Score = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 55/90 (61%), Positives = 70/90 (77%)
Query: 1 KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
K H LSR++IIPLP +ANPET+PEALF +V+ALYPQTTCFY+A++++ P DD
Sbjct: 200 KERHTLSRRRIIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHTPPQRPQDD 259
Query: 61 YELLFEDNSYADNYAPPLGVPQRYVIAYKK 90
Y +LFED SYAD Y+PPL V QRYV+A K+
Sbjct: 260 YSVLFEDTSYADGYSPPLNVAQRYVVACKE 289
Involved in transcriptional regulation, through association with histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes. Specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3). In the SAGA-type complexes, required to recruit complexes to H3K4me. May be involved in MYC-mediated oncogenic transformation. Rattus norvegicus (taxid: 10116)
Score = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 55/90 (61%), Positives = 70/90 (77%)
Query: 1 KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
K H LSR++IIPLP +ANPET+PEALF +V+ALYPQTTCFY+A++++ P DD
Sbjct: 200 KERHTLSRRRIIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHTPPQRPQDD 259
Query: 61 YELLFEDNSYADNYAPPLGVPQRYVIAYKK 90
Y +LFED SYAD Y+PPL V QRYV+A K+
Sbjct: 260 YSVLFEDTSYADGYSPPLNVAQRYVVACKE 289
Involved in transcriptional regulation, through association with histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes. Specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3). In the SAGA-type complexes, required to recruit complexes to H3K4me. May be involved in MYC-mediated oncogenic transformation.
Score = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 54/91 (59%), Positives = 71/91 (78%)
Query: 1 KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
K H LSR+++IPLP +ANPET+PEALF +V+ALYPQTTCFY+A++++ P DD
Sbjct: 200 KERHTLSRRRVIPLPQWKANPETDPEALFQREQLVLALYPQTTCFYRALIHAPPQRPQDD 259
Query: 61 YELLFEDNSYADNYAPPLGVPQRYVIAYKKS 91
Y +LFED SYAD Y+PPL V QRYV+A K++
Sbjct: 260 YSVLFEDTSYADGYSPPLNVAQRYVVACKET 290
Involved in transcriptional regulation, through association with histone acetyltransferase (HAT) SAGA-type complexes. Specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for the trimethylated form (H3K4me3). In the SAGA-type complexes, required to recruit complexes to H3K4me.
Score = 119 bits (298), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 54/90 (60%), Positives = 70/90 (77%)
Query: 1 KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
K H LSR+++IPLP +ANPET+PEALF +V+ALYPQTTCFY+A++++ P DD
Sbjct: 200 KERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDD 259
Query: 61 YELLFEDNSYADNYAPPLGVPQRYVIAYKK 90
Y +LFED SYAD Y+PPL V QRYV+A K+
Sbjct: 260 YSVLFEDTSYADGYSPPLNVAQRYVVACKE 289
Involved in transcriptional regulation, through association with histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes. Specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3). In the SAGA-type complexes, required to recruit complexes to H3K4me. May be involved in MYC-mediated oncogenic transformation.
Homo sapiens (taxid: 9606)
Close Homologs in the Non-Redundant Database Detected by BLAST
Score = 117 (46.2 bits), Expect = 9.8e-07, P = 9.8e-07
Identities = 34/85 (40%), Positives = 47/85 (55%)
Query: 4 HQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTG-TDDYE 62
++LS I+P P KR +P + E + P G V+A+YP TT YKA V S P +D+Y
Sbjct: 183 YKLSMSCILPFP-KRNDPSSTQEFI-P-GKHVLAVYPGTTALYKATVISTPRKRKSDEYL 239
Query: 63 LLFEDNSYADNYAPPLGVPQRYVIA 87
L F+D+ D P VP V+A
Sbjct: 240 LEFDDDE-EDGALPQRTVPFHKVVA 263
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.315 0.134 0.399 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 92 92 0.00091 102 3 11 23 0.40 30
29 0.40 31
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 9
No. of states in DFA: 499 (53 KB)
Total size of DFA: 100 KB (2071 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 24
Search cpu time: 10.39u 0.09s 10.48t Elapsed: 00:00:03
Total cpu time: 10.39u 0.09s 10.48t Elapsed: 00:00:03
Start: Thu Aug 15 13:10:29 2013 End: Thu Aug 15 13:10:32 2013
Score = 119 bits (300), Expect = 1e-36
Identities = 55/90 (61%), Positives = 68/90 (75%), Gaps = 2/90 (2%)
Query: 1 KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
K ++LSRK +IPLP K ANPET P ALFP G++V+ALYPQTTCFY+AIV+S P +D+
Sbjct: 43 KKRYKLSRKDLIPLP-KTANPETSPHALFPKGTIVLALYPQTTCFYRAIVHSPPKRKSDE 101
Query: 61 YELLFEDNSYADNYAPPLGVPQRYVIAYKK 90
Y L FED+ AD Y PP VPQRYV+A+
Sbjct: 102 YRLRFEDDEDADGY-PPREVPQRYVVAFPG 130
This domain is found in the yeast protein SAGA-associated factor 29. This domain is related to members of the Tudor domain superfamily such as pfam05641. The SAGA complex is involved in RNA polymerase II-dependent transcriptional regulation. The membership of the tudor domain superfamily suggests this domain may bind to RNA. Length = 130
MSH6_like The PWWP domain is present in MSH6, a mi
82.47
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes
It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane
It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains
For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
>PF15057 DUF4537: Domain of unknown function (DUF4537)
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix
The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins
The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways
DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []
The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []
Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids
The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []
The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF
This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS
The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
>2equ_A PHD finger protein 20-like 1; tudor domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
>2e5q_A PHD finger protein 19; tudor domain, isoform B, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
>2d9t_A Tudor domain-containing protein 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: b.34.9.1
>2diq_A Tudor and KH domain-containing protein; tudor domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.9.1
>2eqm_A PHD finger protein 20-like 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2jtf_A
>2eqk_A Tudor domain-containing protein 4; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
