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Conserved domains on  [gi|6322010|ref|NP_012086.1|]
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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) ...
1644-1780 2.21e-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: 93.30  E-value: 2.21e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010  1644 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSHLVQEL---NKKPITkg 1719
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010  1720 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1780
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 2.80e-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: 206.83  E-value: 2.80e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENLHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 6322010      97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1303-1532 2.46e-38

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: 146.06  E-value: 2.46e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1303 KTWDtdryydrkEIDP---KRVINSMFIFNRKR--DGT---HKARFVARGDIQHP-----DTYDPGMQSNTVHhyalmTS 1369
Cdd:pfam07727    2 KTWE--------LVPLpkgKKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETFSPVAKLTTIR-----LL 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1370 LSLALDNNYYITQLDISSAYLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLiKQCGMEEV 1446
Cdd:pfam07727   69 LALAAQRGWELHQMDVKTAFLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFL-LKLGFKQS 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1447 RGWSCVF-KNSQ---VTICLFVDDMILFSKDLNANKKIITTLKKQYDTKiiNLGesdnEIQYdILGLEIKYQRGKYM--- 1519
Cdd:pfam07727  148 EADPCLFvKKSGggiIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTSGGIFlsq 220
                          250       260
                   ....*....|....*....|..
gi 6322010    1520 ---------KLGMENSLTEKIP 1532
Cdd:pfam07727  221 rkyakkllkRFGMLDCKPVSTP 242
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
701-820 8.62e-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: 88.16  E-value: 8.62e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010     701 EPFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQASVlVIQMDRGSEYT 780
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 6322010     781 NRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 820
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) ...
1644-1780 2.21e-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: 93.30  E-value: 2.21e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010  1644 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSHLVQEL---NKKPITkg 1719
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010  1720 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1780
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 2.80e-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: 206.83  E-value: 2.80e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENLHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 6322010      97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1303-1532 2.46e-38

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: 146.06  E-value: 2.46e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1303 KTWDtdryydrkEIDP---KRVINSMFIFNRKR--DGT---HKARFVARGDIQHP-----DTYDPGMQSNTVHhyalmTS 1369
Cdd:pfam07727    2 KTWE--------LVPLpkgKKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETFSPVAKLTTIR-----LL 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1370 LSLALDNNYYITQLDISSAYLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLiKQCGMEEV 1446
Cdd:pfam07727   69 LALAAQRGWELHQMDVKTAFLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFL-LKLGFKQS 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1447 RGWSCVF-KNSQ---VTICLFVDDMILFSKDLNANKKIITTLKKQYDTKiiNLGesdnEIQYdILGLEIKYQRGKYM--- 1519
Cdd:pfam07727  148 EADPCLFvKKSGggiIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTSGGIFlsq 220
                          250       260
                   ....*....|....*....|..
gi 6322010    1520 ---------KLGMENSLTEKIP 1532
Cdd:pfam07727  221 rkyakkllkRFGMLDCKPVSTP 242
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
701-820 8.62e-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: 88.16  E-value: 8.62e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010     701 EPFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQASVlVIQMDRGSEYT 780
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 6322010     781 NRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 820
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
52-140 4.92e-05

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: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 46.09  E-value: 4.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      52 SQQTTTPASSAVPEnlhHASPQPASVPPPQNGPYPQQCMMTQN---QANPSGWSFYGHPsmiPYTPYQMsPMYFP--PGP 126
Cdd:pfam07223  126 SQPQPPPAQQPQAQ---QPQPPPQVPQQQQYQSPPQQPQYQQNpppQAQSAPQVSGLYP---EESPYQP-QSYPPnePLP 198
                           90
                   ....*....|....
gi 6322010     127 QSQFPQYPSSVGTP 140
Cdd:pfam07223  199 SSMAMQPPYSGAPP 212
PHA02517 PHA02517
putative transposase OrfB; Reviewed
728-820 6.27e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.54  E-value: 6.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    728 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 793
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 6322010    794 TPCYTTTADSRAHGVAERLNRTLLDDC 820
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 6.71e-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: 40.93  E-value: 6.71e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010       53 QQTTTPASSAVPenLHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 6322010      128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
 
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) ...
1644-1780 2.21e-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: 93.30  E-value: 2.21e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010  1644 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSHLVQEL---NKKPITkg 1719
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010  1720 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1780
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 2.80e-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: 206.83  E-value: 2.80e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENLHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 6322010      97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1303-1532 2.46e-38

