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Conserved domains on  [gi|285814380|tpg|DAA10274|]
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TPA: gag-pol fusion protein [Saccharomyces cerevisiae S288c]

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List of domain hits

Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 6.06e-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: 92.15  E-value: 6.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1681
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380 1682 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1742
Cdd:cd09272    79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 1.48e-61

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: 144563  Cd Length: 98  Bit Score: 207.60  E-value: 1.48e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380    17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQTAQSHSPQNGPYQQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 285814380    97 NPSGWSFYGRPSMIPYTP 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1265-1494 3.87e-36

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: 254387  Cd Length: 246  Bit Score: 139.51  E-value: 3.87e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1265 KTWDtdryydrkEIDP---KRVINSMFIFNRKR--DGT---HKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTS 1331
Cdd:pfam07727    2 KTWE--------LVPLpkgKKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETF-----SPVAKLTTIRLL 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1332 LSLALDNNYYITQLDISSAYLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIQQcGMEEV 1408
Cdd:pfam07727   69 LALAAQRGWELHQMDVKTAFLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFLLKL-GFKQS 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1409 RGWSCVF-KNSQ---VTICLFVDDMVLFSKNLNSNKRIIEKLKMQYDTKiiNLGesdeEIQYdILGLEIKYQRGKYM--- 1481
Cdd:pfam07727  148 EADPCLFvKKSGggiIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTSGGIFlsq 220
                          250       260
                   ....*....|....*....|..
gi 285814380  1482 ---------KLGMENSLTEKIP 1494
Cdd:pfam07727  221 rkyakkllkRFGMLDCKPVSTP 242
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
663-782 9.86e-20

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 250040  Cd Length: 119  Bit Score: 87.77  E-value: 9.86e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380   663 EPFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQASVlVIQMDRGSEYT 742
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 285814380   743 NRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 6.06e-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: 92.15  E-value: 6.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1681
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380 1682 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1742
Cdd:cd09272    79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 1.48e-61

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: 144563  Cd Length: 98  Bit Score: 207.60  E-value: 1.48e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380    17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQTAQSHSPQNGPYQQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 285814380    97 NPSGWSFYGRPSMIPYTP 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1265-1494 3.87e-36

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: 254387  Cd Length: 246  Bit Score: 139.51  E-value: 3.87e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1265 KTWDtdryydrkEIDP---KRVINSMFIFNRKR--DGT---HKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTS 1331
Cdd:pfam07727    2 KTWE--------LVPLpkgKKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETF-----SPVAKLTTIRLL 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1332 LSLALDNNYYITQLDISSAYLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIQQcGMEEV 1408
Cdd:pfam07727   69 LALAAQRGWELHQMDVKTAFLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFLLKL-GFKQS 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1409 RGWSCVF-KNSQ---VTICLFVDDMVLFSKNLNSNKRIIEKLKMQYDTKiiNLGesdeEIQYdILGLEIKYQRGKYM--- 1481
Cdd:pfam07727  148 EADPCLFvKKSGggiIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTSGGIFlsq 220
                          250       260
                   ....*....|....*....|..
gi 285814380  1482 ---------KLGMENSLTEKIP 1494
Cdd:pfam07727  221 rkyakkllkRFGMLDCKPVSTP 242
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
663-782 9.86e-20

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 250040  Cd Length: 119  Bit Score: 87.77  E-value: 9.86e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380   663 EPFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQASVlVIQMDRGSEYT 742
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 285814380   743 NRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
4-171 4.61e-05

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 255446 [Multi-domain]  Cd Length: 768  Bit Score: 46.92  E-value: 4.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380     4 QQLSQHSPISHGSACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQTAQSHSPQNG 83
Cdd:pfam09606  369 HQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQQGQPGMMSSPSPVPQVQTNQSMPQPPQPSVPSPGGPGSQPPQSV 448
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380    84 PyqqqcmmtqNQANPSgwsfygRPSMIPYTPYQMSPMyfpPGPHSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMT 163
Cdd:pfam09606  449 S---------GGMIPS------PPALMPSPSPQMSQS---PASQRTIQQDMVSPGGPLNTPGQSSVNSPANPQEEQLYRE 510
                          170
                   ....*....|.
gi 285814380   164 STK---KYVRP 171
Cdd:pfam09606  511 KYKqlsKYIEP 521
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 6.29e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.16  E-value: 6.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 285814380  756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 6.06e-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: 92.15  E-value: 6.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380 1606 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1681
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380 1682 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1742
Cdd:cd09272    79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 1.48e-61

