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Conserved domains on  [gi|7839176|ref|NP_058163.1|]
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TPA: gag-pol fusion protein [Saccharomyces cerevisiae S288c]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 2.23e-63

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


:

Pssm-ID: 279373  Cd Length: 98  Bit Score: 212.63  E-value: 2.23e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      17 AYASVTSKEVPSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 7839176      97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1489 3.63e-30

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: 285028  Cd Length: 246  Bit Score: 121.92  E-value: 3.63e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176    1296 KKVINSMFIFNKKRD-----GTHKARFVARGDIQHP-----DTYdsdmqSNTVHHYALMTSLSIALDNDYYITQLDISSA 1365
Cdd:pfam07727   13 HKPIGCKWVFKVKQDedgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176    1366 YLYADIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLInCCDMQEVRGWSCVF----KNSQVTIC 1438
Cdd:pfam07727   88 FLNGELDEEVYVKQPPgfeDPGKPNKVCKLKKSLYGLKQAPRAWYSRLDNTLL-SLGFKRSKADTGLFikgkGGGFLILG 166
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 7839176    1439 LFVDDMILFSKDLNANKKIITTLKKQYDTKiiNLGESDNeiqydILGLEIK 1489
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSSEFEMK--DLGELSY-----FLGIEIK 210
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 9.49e-28

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: 111.79  E-value: 9.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176  1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7839176  1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
660-778 1.19e-17

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: 279057  Cd Length: 116  Bit Score: 81.54  E-value: 1.19e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     660 PFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFNARVLVIQMDRGSEYTN 739
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIEFRGPPGPKIIHSDNGSEYTS 77
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 7839176     740 KTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   78 KAFQEFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 116
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 4.87e-06

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


:

Pssm-ID: 290683  Cd Length: 67  Bit Score: 46.21  E-value: 4.87e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7839176     574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 YLDISSVANPVIAvasKDDETWLWHRRLGHPSFKGLKKLSKKGLVPGLPILKDL-------VCESCQLGKQ 67
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 2.23e-63

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


Pssm-ID: 279373  Cd Length: 98  Bit Score: 212.63  E-value: 2.23e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      17 AYASVTSKEVPSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 7839176      97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1489 3.63e-30

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: 285028  Cd Length: 246  Bit Score: 121.92  E-value: 3.63e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176    1296 KKVINSMFIFNKKRD-----GTHKARFVARGDIQHP-----DTYdsdmqSNTVHHYALMTSLSIALDNDYYITQLDISSA 1365
Cdd:pfam07727   13 HKPIGCKWVFKVKQDedgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176    1366 YLYADIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLInCCDMQEVRGWSCVF----KNSQVTIC 1438
Cdd:pfam07727   88 FLNGELDEEVYVKQPPgfeDPGKPNKVCKLKKSLYGLKQAPRAWYSRLDNTLL-SLGFKRSKADTGLFikgkGGGFLILG 166
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 7839176    1439 LFVDDMILFSKDLNANKKIITTLKKQYDTKiiNLGESDNeiqydILGLEIK 1489
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSSEFEMK--DLGELSY-----FLGIEIK 210
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 9.49e-28

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: 111.79  E-value: 9.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176  1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7839176  1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
660-778 1.19e-17

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: 279057  Cd Length: 116  Bit Score: 81.54  E-value: 1.19e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     660 PFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFNARVLVIQMDRGSEYTN 739
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIEFRGPPGPKIIHSDNGSEYTS 77
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 7839176     740 KTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   78 KAFQEFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 116
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 4.87e-06

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


Pssm-ID: 290683  Cd Length: 67  Bit Score: 46.21  E-value: 4.87e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7839176     574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 YLDISSVANPVIAvasKDDETWLWHRRLGHPSFKGLKKLSKKGLVPGLPILKDL-------VCESCQLGKQ 67
DAZAP2 pfam11029
DAZ associated protein 2 (DAZAP2); DAZ associated protein 2 has a highly conserved sequence ...
78-132 3.82e-06

DAZ associated protein 2 (DAZAP2); DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organization and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats.


