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Conserved domains on  [gi|536210|emb|CAA84952|]
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TY1B [Saccharomyces cerevisiae]

Protein Classification

TYA and RNase_HI_RT_Ty1 domain-containing protein (domain architecture ID 12013401)

protein containing domains TYA, rve, RVT_2, and RNase_HI_RT_Ty1

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 4.19e-65

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: 218.80  E-value: 4.19e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 536210       97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1282-1495 1.03e-31

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 311594  Cd Length: 246  Bit Score: 127.70  E-value: 1.03e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1282 KRVINSMFIFNRKRD-----GTHKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTSLSLALDNNYYITQLDISSA 1351
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1352 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1424
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1425 LFVDDMILFSKDLNSNKRIIAKLKMQYDTKiiNLGESddeiqHDILGLEIKYQRGKYM------------KLGMENSLTE 1492
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSKEFEMK--DLGEL-----SYFLGIEIKQTPGGITlsqskyikklleRFGMTDCKPV 239

                   ...
gi 536210     1493 KIP 1495
Cdd:pfam07727  240 STP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1607-1743 1.06e-20

Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms including bacteria, archaea, and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD) are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1, and the vertebrate retroviruses. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260004  Cd Length: 140  Bit Score: 92.53  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210   1607 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1682
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210   1683 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1743
Cdd:cd09272   79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 6.79e-19

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


:

Pssm-ID: 307008  Cd Length: 114  Bit Score: 86.54  E-value: 6.79e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210      664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 536210      744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
PAT1 super family cl25764
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
51-186 1.57e-04

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


The actual alignment was detected with superfamily member pfam07223:

Pssm-ID: 330585  Cd Length: 389  Bit Score: 46.01  E-value: 1.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 536210      117 MSPMYFPPGPQSQFPQYPSSVGTPlSTPSPESGNTFTDSSSADSDMTSTkKYVR----PPPmlTSPNDFPNWVK 186
Cdd:pfam07223  212 VPPVYPPYSPIRQPPNPSPEPLPG-SMPMQQFYSGPPPPQSRHHSGAPS-GYGQggtiGPP--SGPGQQPQQLK 281
 
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 4.19e-65

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: 218.80  E-value: 4.19e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 536210       97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1282-1495 1.03e-31

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 311594  Cd Length: 246  Bit Score: 127.70  E-value: 1.03e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1282 KRVINSMFIFNRKRD-----GTHKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTSLSLALDNNYYITQLDISSA 1351
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1352 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1424
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1425 LFVDDMILFSKDLNSNKRIIAKLKMQYDTKiiNLGESddeiqHDILGLEIKYQRGKYM------------KLGMENSLTE 1492
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSKEFEMK--DLGEL-----SYFLGIEIKQTPGGITlsqskyikklleRFGMTDCKPV 239

                   ...
gi 536210     1493 KIP 1495
Cdd:pfam07727  240 STP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1607-1743 1.06e-20

Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms including bacteria, archaea, and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD) are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1, and the vertebrate retroviruses. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260004  Cd Length: 140  Bit Score: 92.53  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210   1607 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1682
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210   1683 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1743
Cdd:cd09272   79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 6.79e-19

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


Pssm-ID: 307008  Cd Length: 114  Bit Score: 86.54  E-value: 6.79e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210      664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 536210      744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 1.01e-04

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


Pssm-ID: 197891  Cd Length: 165  Bit Score: 44.40  E-value: 1.01e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210        53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 536210       128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
51-186 1.57e-04

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


Pssm-ID: 311273  Cd Length: 389  Bit Score: 46.01  E-value: 1.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 536210      117 MSPMYFPPGPQSQFPQYPSSVGTPlSTPSPESGNTFTDSSSADSDMTSTkKYVR----PPPmlTSPNDFPNWVK 186
Cdd:pfam07223  212 VPPVYPPYSPIRQPPNPSPEPLPG-SMPMQQFYSGPPPPQSRHHSGAPS-GYGQggtiGPP--SGPGQQPQQLK 281
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 1.48e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853  Cd Length: 277  Bit Score: 42.54  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 536210     756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 4.19e-65

