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Conserved domains on  [gi|398365961|ref|NP_058165|]
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gag-pol fusion protein [Saccharomyces cerevisiae S288C]

Protein Classification

TYA and RNase_HI_RT_Ty1 domain-containing protein( domain architecture ID 10470241)

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
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a ...
 17-400 0e+00

Ty transposon capsid 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. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.


:

Pssm-ID: 425992  Cd Length: 384  Bit Score: 778.75  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLQEYDKDSTKANSQQTTTPGSSAVPENHHHASPQPASVPPPQNGPYSQQCMMTPNQA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    97 NPSGWSFYGHPSMIPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLT 176
Cdd:pfam01021   81 NPSGWPFYGHPSMMPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSAKSDMTSTNKYVRPPPILT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   177 SPNDFPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDILSVDYTDIMKILSKSI 256
Cdd:pfam01021  161 SPNDFLNWVKTYIKFLQNSNLGDIIPTATGKAVRQMTDDEHTFLYNTFQLFAPSQFLPTWVKDILSVDYTDIMKILSKSI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   257 EKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIIDRLNNNGIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTV 336
Cdd:pfam01021  241 EKMQSDTQEVNDIITLANLHYNGSTPADTFETTVTNIIDRLNNNGININDKVACQLIMRGLSGEYKFLRYTRHRHINMTV 320

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398365961   337 AELFLDIHAIYEEQQGSRNSKPNYRRNPSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARA 400
Cdd:pfam01021  321 ADLFSDIHAIYEEQQESKRNKPTYRRNPSDEKNDSRTYTNTTKTKVITRNSQKTNNSKSRTAKA 384
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1265-1498 1.59e-22

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: 400190  Cd Length: 243  Bit Score: 98.43  E-value: 1.59e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1265 NTWD-TDKYYDRKEIdPKRVINSMFIfNRKRDGTHKARFVARGDIQHPDTYDSGMQSNTVHHYALMTSLSLALDNNYYIT 1343
Cdd:pfam07727    2 ETWTlVKLPKNVKPI-GTTWVHTHKI-NDLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1344 QLDISSAYLYADIKEELYIRPPPHL---GMNDKLIRLKKSLYGLKQSGANWYETIKSYLIK--------QCGMeEVRGws 1412
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFnidNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDlnfepdtaESGM-YCRG-- 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1413 cvFKNSQVTICLFVDDMILFSKDLNSNKRIIAKLKMQYDTKiiNLGESDdeiqyDILGLEIKYQRGKYmKLGMENSLTEK 1492
Cdd:pfam07727  157 --FGENKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMK--DLGDIS-----EFLGIEFIQIAGGI-RLSQHNYLNSV 226


                   ....*.
gi 398365961  1493 IPKLNV 1498
Cdd:pfam07727  227 IKKFNL 232
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1606-1742 1.47e-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: 1.47e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1681
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961 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 ...
 664-765 4.91e-12

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 63.87  E-value: 4.91e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQaSVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNQLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWAL--SSEMDAELVLDALERAIAFRGG-VPLIIHSDNGSEYTS 76

                           90       100
                   ....*....|....*....|..
gi 398365961   744 RTLHKFLEKNGITPCYTTTADS 765
Cdd:pfam00665   77 KAFREFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
TYA pfam01021
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a ...
 17-400 0e+00

Ty transposon capsid 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. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.


Pssm-ID: 425992  Cd Length: 384  Bit Score: 778.75  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLQEYDKDSTKANSQQTTTPGSSAVPENHHHASPQPASVPPPQNGPYSQQCMMTPNQA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    97 NPSGWSFYGHPSMIPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLT 176
Cdd:pfam01021   81 NPSGWPFYGHPSMMPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSAKSDMTSTNKYVRPPPILT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   177 SPNDFPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDILSVDYTDIMKILSKSI 256
Cdd:pfam01021  161 SPNDFLNWVKTYIKFLQNSNLGDIIPTATGKAVRQMTDDEHTFLYNTFQLFAPSQFLPTWVKDILSVDYTDIMKILSKSI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   257 EKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIIDRLNNNGIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTV 336
Cdd:pfam01021  241 EKMQSDTQEVNDIITLANLHYNGSTPADTFETTVTNIIDRLNNNGININDKVACQLIMRGLSGEYKFLRYTRHRHINMTV 320

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398365961   337 AELFLDIHAIYEEQQGSRNSKPNYRRNPSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARA 400
Cdd:pfam01021  321 ADLFSDIHAIYEEQQESKRNKPTYRRNPSDEKNDSRTYTNTTKTKVITRNSQKTNNSKSRTAKA 384
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1265-1498 1.59e-22

