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Conserved domains on  [gi|1370534|emb|CAA97988.1|]
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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 4.47e-64

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: 215.71  E-value: 4.47e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      17 ACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 1370534      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 ...
1281-1494 5.33e-32

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: 128.47  E-value: 5.33e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1281 KRVINSMFIFNKKRD-----GTHKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTSLSLALDNNYYITQLDISSA 1350
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1351 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1423
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1424 LFVDDMILFSKDlnanKKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIKYQRGKYM------------KLGMEN 1487
Cdd:pfam07727  167 LYVDDILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIKQTPGGITlsqskyikklleRFGMTD 235

                   ....*..
gi 1370534    1488 SLTEKIP 1494
Cdd:pfam07727  236 CKPVSTP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 7.53e-26

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: 107.55  E-value: 7.53e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534  1606 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQEL---NKKPIIkg 1681
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370534  1682 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1742
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 1.79e-18

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: 85.00  E-value: 1.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534     664 PFQYLHTDIFgPVHNLPNSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1370534     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 2.70e-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: 45.24  E-value: 2.70e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370534     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 4.47e-64

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: 215.71  E-value: 4.47e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      17 ACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 1370534      97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1281-1494 5.33e-32

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: 128.47  E-value: 5.33e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1281 KRVINSMFIFNKKRD-----GTHKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTSLSLALDNNYYITQLDISSA 1350
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1351 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1423
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1424 LFVDDMILFSKDlnanKKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIKYQRGKYM------------KLGMEN 1487
Cdd:pfam07727  167 LYVDDILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIKQTPGGITlsqskyikklleRFGMTD 235

                   ....*..
gi 1370534    1488 SLTEKIP 1494
Cdd:pfam07727  236 CKPVSTP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 7.53e-26

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: 107.55  E-value: 7.53e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534  1606 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQEL---NKKPIIkg 1681
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370534  1682 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1742
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 1.79e-18

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: 85.00  E-value: 1.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534     664 PFQYLHTDIFgPVHNLPNSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1370534     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 1.86e-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: 43.62  E-value: 1.86e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534       53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 1370534      128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
51-186 2.70e-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: 45.24  E-value: 2.70e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370534     117 MSPMYFPPGPQSQFPQYPSSVGTPlSTPSPESGNTFTDSSSADSDMTSTkKYVR----PPPmlTSPNDFPNWVK 186
Cdd:pfam07223  212 VPPVYPPYSPIRQPPNPSPEPLPG-SMPMQQFYSGPPPPQSRHHSGAPS-GYGQggtiGPP--SGPGQQPQQLK 281
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 1.47e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853  Cd Length: 277  Bit Score: 42.54  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 1370534    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 4.47e-64

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: 215.71  E-value: 4.47e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      17 ACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 1370534      97 NPSGWSFYGHPSMIPYTP 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1281-1494 5.33e-32

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: 128.47  E-value: 5.33e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1281 KRVINSMFIFNKKRD-----GTHKARFVARGDIQHP-----DTYdsgmqSNTVHHYALMTSLSLALDNNYYITQLDISSA 1350
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgidydETF-----SPVARLESIRLLLALAAQRGWELHQMDVKSA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1351 YLYADIKEELYIRPPP---HLGMNDKLIRLKKSLYGLKQSGANWYETIKSYLIKQcGMEEVRGWSCVF----KNSQVTIC 1423
Cdd:pfam07727   88 FLNGELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLLSL-GFKRSKHDHGLFikgkGDGFLIVG 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    1424 LFVDDMILFSKDlnanKKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIKYQRGKYM------------KLGMEN 1487
Cdd:pfam07727  167 LYVDDILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIKQTPGGITlsqskyikklleRFGMTD 235

                   ....*..
gi 1370534    1488 SLTEKIP 1494
Cdd:pfam07727  236 CKPVSTP 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1606-1742 7.53e-26

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: 107.55  E-value: 7.53e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534  1606 VAISDASYGNQPY-YKSQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQEL---NKKPIIkg 1681
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370534  1682 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1742
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
664-782 1.79e-18

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: 85.00  E-value: 1.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534     664 PFQYLHTDIFgPVHNLPNSAPSYFISFTDETTKFRWVYPLhdRREDSILDVFTTILAFIKNQFQasVLVIQMDRGSEYTN 743
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRGG--PKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1370534     744 RTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
Cytadhesin_P30 pfam07271
Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 ...
33-149 4.38e-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: 50.62  E-value: 4.38e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      33 LDVSASKTEECEK-ASTKANSQQTTTPASSAVPENPHHASPQPASvpPPQNGPYPQQCMMTQNQANPSGWSFYG------ 105
Cdd:pfam07271  124 IEAEQEEQEAIEQqAAAEAHAEAETEPAGQNVANNPQMGINQPQI--NINFGPNPQQRINPQCFGFPMQPGQMAmrpgfn 201
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1370534     106 ----HPSMIPYTPYQMSPMY--FPP-----GPQSQFPQYPSSVGTPLSTPSPESG 149
Cdd:pfam07271  202 qmppHMGGAPPNQMGMRPGFnqMPPqmggmAPRPGFPNHMPGMNAPRPGFPPQPG 256
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
41-141 9.08e-05