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: 218.80  E-value: 4.19e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       17 ACASVTSKEVHTNQDPLDVSASKIQEYDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 536210       97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1282-1495 1.03e-31

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 311594  Cd Length: 246  Bit Score: 127.70  E-value: 1.03e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1282 KRVINSMFIFNRKRD-----GTHKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTSLSLALDNNYYITQLDISSA 1351
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1352 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1424
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     1425 LFVDDMILFSKDLNSNKRIIAKLKMQYDTKiiNLGESddeiqHDILGLEIKYQRGKYM------------KLGMENSLTE 1492
Cdd:pfam07727  167 LYVDDILITGSSEKEINEFKEELSKEFEMK--DLGEL-----SYFLGIEIKQTPGGITlsqskyikklleRFGMTDCKPV 239

                   ...
gi 536210     1493 KIP 1495
Cdd:pfam07727  240 STP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1607-1743 1.06e-20

Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms including bacteria, archaea, and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD) are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1, and the vertebrate retroviruses. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260004  Cd Length: 140  Bit Score: 92.53  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210   1607 VVISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELD---KKPITkg 1682
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGiplDGPTT-- 78
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210   1683 LLTDskstisiiisN-------NEEKF--RNRFFGTKAMRLRDEVSGNHLHVCYIETKKNIADVMTKPLP 1743
Cdd:cd09272   79 IYCD----------NqsaialaKNPVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 6.79e-19

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


Pssm-ID: 307008  Cd Length: 114  Bit Score: 86.54  E-value: 6.79e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210      664 PFQYLHTDIFgPVHNLPKSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 536210      744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
Cytadhesin_P30 pfam07271
Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 ...
45-149 6.12e-06

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


Pssm-ID: 284643  Cd Length: 308  Bit Score: 50.23  E-value: 6.12e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       45 KASTKANSQQTTTPASSAVPENPHHASPQPASvpPPQNGPYPQQCMMTQNQANPSGWSFYG----------HPSMIPYTP 114
Cdd:pfam07271  137 QAAAEAHAEAETEPAGQNVANNPQMGINQPQI--NINFGPNPQQRINPQCFGFPMQPGQMAmrpgfnqmppHMGGAPPNQ 214
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 536210      115 YQMSPMY--FPP-----GPQSQFPQYPSSVGTPLSTPSPESG 149
Cdd:pfam07271  215 MGMRPGFnqMPPqmggmAPRPGFPNHMPGMNAPRPGFPPQPG 256
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 1.01e-04

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


Pssm-ID: 197891  Cd Length: 165  Bit Score: 44.40  E-value: 1.01e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210        53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 536210       128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
51-186 1.57e-04

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


Pssm-ID: 311273  Cd Length: 389  Bit Score: 46.01  E-value: 1.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 536210      117 MSPMYFPPGPQSQFPQYPSSVGTPlSTPSPESGNTFTDSSSADSDMTSTkKYVR----PPPmlTSPNDFPNWVK 186
Cdd:pfam07223  212 VPPVYPPYSPIRQPPNPSPEPLPG-SMPMQQFYSGPPPPQSRHHSGAPS-GYGQggtiGPP--SGPGQQPQQLK 281
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
52-178 1.84e-04

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


Pssm-ID: 308660  Cd Length: 938  Bit Score: 46.24  E-value: 1.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       52 SQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGwsfyghPSMIPYTPYQMSPMYFPPGPQSQFP 131
Cdd:pfam03154  181 QQPAPTPATPLPSQTPPPMTSQPQPLPVASPSTITTATSTTTTSRVVSP------VDPNPDPPSIIAPQSAQRGPEGPPT 254
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 536210      132 QYPSSVGTPLSTPSPESGNTFTDSSSAdsdmtstkkyvrPPPMLTSP 178
Cdd:pfam03154  255 PQPHSLQGPPSFPGPAQGPGQGQGQSP------------PPPSLYPP 289
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
46-141 5.25e-04