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: 400190  Cd Length: 243  Bit Score: 98.43  E-value: 1.59e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1265 NTWD-TDKYYDRKEIdPKRVINSMFIfNRKRDGTHKARFVARGDIQHPDTYDSGMQSNTVHHYALMTSLSLALDNNYYIT 1343
Cdd:pfam07727    2 ETWTlVKLPKNVKPI-GTTWVHTHKI-NDLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1344 QLDISSAYLYADIKEELYIRPPPHL---GMNDKLIRLKKSLYGLKQSGANWYETIKSYLIK--------QCGMeEVRGws 1412
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFnidNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDlnfepdtaESGM-YCRG-- 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1413 cvFKNSQVTICLFVDDMILFSKDLNSNKRIIAKLKMQYDTKiiNLGESDdeiqyDILGLEIKYQRGKYmKLGMENSLTEK 1492
Cdd:pfam07727  157 --FGENKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMK--DLGDIS-----EFLGIEFIQIAGGI-RLSQHNYLNSV 226


                   ....*.
gi 398365961  1493 IPKLNV 1498
Cdd:pfam07727  227 IKKFNL 232
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1606-1742 1.47e-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: 1.47e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1681
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961 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 ...
 664-765 4.91e-12

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 63.87  E-value: 4.91e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQaSVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNQLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWAL--SSEMDAELVLDALERAIAFRGG-VPLIIHSDNGSEYTS 76

                           90       100
                   ....*....|....*....|..
gi 398365961   744 RTLHKFLEKNGITPCYTTTADS 765
Cdd:pfam00665   77 KAFREFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
663-782 5.26e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 56.70  E-value: 5.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  663 EPFQYLHTDIFgpvhnlpksapsYFisftdeTTKFRWVYPLhdrredSILDVFT-TILAF------------------IK 723
Cdd:COG2801   147 APNQVWVTDIT------------YI------PTAEGWLYLA------AVIDLFSrEIVGWsvsdsmdaelvvdalemaIE 202

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 398365961  724 NQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:COG2801   203 RRGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
transpos_IS481 NF033577
IS481 family transposase; null
 652-780 6.44e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 56.06  E-value: 6.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  652 KGSRLKYQNSYePFQYLHTDIFGpVHNLPKSAPSYFISFTDETTKFRWVYPLHDRREDSILDVFTTILAfiknQFQASVL 731
Cdd:NF033577  116 TGKVKRYERAH-PGELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFA----EHGIPIR 189

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 398365961  732 VIQMDRGSEYTNRT--LHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLD 780
Cdd:NF033577  190 RVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
722-782 1.64e-06

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 52.18  E-value: 1.64e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398365961  722 IKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:NF033516  268 IEWRGKPEGLILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKREC 328
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 53-146 1.23e-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 [Multi-domain]  Cd Length: 165  Bit Score: 44.40  E-value: 1.23e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961     53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109

                            90
                    ....*....|....*....
gi 398365961    128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 690-782 1.69e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.54  E-value: 1.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195

                          90       100
                  ....*....|....*....|....*..
gi 398365961  756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
Name Accession Description Interval E-value
TYA pfam01021
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a ...
 17-400 0e+00

Ty transposon capsid 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. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.


Pssm-ID: 425992  Cd Length: 384  Bit Score: 778.75  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLQEYDKDSTKANSQQTTTPGSSAVPENHHHASPQPASVPPPQNGPYSQQCMMTPNQA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    97 NPSGWSFYGHPSMIPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLT 176
Cdd:pfam01021   81 NPSGWPFYGHPSMMPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSAKSDMTSTNKYVRPPPILT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   177 SPNDFPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDILSVDYTDIMKILSKSI 256
Cdd:pfam01021  161 SPNDFLNWVKTYIKFLQNSNLGDIIPTATGKAVRQMTDDEHTFLYNTFQLFAPSQFLPTWVKDILSVDYTDIMKILSKSI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   257 EKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIIDRLNNNGIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTV 336
Cdd:pfam01021  241 EKMQSDTQEVNDIITLANLHYNGSTPADTFETTVTNIIDRLNNNGININDKVACQLIMRGLSGEYKFLRYTRHRHINMTV 320

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398365961   337 AELFLDIHAIYEEQQGSRNSKPNYRRNPSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARA 400
Cdd:pfam01021  321 ADLFSDIHAIYEEQQESKRNKPTYRRNPSDEKNDSRTYTNTTKTKVITRNSQKTNNSKSRTAKA 384
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1265-1498 1.59e-22