Pssm-ID: 287943 [Multi-domain]  Cd Length: 130  Bit Score: 47.42  E-value: 3.82e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7839176      78 PPPQNGQYQQHGMMTPNKAMASN--WAHYQQPSMMTCSHYQTSP----AYYQPDPHYPLPQ 132
Cdd:pfam11029    4 YPPAYSQIYQPRYAHPPYAASYApqYGPPYPAQQMYPPMAQMGPpppmAYQPPGPAQPPPQ 64
PRK10263 PRK10263
DNA translocase FtsK; Provisional
55-158 1.76e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.54  E-value: 1.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     55 ETTPGTSAVPENHHHVSPQPasVPPPQngQYQQhgmmtPNKAMASNWaHYQQPSMMTCSHyqtsPAYYQPD-PHYPLPQY 133
Cdd:PRK10263  752 VQQPQQPVAPQQQYQQPQQP--VAPQP--QYQQ-----PQQPVAPQP-QYQQPQQPVAPQ----PQYQQPQqPVAPQPQY 817
                          90       100
                  ....*....|....*....|....*
gi 7839176    134 IPPLSTSSPDPIDSQNQHSEVPQAE 158
Cdd:PRK10263  818 QQPQQPVAPQPQYQQPQQPVAPQPQ 842
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
52-144 2.79e-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: 42.08  E-value: 2.79e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176       52 SQQetTPGTSAVPEnHHHVSPQPASVP-PPQNGQYQQ--HGMMTPNKAMASNW-AHYQQPSMMTcshYQTSPAYYQPDPH 127
Cdd:smart00818   43 SQQ--HPPTHTLQP-HHHIPVLPAQQPvVPQQPLMPVpgQHSMTPTQHHQPNLpQPAQQPFQPQ---PLQPPQPQQPMQP 116
                            90
                    ....*....|....*..
gi 7839176      128 YPLPQYIPPLSTSSPDP 144
Cdd:smart00818  117 QPPVHPIPPLPPQPPLP 133
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 2.23e-63

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


Pssm-ID: 279373  Cd Length: 98  Bit Score: 212.63  E-value: 2.23e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      17 AYASVTSKEVPSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 7839176      97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1489 3.63e-30

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: 285028  Cd Length: 246  Bit Score: 121.92  E-value: 3.63e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176    1296 KKVINSMFIFNKKRD-----GTHKARFVARGDIQHP-----DTYdsdmqSNTVHHYALMTSLSIALDNDYYITQLDISSA 1365
Cdd:pfam07727   13 HKPIGCKWVFKVKQDedgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176    1366 YLYADIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLInCCDMQEVRGWSCVF----KNSQVTIC 1438
Cdd:pfam07727   88 FLNGELDEEVYVKQPPgfeDPGKPNKVCKLKKSLYGLKQAPRAWYSRLDNTLL-SLGFKRSKADTGLFikgkGGGFLILG 166
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 7839176    1439 LFVDDMILFSKDLNANKKIITTLKKQYDTKiiNLGESDNeiqydILGLEIK 1489
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSSEFEMK--DLGELSY-----FLGIEIK 210
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 9.49e-28

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: 111.79  E-value: 9.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176  1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7839176  1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
660-778 1.19e-17

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: 279057  Cd Length: 116  Bit Score: 81.54  E-value: 1.19e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     660 PFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFNARVLVIQMDRGSEYTN 739
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIEFRGPPGPKIIHSDNGSEYTS 77
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 7839176     740 KTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   78 KAFQEFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 116
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 4.87e-06

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


Pssm-ID: 290683  Cd Length: 67  Bit Score: 46.21  E-value: 4.87e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7839176     574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 YLDISSVANPVIAvasKDDETWLWHRRLGHPSFKGLKKLSKKGLVPGLPILKDL-------VCESCQLGKQ 67
Sox_C_TAD pfam12067
Sox C-terminal transactivation domain; This domain is found at the C-terminus of the Sox ...
60-153 9.74e-04

Sox C-terminal transactivation domain; This domain is found at the C-terminus of the Sox family of transcription factors. It is found associated with pfam00505. It binds to the Armadillo repeats (pfam00514) in Catenin beta-1 (CTNNB1), which is involved in transcriptional regulation. It functions as a transactivating domain (TAD).


