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Conserved domains on  [gi|74627262|sp|Q12088|]
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RecName: Full=Transposon Ty1-LR1 Gag-Pol polyprotein; AltName: Full=Gag-Pol-p199; AltName: Full=TY1A-TY1B; AltName: Full=Transposon Ty1 TYA-TYB polyprotein; AltName: Full=p190; Contains: RecName: Full=Capsid protein; Short=CA; AltName: Full=Gag-p45; AltName: Full=p54; Contains: RecName: Full=Ty1 protease; Short=PR; AltName: Full=Pol-p20; AltName: Full=p23; Contains: RecName: Full=Integrase; Short=IN; AltName: Full=Pol-p71; AltName: Full=p84; AltName: Full=p90; Contains: RecName: Full=Reverse transcriptase/ribonuclease H; Short=RT; Short=RT-RH; AltName: Full=Pol-p63; AltName: Full=p60

Protein Classification

TYA and RNase_HI_RT_Ty1 domain-containing protein (domain architecture ID 12013406)

protein containing domains TYA, rve, RVT_2, and RNase_HI_RT_Ty1

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 1.74e-64

TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.


:

Pssm-ID: 279373  Cd Length: 98  Bit Score: 216.87  E-value: 1.74e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 74627262     97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1281-1494 6.18e-33

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 311594  Cd Length: 246  Bit Score: 131.17  E-value: 6.18e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1281 KRVINSMFIFNRKRG-----GTHKARFVARGDIQHP-----DTYDPGMQSNTVHhyalmTSLSLASDNNYYITQLDISSA 1350
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETFSPVARLESIR-----LLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1351 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1423
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1424 LFVDDMILFSKDlnanKKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIKYQRGKYM------------KLGMEN 1487
Cdd:pfam07727  167 LYVDDILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIKQTPGGITlsqskyikklleRFGMTD 235

                   ....*..
gi 74627262   1488 SLTEKIP 1494
Cdd:pfam07727  236 CKPVSTP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 9.69e-21

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 92.53  E-value: 9.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSHLVQEL---NKKPITkg 1681
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262 1682 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1742
Cdd:cd09272   79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 6.79e-19

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: 307008  Cd Length: 114  Bit Score: 86.54  E-value: 6.79e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262    664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 74627262    744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
Atrophin-1 super family cl26464
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
52-178 2.24e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 331285  Cd Length: 938  Bit Score: 45.86  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     52 SQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGwsfyghPSMIPYTPYQMSPMYFPPGPQSQFP 131
Cdd:pfam03154  181 QQPAPTPATPLPSQTPPPMTSQPQPLPVASPSTITTATSTTTTSRVVSP------VDPNPDPPSIIAPQSAQRGPEGPPT 254
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 74627262    132 QYPSSVGTPLSTPSPESGNTFTDSSSAdsdmtstkkyvrPPPMLTSP 178
Cdd:pfam03154  255 PQPHSLQGPPSFPGPAQGPGQGQGQSP------------PPPSLYPP 289
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 1.74e-64

TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.


Pssm-ID: 279373  Cd Length: 98  Bit Score: 216.87  E-value: 1.74e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 74627262     97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1281-1494 6.18e-33

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 311594  Cd Length: 246  Bit Score: 131.17  E-value: 6.18e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1281 KRVINSMFIFNRKRG-----GTHKARFVARGDIQHP-----DTYDPGMQSNTVHhyalmTSLSLASDNNYYITQLDISSA 1350
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETFSPVARLESIR-----LLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1351 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1423
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1424 LFVDDMILFSKDlnanKKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIKYQRGKYM------------KLGMEN 1487
Cdd:pfam07727  167 LYVDDILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIKQTPGGITlsqskyikklleRFGMTD 235

                   ....*..
gi 74627262   1488 SLTEKIP 1494
Cdd:pfam07727  236 CKPVSTP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 9.69e-21

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 92.53  E-value: 9.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSHLVQEL---NKKPITkg 1681
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262 1682 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1742
Cdd:cd09272   79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 6.79e-19

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: 307008  Cd Length: 114  Bit Score: 86.54  E-value: 6.79e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262    664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 74627262    744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 1.36e-04

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891  Cd Length: 165  Bit Score: 44.01  E-value: 1.36e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262      53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 74627262     128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
52-178 2.24e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 308660  Cd Length: 938  Bit Score: 45.86  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     52 SQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGwsfyghPSMIPYTPYQMSPMYFPPGPQSQFP 131
Cdd:pfam03154  181 QQPAPTPATPLPSQTPPPMTSQPQPLPVASPSTITTATSTTTTSRVVSP------VDPNPDPPSIIAPQSAQRGPEGPPT 254
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 74627262    132 QYPSSVGTPLSTPSPESGNTFTDSSSAdsdmtstkkyvrPPPMLTSP 178
Cdd:pfam03154  255 PQPHSLQGPPSFPGPAQGPGQGQGQSP------------PPPSLYPP 289
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 1.47e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853  Cd Length: 277  Bit Score: 42.54  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 74627262   756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 1.74e-64

TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.