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: 400190  Cd Length: 243  Bit Score: 98.43  E-value: 1.59e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1265 NTWD-TDKYYDRKEIdPKRVINSMFIfNRKRDGTHKARFVARGDIQHPDTYDSGMQSNTVHHYALMTSLSLALDNNYYIT 1343
Cdd:pfam07727    2 ETWTlVKLPKNVKPI-GTTWVHTHKI-NDLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1344 QLDISSAYLYADIKEELYIRPPPHL---GMNDKLIRLKKSLYGLKQSGANWYETIKSYLIK--------QCGMeEVRGws 1412
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFnidNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDlnfepdtaESGM-YCRG-- 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  1413 cvFKNSQVTICLFVDDMILFSKDLNSNKRIIAKLKMQYDTKiiNLGESDdeiqyDILGLEIKYQRGKYmKLGMENSLTEK 1492
Cdd:pfam07727  157 --FGENKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMK--DLGDIS-----EFLGIEFIQIAGGI-RLSQHNYLNSV 226


                   ....*.
gi 398365961  1493 IPKLNV 1498
Cdd:pfam07727  227 IKKFNL 232
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1606-1742 1.47e-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: 1.47e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1681
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961 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 ...
 664-765 4.91e-12

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 63.87  E-value: 4.91e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQaSVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNQLWQGDFT-YIRIPGGGGKLYLLVIVDDFSREILAWAL--SSEMDAELVLDALERAIAFRGG-VPLIIHSDNGSEYTS 76

                           90       100
                   ....*....|....*....|..
gi 398365961   744 RTLHKFLEKNGITPCYTTTADS 765
Cdd:pfam00665   77 KAFREFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
663-782 5.26e-08

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 56.70  E-value: 5.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  663 EPFQYLHTDIFgpvhnlpksapsYFisftdeTTKFRWVYPLhdrredSILDVFT-TILAF------------------IK 723
Cdd:COG2801   147 APNQVWVTDIT------------YI------PTAEGWLYLA------AVIDLFSrEIVGWsvsdsmdaelvvdalemaIE 202

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 398365961  724 NQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:COG2801   203 RRGPPKPLILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYEL 261
transpos_IS481 NF033577
IS481 family transposase; null
 652-780 6.44e-08

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 56.06  E-value: 6.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  652 KGSRLKYQNSYePFQYLHTDIFGpVHNLPKSAPSYFISFTDETTKFRWVYPLHDRREDSILDVFTTILAfiknQFQASVL 731
Cdd:NF033577  116 TGKVKRYERAH-PGELWHIDIKK-LGRIPDVGRLYLHTAIDDHSRFAYAELYPDETAETAADFLRRAFA----EHGIPIR 189

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 398365961  732 VIQMDRGSEYTNRT--LHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLD 780
Cdd:NF033577  190 RVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 35-197 2.14e-07

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 characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 55.93  E-value: 2.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    35 VSASKIQEYDKASTKANSQQTTTPASSAVPeNPHHA-SPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMIPY- 112
Cdd:pfam03154  214 TSQPPNQTQSTAAPHTLIQQTPTLHPQRLP-SPHPPlQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHp 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961   113 -------TPYQMSPMYFPPGPQSQFP-QYPSSVGTPLSTPSPESGNTFTDSSSADSDMtsTKKYVRPPPmlTSP------ 178
Cdd:pfam03154  293 vppqpfpLTPQSSQSQVPPGPSPAAPgQSQQRIHTPPSQSQLQSQQPPREQPLPPAPL--SMPHIKPPP--TTPipqlpn 368

                          170       180
                   ....*....|....*....|..
gi 398365961   179 ---NDFPNWVKTYIKFLQNSNL 197
Cdd:pfam03154  369 pqsHKHPPHLSGPSPFQMNSNL 390
transpos_IS3 NF033516
IS3 family transposase;
722-782 1.64e-06

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 52.18  E-value: 1.64e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398365961  722 IKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:NF033516  268 IEWRGKPEGLILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKREC 328
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 53-146 1.23e-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 [Multi-domain]  Cd Length: 165  Bit Score: 44.40  E-value: 1.23e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961     53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109

                            90
                    ....*....|....*....
gi 398365961    128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 690-782 1.69e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.54  E-value: 1.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961  690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195

                          90       100
                  ....*....|....*....|....*..
gi 398365961  756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 46-141 7.99e-03

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


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 41.17  E-value: 7.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398365961    46 ASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMI----PYTPYQMSPMY 121
Cdd:pfam09770  201 AAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTIlqrpQSPQPDPAQPS 280

                           90       100
                   ....*....|....*....|
gi 398365961   122 FPPGPQSQFPQYPSSVGTPL 141
Cdd:pfam09770  281 IQPQAQQFHQQPPPVPVQPT 300
 
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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