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: 144563  Cd Length: 98  Bit Score: 207.60  E-value: 1.48e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380    17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQTAQSHSPQNGPYQQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 285814380    97 NPSGWSFYGRPSMIPYTP 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1265-1494 3.87e-36

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: 254387  Cd Length: 246  Bit Score: 139.51  E-value: 3.87e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1265 KTWDtdryydrkEIDP---KRVINSMFIFNRKR--DGT---HKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTS 1331
Cdd:pfam07727    2 KTWE--------LVPLpkgKKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETF-----SPVAKLTTIRLL 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1332 LSLALDNNYYITQLDISSAYLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIQQcGMEEV 1408
Cdd:pfam07727   69 LALAAQRGWELHQMDVKTAFLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFLLKL-GFKQS 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  1409 RGWSCVF-KNSQ---VTICLFVDDMVLFSKNLNSNKRIIEKLKMQYDTKiiNLGesdeEIQYdILGLEIKYQRGKYM--- 1481
Cdd:pfam07727  148 EADPCLFvKKSGggiIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTSGGIFlsq 220
                          250       260
                   ....*....|....*....|..
gi 285814380  1482 ---------KLGMENSLTEKIP 1494
Cdd:pfam07727  221 rkyakkllkRFGMLDCKPVSTP 242
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
663-782 9.86e-20

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 250040  Cd Length: 119  Bit Score: 87.77  E-value: 9.86e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380   663 EPFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQASVlVIQMDRGSEYT 742
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 285814380   743 NRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
MFMR pfam07777
G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 ...
37-167 4.61e-05

G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals.


Pssm-ID: 254423  Cd Length: 189  Bit Score: 44.84  E-value: 4.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380    37 ASKIQEYDKASTKANSQQTTTP--------ASSAVPENPHHASPQTAQSHSPQngPY---QQQCMMTqnqanPsgwsfYG 105
Cdd:pfam07777    6 EGKPSKSSPKTSVQEDTPTPTVypdwsamqAYYGPRPPPPYFNSSVASSPQPH--PYmwgPQQPMMP-----P-----YG 73
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380   106 RPsmIPY-------TPYQMSPMyfPPGPHSQFPQYPSSVGTPLSTPspesGNTFTDS-SSADSDMTSTKK 167
Cdd:pfam07777   74 TP--PPYaamyppgGVYAHPSM--PPGSHPFSPYAMPSAEVPGSTP----LSMETDAkSSDNKDKGSIKK 135
Hpr_kinase_C pfam07475
HPr Serine kinase C-terminal domain; This family represents the C terminal kinase domain of ...
1454-1508 8.34e-03

HPr Serine kinase C-terminal domain; This family represents the C terminal kinase domain of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria. This kinase in unusual in that it recognizes the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller.


Pssm-ID: 148849  Cd Length: 171  Bit Score: 37.79  E-value: 8.34e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 285814380  1454 IINLGESDEEIQYDILGLEIKYQRgkymKLGMenslteKIPKLNVPLNPkGRKLS 1508
Cdd:pfam07475  101 VIELEEWDPDKNYDRLGLDEETQE----ILGV------KIPKVTIPVRP-GRNLA 144
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
4-171 4.61e-05

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 255446 [Multi-domain]  Cd Length: 768  Bit Score: 46.92  E-value: 4.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380     4 QQLSQHSPISHGSACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQTAQSHSPQNG 83
Cdd:pfam09606  369 HQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQQGQPGMMSSPSPVPQVQTNQSMPQPPQPSVPSPGGPGSQPPQSV 448
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380    84 PyqqqcmmtqNQANPSgwsfygRPSMIPYTPYQMSPMyfpPGPHSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMT 163
Cdd:pfam09606  449 S---------GGMIPS------PPALMPSPSPQMSQS---PASQRTIQQDMVSPGGPLNTPGQSSVNSPANPQEEQLYRE 510
                          170
                   ....*....|.
gi 285814380   164 STK---KYVRP 171
Cdd:pfam09606  511 KYKqlsKYIEP 521
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 6.29e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.16  E-value: 6.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285814380  690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 285814380  756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.11
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • 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 et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • 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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