Pssm-ID: 288887  Cd Length: 202  Bit Score: 41.15  E-value: 9.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      60 TSAVPENHHHVspqPASVPPPQNGQYQQH-----------GMMTPNKAMASNWAHYQQPSMMTCSHYQTSPAYYQPDPHY 128
Cdd:pfam12067   40 PSHMQEDCQMM---PPYSYHPYASEYSGQpephcgpshplGQEPAGSSLPGLMGPPSPLHMYYGQMYSPQAGKHHPGHQP 116
                           90       100
                   ....*....|....*....|....*
gi 7839176     129 PLPQYIPPLSTSSPDPIDsQNQHSE 153
Cdd:pfam12067  117 HLGQLSPPPEAPHLDTLD-QLSPAE 140
DAZAP2 pfam11029
DAZ associated protein 2 (DAZAP2); DAZ associated protein 2 has a highly conserved sequence ...
78-132 3.82e-06

DAZ associated protein 2 (DAZAP2); DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organization and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats.


Pssm-ID: 287943 [Multi-domain]  Cd Length: 130  Bit Score: 47.42  E-value: 3.82e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7839176      78 PPPQNGQYQQHGMMTPNKAMASN--WAHYQQPSMMTCSHYQTSP----AYYQPDPHYPLPQ 132
Cdd:pfam11029    4 YPPAYSQIYQPRYAHPPYAASYApqYGPPYPAQQMYPPMAQMGPpppmAYQPPGPAQPPPQ 64
PRK10263 PRK10263
DNA translocase FtsK; Provisional
55-158 1.76e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.54  E-value: 1.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     55 ETTPGTSAVPENHHHVSPQPasVPPPQngQYQQhgmmtPNKAMASNWaHYQQPSMMTCSHyqtsPAYYQPD-PHYPLPQY 133
Cdd:PRK10263  752 VQQPQQPVAPQQQYQQPQQP--VAPQP--QYQQ-----PQQPVAPQP-QYQQPQQPVAPQ----PQYQQPQqPVAPQPQY 817
                          90       100
                  ....*....|....*....|....*
gi 7839176    134 IPPLSTSSPDPIDSQNQHSEVPQAE 158
Cdd:PRK10263  818 QQPQQPVAPQPQYQQPQQPVAPQPQ 842
PRK10263 PRK10263
DNA translocase FtsK; Provisional
9-147 1.99e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.16  E-value: 1.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      9 NPHSLHGSAYASVTS--KEVPSnqDPLaVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHvSPQPASVPPPQNGQYQ 86
Cdd:PRK10263  720 NPFSLDDFEFSPMKAllDDGPH--EPL-FTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQ-QPQQPVAPQPQYQQPQ 795
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 7839176     87 QHGMMTPnkamasNWAHYQQPSmmtcshyQTSPAYYQP-DPHYPLPQYIPPLSTSSPDPIDS 147
Cdd:PRK10263  796 QPVAPQP------QYQQPQQPV-------APQPQYQQPqQPVAPQPQYQQPQQPVAPQPQDT 844
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
3-158 3.17e-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: 284607 [Multi-domain]  Cd Length: 389  Bit Score: 47.11  E-value: 3.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176       3 SQQLHQNPHSLHGSAYA-SVTSKEVPSNQdpLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQ-PASVPPP 80
Cdd:pfam07223  103 PTQFPQQQIPQQEPYYMpPQQHPENTQQQ--YQLPPAQQPQLPQYPSQAPHQYYQPQPQAPPQPPQQLQSQQfPQYSQPP 180
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      81 QNGQYQQHGMMTPNKAMASnwahyQQPSMMTCSHYQTSPAYYQPDPHYPLPQYIPPLSTSSP--DPIDSQNQHSEVPQAE 158
Cdd:pfam07223  181 QQQQQQPSPQVNPQQVQQP-----PSPHHQEESAPQSPPVYPPYPSQQQPANPPPEPLPGSMpmQQFYSGPPQPQSRHHS 255
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
52-144 2.79e-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: 42.08  E-value: 2.79e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176       52 SQQetTPGTSAVPEnHHHVSPQPASVP-PPQNGQYQQ--HGMMTPNKAMASNW-AHYQQPSMMTcshYQTSPAYYQPDPH 127
Cdd:smart00818   43 SQQ--HPPTHTLQP-HHHIPVLPAQQPvVPQQPLMPVpgQHSMTPTQHHQPNLpQPAQQPFQPQ---PLQPPQPQQPMQP 116
                            90
                    ....*....|....*..
gi 7839176      128 YPLPQYIPPLSTSSPDP 144
Cdd:smart00818  117 QPPVHPIPPLPPQPPLP 133
PRK10263 PRK10263
DNA translocase FtsK; Provisional
53-155 4.55e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 43.92  E-value: 4.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     53 QQETTPGTSAVPENHHHVSPQPASVP-PPQNGQYQQHGMMTPNKAMASNWAHYQQPSMMTC-SHYQTSPAYYQP---DPH 127
Cdd:PRK10263  398 QQPVQPQQPYYAPAAEQPAQQPYYAPaPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPqSTYQTEQTYQQPaaqEPL 477
                          90       100
                  ....*....|....*....|....*...
gi 7839176    128 YPLPQYIPPLSTSSPDPIDSQNQHSEVP 155
Cdd:PRK10263  478 YQQPQPVEQQPVVEPEPVVEETKPARPP 505
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
19-170 4.87e-04