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: 47.31  E-value: 9.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      41 EECEkASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMI----PYTPYQ 116
Cdd:pfam09770  192 EEVE-AAMRAQAKKPAQQPAPAPPQQPQAPPAQQQQQQQQFPPQQQQQQQPQQQPQQPQQHPGQGHPVTIlqrpQSKQPD 270
                           90       100
                   ....*....|....*....|....*
gi 1370534     117 MSPMYFPPGPQSQFPQYPSSVGTPL 141
Cdd:pfam09770  271 PPQPSPQPQAQPFHQQPPPVPVQPT 295
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
53-146 1.86e-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: 43.62  E-value: 1.86e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534       53 QQTTTPASSAVPenPHHASPQPASVP--PPQNGPYPQQCMMT---QNQANPSGwsfyGHPSMIPYTPYQMSPMYFPPGPQ 127
Cdd:smart00818   36 HHQIIPVSQQHP--PTHTLQPHHHIPvlPAQQPVVPQQPLMPvpgQHSMTPTQ----HHQPNLPQPAQQPFQPQPLQPPQ 109
                            90
                    ....*....|....*....
gi 1370534      128 SQFPQYPSSVGTPLSTPSP 146
Cdd:smart00818  110 PQQPMQPQPPVHPIPPLPP 128
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
51-186 2.70e-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: 45.24  E-value: 2.70e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      51 NSQQTTTPASSAVPENPHHASPQPA-----SVPPPQNGPYPQQCMMTQNQANPSgwsfyGHPSMIPYTPY---------Q 116
Cdd:pfam07223  137 AQQPQLPQYPPQAPHQYYQPPPQWQhqtgqQVQSQQFPQYSQPPQLQQQQYNQQ-----VNPQQVQPPPSphhqeesapY 211
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370534     117 MSPMYFPPGPQSQFPQYPSSVGTPlSTPSPESGNTFTDSSSADSDMTSTkKYVR----PPPmlTSPNDFPNWVK 186
Cdd:pfam07223  212 VPPVYPPYSPIRQPPNPSPEPLPG-SMPMQQFYSGPPPPQSRHHSGAPS-GYGQggtiGPP--SGPGQQPQQLK 281
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
2-135 9.15e-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: 43.31  E-value: 9.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534       2 ESQQLSQHSPISHGSACASVTSKEVHTNQDpldvsaskteecekastkaNSQQTTTPASSAVPENPHHASPQPASVPPPQ 81
Cdd:pfam07223   33 ESQQSSNSQSGQEDSAQSVSASKPQDNSQS-------------------HQQLPLPLALPHQVNAPNAPPPQFQSPPPLI 93
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1370534      82 NG---PYPQQCMMTQNQANPSGwSFYGHPSMIPYTPYQmsPMYFPPGPQSQFPQYPS 135
Cdd:pfam07223   94 LQqlvPVQLPTQLPQQQINQQE-PYYMPPQQHPENTHQ--QYQVPPAQQPQLPQYPP 147
PHA02517 PHA02517
putative transposase OrfB; Reviewed
690-782 1.47e-03

putative transposase OrfB; Reviewed


Pssm-ID: 222853  Cd Length: 277  Bit Score: 42.54  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534    690 FTDETTKFRWVY-----PLHDRR---------EDSILdVFTTILAFIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGI 755
Cdd:PHA02517  117 FTYVSTWQGWVYvafiiDVFARRivgwrvsssMDTDF-VLDALEQALWARGRPGGLIHHSDKGSQYVSLAYTQRLKEAGI 195
                          90       100
                  ....*....|....*....|....*..
gi 1370534    756 TPCYTTTADSRAHGVAERLNRTLLDDC 782
Cdd:PHA02517  196 RASTGSRGDSYDNAPAESINGLYKAEV 222
SOBP pfam15279
Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual ...
10-183 9.33e-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: 39.76  E-value: 9.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      10 SPISHGSACASVTSkEVHTNQDPLDVSASkteeCEKAStkansqQTTTPASSAVPENPHHASPQPASVPPPQN------- 82
Cdd:pfam15279   83 SPASVRSESVSPPP-SSRTSPSPSPTSSS----SSKPL------ISVAPSSKLLSPRPPEPPSLVPPPLPPKLlrkrpgl 151
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370534      83 GPYPQQCM-----------MTQNQANPSGWSFYGHPSMIPYTPyqMSPMyfPPGPQSQFPQYPSSVGTPLSTPSPesGNT 151
Cdd:pfam15279  152 RPPPGVPPgsppmsmtprgPLQKPQPPLPLPAFMEGSSMPPPF--LRPP--PSIGNLQGPLPNQSLPPIGPPPKP--PRT 225
                          170       180       190
                   ....*....|....*....|....*....|..
gi 1370534     152 FTDSSSAdsdMTSTKKYVRPPPMLTSPNDFPN 183
Cdd:pfam15279  226 LGPPSNP---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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