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: 146.06  E-value: 2.46e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1303 KTWDtdryydrkEIDP---KRVINSMFIFNRKR--DGT---HKARFVARGDIQHP-----DTYDPGMQSNTVHhyalmTS 1369
Cdd:pfam07727    2 KTWE--------LVPLpkgKKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETFSPVAKLTTIR-----LL 68
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1370 LSLALDNNYYITQLDISSAYLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLiKQCGMEEV 1446
Cdd:pfam07727   69 LALAAQRGWELHQMDVKTAFLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFL-LKLGFKQS 147
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    1447 RGWSCVF-KNSQ---VTICLFVDDMILFSKDLNANKKIITTLKKQYDTKiiNLGesdnEIQYdILGLEIKYQRGKYM--- 1519
Cdd:pfam07727  148 EADPCLFvKKSGggiIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTSGGIFlsq 220
                          250       260
                   ....*....|....*....|..
gi 6322010    1520 ---------KLGMENSLTEKIP 1532
Cdd:pfam07727  221 rkyakkllkRFGMLDCKPVSTP 242
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
701-820 8.62e-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: 88.16  E-value: 8.62e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010     701 EPFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQASVlVIQMDRGSEYT 780
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 6322010     781 NRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 820
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
MFMR pfam07777
G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 ...
42-167 1.13e-03

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: 40.60  E-value: 1.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      42 EYDKASTK--ANSQQTTTPASSAVPE----------NLHHASPQPASVPPPQNGPY---PQQCMMTqnqanpsgwsfygh 106
Cdd:pfam07777    5 EEGKPSKSspKTSVQEDTPTPTVYPDwsamqayygpRPPPPYFNSSVASSPQPHPYmwgPQQPMMP-------------- 70
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6322010     107 psmiPY-TPYQMSPMY----------FPPGPQSQFPQYPSSVGTPLSTPspesGNTFTDS-SSADSDMTSTKK 167
Cdd:pfam07777   71 ----PYgTPPPYAAMYppggvyahpsMPPGSHPFSPYAMPSAEVPGSTP----LSMETDAkSSDNKDKGSIKK 135
YppG pfam14179
YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which ...
73-148 9.12e-03

YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important.


Pssm-ID: 258379  Cd Length: 110  Bit Score: 36.64  E-value: 9.12e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6322010      73 QPASVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMiPYTPYQMSPMYFPPGPQSQFPQYPSSVGTPLSTPSPES 148
Cdd:pfam14179    1 NMYQQNHNPYLPYNQQQQPYQQQPYHQ-----QMPPP-PYSPPQQQQAHFMPPQPQPYPKPSPQQQQPSQFSSFMS 70
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
52-140 4.92e-05

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: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 46.09  E-value: 4.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      52 SQQTTTPASSAVPEnlhHASPQPASVPPPQNGPYPQQCMMTQN---QANPSGWSFYGHPsmiPYTPYQMsPMYFP--PGP 126
Cdd:pfam07223  126 SQPQPPPAQQPQAQ---QPQPPPQVPQQQQYQSPPQQPQYQQNpppQAQSAPQVSGLYP---EESPYQP-QSYPPnePLP 198
                           90
                   ....*....|....
gi 6322010     127 QSQFPQYPSSVGTP 140
Cdd:pfam07223  199 SSMAMQPPYSGAPP 212
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
23-178 2.21e-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: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 44.16  E-value: 2.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      23 SKEVHTNQ-DPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENLHHASPQPASVPPPQN----GPYPQQCMMTQNQAN 97
Cdd:pfam07223   36 SSEAHSFHvDSTKQPPAPEQVAKHELADAPLQQVNAALPPAPAPQSPQPDQQQQSQAPPSHqypsQLPPQQVQSVPQQPT 115
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      98 PSGWSFY------GHPSMIPYTPYQMSPMYFPPGPQS-----QFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTK 166
Cdd:pfam07223  116 PQQEPYYpppsqpQPPPAQQPQAQQPQPPPQVPQQQQyqsppQQPQYQQNPPPQAQSAPQVSGLYPEESPYQPQSYPPNE 195
                          170
                   ....*....|..
gi 6322010     167 KyvRPPPMLTSP 178
Cdd:pfam07223  196 P--LPSSMAMQP 205
PHA02517 PHA02517
putative transposase OrfB; Reviewed
728-820 6.27e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 42.54  E-value: 6.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010    728 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 793
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 6322010    794 TPCYTTTADSRAHGVAERLNRTLLDDC 820
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 6.71e-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: 40.93  E-value: 6.71e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010       53 QQTTTPASSAVPenLHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 6322010      128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
52-183 1.72e-03

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


Pssm-ID: 255543 [Multi-domain]  Cd Length: 806  Bit Score: 41.69  E-value: 1.72e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322010      52 SQQTTTPASSAVPENLHHASPQPASVPPPQNGPYPQQCMMTQNQANPSgwsfyghpsmiPYTPYQMSPMYFPPGPQSQFP 131
Cdd:pfam09770  201 PGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQF-----------PGLSQQMPPPPPQPPQQQQQP 269
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 6322010     132 QYPSSVGTPLSTPSPESGNtftdsssadsdmtsTKKYVRPPPMLTSPNDFPN 183
Cdd:pfam09770  270 PQPQAQPPPQNQPTPHPGL--------------PQGQNAPLPPPQQPQLLPL 307
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.14
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • 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 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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