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


Pssm-ID: 281189 [Multi-domain]  Cd Length: 982  Bit Score: 43.47  E-value: 4.87e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      19 ASVTSKEVPSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQN-GQYQQ----HGMMTP 93
Cdd:pfam03154  195 PAPTPATTLPPQPSPPTTSQPPQPIPQASPHTLIQQTPTLHPQRLPSPHPPLQPMPQPDPPSQApPQSAPqpglHGPPPP 274
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      94 NKAMASNWAHYQQP---SMMTCSHYQTSPAYYQPDPHYPLpQYIPPLSTSSPDPIDSQNQHseVPQAETKVRNNVLPPHT 170
Cdd:pfam03154  275 TPHSLQGPPHLPHPlppQPFGQGQVPPPPSFQAPHPSSQL-QCQPPSQSSGPSPQPPREQP--LPPAPLSMPHIKPPPTT 351
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
47-169 1.38e-03

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


Pssm-ID: 284607 [Multi-domain]  Cd Length: 389  Bit Score: 41.71  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176      47 STKVNSQQET--TPGTSAVPENHHHVSP-----QPASVPPPQNGQYQQHGMMTPNKAMASNWAHY-QQPS-------MMT 111
Cdd:pfam07223   42 SGEEDSAQSVfsPRENDNSQSHQQQELAlapphQVNAPQSPAPPFQPPPPLQLQQLPPVQLPTQFpQQQIpqqepyyMPP 121
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 7839176     112 CSHYQTSPAYYQ--PDPHYPLPQYIPPLSTSSPDPIDsQNQHSEVPQAETKVRNNVLPPH 169
Cdd:pfam07223  122 QQHPENTQQQYQlpPAQQPQLPQYPSQAPHQYYQPQP-QAPPQPPQQLQSQQFPQYSQPP 180
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.15
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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