA 1638
Cdd:cd09274      1 ILETDASDYGIGAV----LSQEDDDGKERPIAFFSRKLtpaERNYSTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2254927262 1639 IIGFYNKsnQHKPSRV-RWIgf*DFIngSGJT*HFEHIEGKNNTLADTLSRL 1689
Cdd:cd09274     76 LKYLLTQ--KDLNGRLaRWL---LLL--SEFDFEIEYRPGKENVVADALSRL 120
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1273-1466 4.28e-16

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: 79.25  E-value: 4.28e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1273 IDSLLELGVIRPSKSRHRTMAIIVysgttvdaetrR*TKGKERMVCNYRTLNDNTyKDQYSL-PGIN--TIIZKVGNSTI 1349
Cdd:cd01645     21 VTEQLKEGHIEPSTSPWNTPVFVI-----------KKKSGKWRLLHDLRAVNAQT-QDMGALqPGLPhpAALPKGWPLIV 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1350 FskfDLKSGFHQVAMAEESIPWTAFI-------TPGGLYEWLVMPFGLKNAPAIFQRKMD-------ECFKDCQdfIAVY 1415
Cdd:cd01645     89 L---DLKDCFFSIPLHPDDRERFAFTvpsinnkGPAKRYQWKVLPQGMKNSPTICQSFVAqalepfrKQYPDIV--IYHY 163

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2254927262 1416 IDDILVFSRNEKEHAEHL*KMLKICEKEGLILSPTKMKIAvEEIEFLGAII 1466
Cdd:cd01645    164 MDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKE-PPFQYLGYEL 213
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1353-1466 1.07e-12

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: 66.60  E-value: 1.07e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1353 FDLKSGFHQVAMAEESIPWTAFITPGGLYEWLVMPFGLKNAPAIFQRKMDECFKDCQDF---IAVYIDDILVFSRNEKeH 1429
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLgvrIFSYLDDLLIIASSIK-T 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2254927262 1430 AEHL*KMLKI--CEKEGLILSPTKMKIA-VEEIEFLGAII 1466
Cdd:cd03714     80 SEAVLRHLRAtlLANLGFTLNLEKSKLGpTQRITFLGLEL 119
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1561-1656 8.65e-10

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: 57.52  E-value: 8.65e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1561 IIIE*DGCMDGWGAVCKwkhkRMDPRSKEKICAYASGKF---QQ*KSTIDAEIHAVMEA*QSFKiYYLDKEEVTIRTDCQ 1637
Cdd:pfam17917    6 FILETDASDYGIGAVLS----QKDEDGKERPIAYASRKLtpaERNYSTTEKELLAIVWALKKFR-HYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|
gi 2254927262 1638 AIIGFynKSNQHKPSRV-RW 1656
Cdd:pfam17917   81 PLKYL--FTPKELNGRLaRW 98
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1540-1632 1.02e-06

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 48.65  E-value: 1.02e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1540 KQIKRQVQNLPD*EIPPATAAIIIE*DGCMDGWGAVCkwKHKRMDprSKEKICAYASGKF---QQ*KSTIDAEIHAVMEA 1616
Cdd:pfam17919   10 EKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVL--SQEDDD--GGERPIAYASRKLspaERNYSTTEKELLAIVFA 85

                           90
                   ....*....|....*.
gi 2254927262 1617 *QSFKiYYLDKEEVTI 1632
Cdd:pfam17919   86 LKKFR-HYLLGRKFTV 100
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1353-1466 2.11e-05

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: 45.03  E-value: 2.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1353 FDLKSGFHQVAMaeesipwtafitpgglyewlvmPFGLKNAPAIFQRKMDECFKD----CQD-FIAVYIDDILVFSRNEk 1427
Cdd:cd00304      1 FDVKSFFTSIPL----------------------PQGSPLSPALANLYMEKLEAPilkqLLDiTLIRYVDDLVVIAKSE- 57

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2254927262 1428 EHAEHL*KMLKICEKEGLILSPTKMKIAVEE--IEFLGAII 1466
Cdd:cd00304     58 QQAVKKRELEEFLARLGLNLSDEKTQFTEKEkkFKFLGILV 98
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 809-826 4.80e-05

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 41.74  E-value: 4.80e-05
                           10
                   ....*....|....*...
gi 2254927262  809 CKCYICGK*GHFARDCTS 826
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
810-826 5.98e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 5.98e-05
                            10
                    ....*....|....*..
gi 2254927262   810 KCYICGK*GHFARDCTS 826
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 1354-1475 1.00e-03

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: 42.68  E-value: 1.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1354 DLKSGFHQVAMAEESIPWTAF-------ITPGGLYEWLVMPFGLKNAPAIFQRKMDECFKDCQDFIAV-------YIDDI 1419
Cdd:cd01644     65 DIEKMFHQVKVRPEDRDVLRFlwrkdgdEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAkiikrnfYVDDI 144

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2254927262 1420 LVFSRNEKEHAEHL*KMLKICEKEGLILSptkmKIAVEEIEFLGAIIGRNRVKLQP 1475
Cdd:cd01644    145 LVSTDTLNEAVNVAKRLIALLKKGGFNLR----KWASNSQEVLDDLPEERVLLDRD 196
Peptidase_A3 pfam02160
Cauliflower mosaic virus peptidase (A3);
1057-1148 9.26e-03

Cauliflower mosaic virus peptidase (A3);


Pssm-ID: 280345  Cd Length: 208  Bit Score: 39.70  E-value: 9.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2254927262 1057 GVKEFKVQAIMDTG*TTCC*NIGSVPEEALEDSPIPTRFT-GINSRDLATKKLKGGQMRIEGNKFRIPFVYafsMMTDGI 1135
Cdd:pfam02160   15 GFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIiADGSKHTIREACKDIDLIIAGEEFLIPIIY---LHDSGI 91

                           90
                   ....*....|...
gi 2254927262 1136 EMLIGCNFIRAMQ 1148
Cdd:pfam02160   92 DFIIGNNFCKLYE 104
 
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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