Pssm-ID: 279373  Cd Length: 98  Bit Score: 216.87  E-value: 1.74e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 74627262     97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1281-1494 6.18e-33

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 311594  Cd Length: 246  Bit Score: 131.17  E-value: 6.18e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1281 KRVINSMFIFNRKRG-----GTHKARFVARGDIQHP-----DTYDPGMQSNTVHhyalmTSLSLASDNNYYITQLDISSA 1350
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETFSPVARLESIR-----LLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1351 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1423
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   1424 LFVDDMILFSKDlnanKKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIKYQRGKYM------------KLGMEN 1487
Cdd:pfam07727  167 LYVDDILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIKQTPGGITlsqskyikklleRFGMTD 235

                   ....*..
gi 74627262   1488 SLTEKIP 1494
Cdd:pfam07727  236 CKPVSTP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 9.69e-21

Ty1/Copia 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 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 Ty1/Copia family is 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: 260004  Cd Length: 140  Bit Score: 92.53  E-value: 9.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSHLVQEL---NKKPITkg 1681
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262 1682 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1742
Cdd:cd09272   79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 6.79e-19

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: 307008  Cd Length: 114  Bit Score: 86.54  E-value: 6.79e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262    664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 74627262    744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
Cytadhesin_P30 pfam07271
Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 ...
45-149 7.36e-06

Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localized on the tip organelle. It is thought that it is important in cytadherence and virulence.


Pssm-ID: 284643  Cd Length: 308  Bit Score: 49.85  E-value: 7.36e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     45 KASTKANSQQTTTPASSAVPENPHHASPQPASvpPPQNGPYPQQCMMTQNQANPSGWSFYG----------HPSMIPYTP 114
Cdd:pfam07271  137 QAAAEAHAEAETEPAGQNVANNPQMGINQPQI--NINFGPNPQQRINPQCFGFPMQPGQMAmrpgfnqmppHMGGAPPNQ 214
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 74627262    115 YQMSPMY--FPP-----GPQSQFPQYPSSVGTPLSTPSPESG 149
Cdd:pfam07271  215 MGMRPGFnqMPPqmggmAPRPGFPNHMPGMNAPRPGFPPQPG 256
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 1.36e-04

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891  Cd Length: 165  Bit Score: 44.01  E-value: 1.36e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262      53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 74627262     128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
52-178 2.24e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 308660  Cd Length: 938  Bit Score: 45.86  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     52 SQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGwsfyghPSMIPYTPYQMSPMYFPPGPQSQFP 131
Cdd:pfam03154  181 QQPAPTPATPLPSQTPPPMTSQPQPLPVASPSTITTATSTTTTSRVVSP------VDPNPDPPSIIAPQSAQRGPEGPPT 254
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 74627262    132 QYPSSVGTPLSTPSPESGNTFTDSSSAdsdmtstkkyvrPPPMLTSP 178
Cdd:pfam03154  255 PQPHSLQGPPSFPGPAQGPGQGQGQSP------------PPPSLYPP 289
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
51-186 2.66e-04

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 311273  Cd Length: 389  Bit Score: 45.24  E-value: 2.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 74627262    117 MSPMYFPPGPQSQFPQYPSSVGTPlSTPSPESGNTFTDSSSADSDMTSTkKYVR----PPPmlTSPNDFPNWVK 186
Cdd:pfam07223  212 VPPVYPPYSPIRQPPNPSPEPLPG-SMPMQQFYSGPPPPQSRHHSGAPS-GYGQggtiGPP--SGPGQQPQQLK 281
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
46-141 5.56e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 313063  Cd Length: 837  Bit Score: 44.61  E-value: 5.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     46 ASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMI----PYTPYQMSPMY 121
Cdd:pfam09770  196 AAMRAQAKKPAQQPAPAPPQQPQAPPAQQQQQQQQFPPQQQQQQQPQQQPQQPQQHPGQGHPVTIlqrpQSKQPDPPQPS 275
                           90       100
                   ....*....|....*....|
gi 74627262    122 FPPGPQSQFPQYPSSVGTPL 141
Cdd:pfam09770  276 PQPQAQPFHQQPPPVPVQPT 295
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 1.47e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853  Cd Length: 277  Bit Score: 42.54  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262   690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 74627262   756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
2-135 2.79e-03

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 311273  Cd Length: 389  Bit Score: 41.77  E-value: 2.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262      2 ESQQLSNYPHISHGSACASVTSKEVHTNQDpldvsaskiqeydkastkaNSQQTTTPASSAVPENPHHASPQPASVPPPQ 81
Cdd:pfam07223   33 ESQQSSNSQSGQEDSAQSVSASKPQDNSQS-------------------HQQLPLPLALPHQVNAPNAPPPQFQSPPPLI 93
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 74627262     82 NG---PYPQQCMMTQNQANPSGwSFYGHPSMIPYTPYQmsPMYFPPGPQSQFPQYPS 135
Cdd:pfam07223   94 LQqlvPVQLPTQLPQQQINQQE-PYYMPPQQHPENTHQ--QYQVPPAQQPQLPQYPP 147
PARM pfam17061
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ...
32-178 4.49e-03

PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta. It has been shown to be induced and expressed in prostate after castration and may have a role in cell proliferation and immortalisation in prostate cancer.


Pssm-ID: 319112  Cd Length: 296  Bit Score: 40.98  E-value: 4.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     32 PLDVS-ASKIQEydKASTKANSQQTTTPASSAVPENPHHAS--PQPASV---PPPQN-----------GPYPQQCMMTQN 94
Cdd:pfam17061   12 PLPVSlPAKITP--PTATWTSSPQNTAAVTASPTSGTHNNSvlPVTASAptsPLPKNisvepreeeptSPASNWEGTNTD 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74627262     95 QANPSGWSFYG--HPSMIPYTPYQMSPMYFPP--GPQS--QFP-----QYPSSVGTPLSTPSPESgntftDSSSADSDMT 163
Cdd:pfam17061   90 PSPPGLSPTSGgvHLTPTPEEHSSGTPEASVPatGSQSpaESPtltspQAPASSPSSLSTSPPEV-----SSASVTTNHS 164
                          170
                   ....*....|....*
gi 74627262    164 STKKYVRPPPMLTSP 178
Cdd:pfam17061  165 STETSTQPTGAPTTP 179
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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