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


Pssm-ID: 313063  Cd Length: 837  Bit Score: 44.61  E-value: 5.25e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       46 ASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMI----PYTPYQMSPMY 121
Cdd:pfam09770  196 AAMRAQAKKPAQQPAPAPPQQPQAPPAQQQQQQQQFPPQQQQQQQPQQQPQQPQQHPGQGHPVTIlqrpQSKQPDPPQPS 275
                           90       100
                   ....*....|....*....|
gi 536210      122 FPPGPQSQFPQYPSSVGTPL 141
Cdd:pfam09770  276 PQPQAQPFHQQPPPVPVQPT 295
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 1.48e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853  Cd Length: 277  Bit Score: 42.54  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210     690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 536210     756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
2-135 1.80e-03

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


Pssm-ID: 311273  Cd Length: 389  Bit Score: 42.54  E-value: 1.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210        2 ESQQLSNYPHISHGSACASVTSKEVHTNQDpldvsaskiqeydkastkaNSQQTTTPASSAVPENPHHASPQPASVPPPQ 81
Cdd:pfam07223   33 ESQQSSNSQSGQEDSAQSVSASKPQDNSQS-------------------HQQLPLPLALPHQVNAPNAPPPQFQSPPPLI 93
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 536210       82 NG---PYPQQCMMTQNQANPSGwSFYGHPSMIPYTPYQmsPMYFPPGPQSQFPQYPS 135
Cdd:pfam07223   94 LQqlvPVQLPTQLPQQQINQQE-PYYMPPQQHPENTHQ--QYQVPPAQQPQLPQYPP 147
PARM pfam17061
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ...
32-178 2.64e-03

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


Pssm-ID: 319112  Cd Length: 296  Bit Score: 41.75  E-value: 2.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       32 PLDVS-ASKIQEydKASTKANSQQTTTPASSAVPENPHHAS--PQPASV---PPPQN-----------GPYPQQCMMTQN 94
Cdd:pfam17061   12 PLPVSlPAKITP--PTATWTSSPQNTAAVTASPTSGTHNNSvlPVTASAptsPLPKNisvepreeeptSPASNWEGTNTD 89
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       95 QANPSGWSFYG--HPSMIPYTPYQMSPMYFPP--GPQS--QFP-----QYPSSVGTPLSTPSPESgntftDSSSADSDMT 163
Cdd:pfam17061   90 PSPPGLSPTSGgvHLTPTPEEHSSGTPEASVPatGSQSpaESPtltspQAPASSPSSLSTSPPEV-----SSASVTTNHS 164
                          170
                   ....*....|....*
gi 536210      164 STKKYVRPPPMLTSP 178
Cdd:pfam17061  165 STETSTQPTGAPTTP 179
SOBP pfam15279
Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual ...
19-183 8.78e-03

Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteristic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein.


Pssm-ID: 317654  Cd Length: 303  Bit Score: 40.14  E-value: 8.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       19 ASVTSKEVHTNQDPLDVSASKIQEyDKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQN-------GPYPQQCM- 90
Cdd:pfam15279   82 ASPASVRSESVSPPPSSRTSPSPS-PTSSSSSKPLISVAPSSKLLSPRPPEPPSLVPPPLPPKLlrkrpglRPPPGVPPg 160
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536210       91 ----------MTQNQANPSGWSFYGHPSMIPYTPyqMSPMyfPPGPQSQFPQYPSSVGTPLSTPSPesGNTFTDSSSAds 160
Cdd:pfam15279  161 sppmsmtprgPLQKPQPPLPLPAFMEGSSMPPPF--LRPP--PSIGNLQGPLPNQSLPPIGPPPKP--PRTLGPPSNP-- 232
                          170       180
                   ....*....|....*....|...
gi 536210      161 dMTSTKKYVRPPPMLTSPNDFPN 183
Cdd:pfam15279  233 -MHRPPFSPHPPPPPTPSGNPPG 254
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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