RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3970
(104 letters)
>gnl|CDD|216497 pfam01429, MBD, Methyl-CpG binding domain. The Methyl-CpG
binding domain (MBD) binds to DNA that contains one or
more symmetrically methylated CpGs. DNA methylation in
animals is associated with alterations in chromatin
structure and silencing of gene expression. MBD has
negligible non-specific affinity for DNA. In vitro
foot-printing with MeCP2 showed the MBD can protect a
12 nucleotide region surrounding a methyl CpG pair.
MBDs are found in several Methyl-CpG binding proteins
and also DNA demethylase.
Length = 75
Score = 73.9 bits (182), Expect = 5e-19
Identities = 34/72 (47%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 20 TKKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGV- 78
+KR +CP LPPGW REE R G S GKVDV+YYSP GKK R++SE+++ + N
Sbjct: 1 RRKREDCPPLPPGWRREERQRKSGSSAGKVDVYYYSPTGKKFRSKSELIRYLEKNGDTSL 60
Query: 79 ---SFDFRSGKL 87
FDF
Sbjct: 61 KLEDFDFTVRSE 72
>gnl|CDD|238690 cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and MBD4 are members
of a protein family that share the methyl-CpG-binding
domain (MBD). The MBD, consists of about 70 residues
and is defined as the minimal region required for
binding to methylated DNA by a methyl-CpG-binding
protein which binds specifically to methylated DNA. The
MBD can recognize a single symmetrically methylated CpG
either as naked DNA or within chromatin. MeCP2, MBD1
and MBD2 (and likely MBD3) form complexes with histone
deacetylase and are involved in histone
deacetylase-dependent repression of transcription. MBD4
is an endonuclease that forms a complex with the DNA
mismatch-repair protein MLH1.
Length = 77
Score = 65.1 bits (159), Expect = 1e-15
Identities = 31/69 (44%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 23 RYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGV---- 78
+ E P+LPPGW RE V R K S GK DV+Y SP GKK R++ E+ + + N P
Sbjct: 1 KPEDPRLPPGWKRELVPR-KSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLS 59
Query: 79 SFDFRSGKL 87
FDF K
Sbjct: 60 DFDFTVPKK 68
>gnl|CDD|128673 smart00391, MBD, Methyl-CpG binding domain. Methyl-CpG binding
domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1)
domain.
Length = 77
Score = 63.9 bits (156), Expect = 4e-15
Identities = 29/73 (39%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 21 KKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGN----IP 76
P LP GW RE R G S GK DV+Y SPCGKKLR++SE+ + + N +
Sbjct: 1 GDPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLD 59
Query: 77 GVSFDFRSGKLNS 89
FDF +
Sbjct: 60 LECFDFNATVPVG 72
>gnl|CDD|238069 cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and
BAZ2A-like proteins constitute a family of proteins
that share the methyl-CpG-binding domain (MBD). The MBD
consists of about 70 residues and is defined as the
minimal region required for binding to methylated DNA
by a methyl-CpG-binding protein which binds
specifically to methylated DNA. The MBD can recognize a
single symmetrically methylated CpG either as naked DNA
or within chromatin. MeCP2, MBD1 and MBD2 (and likely
MBD3) form complexes with histone deacetylase and are
involved in histone deacetylase-dependent repression of
transcription. MBD4 is an endonuclease that forms a
complex with the DNA mismatch-repair protein MLH1. The
MBDs present in putative chromatin remodelling subunit,
BAZ2A, and putative histone methyltransferase, CLLD8,
represent two phylogenetically distinct groups within
the MBD protein family.
Length = 62
Score = 61.2 bits (149), Expect = 3e-14
Identities = 31/63 (49%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 24 YECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGV----S 79
P LPPGW RE V R G S GK DV+YYSPCGKKLR++ EV + + P +
Sbjct: 2 LRDP-LPPGWKRELVIRKSG-SAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLEN 59
Query: 80 FDF 82
F F
Sbjct: 60 FSF 62
>gnl|CDD|238691 cd01397, HAT_MBD, Methyl-CpG binding domains (MBD) present in
putative chromatin remodelling factor such as BAZ2A;
BAZ2A contains a MBD, DDT, PHD-type zinc finger and
Bromo domain suggesting that BAZ2A might be associated
with histone acetyltransferase (HAT) activity. The
Drosophila melanogaster toutatis protein, a putative
subunit of the chromatin-remodeling complex, and other
such proteins in this group share a similar domain
architecture with BAZ2A, as does the Caenorhabditis
elegans flectin homolog.
Length = 73
Score = 42.0 bits (99), Expect = 1e-06
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 29 LPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIP 76
L GW RE R G + + +V YY+PCGKKLR EV++ + N
Sbjct: 6 LELGWRRETRIRGLGGRI-QGEVAYYAPCGKKLRQYPEVIKYLSKNGI 52
>gnl|CDD|238689 cd01395, HMT_MBD, Methyl-CpG binding domains (MBD) present in
putative histone methyltransferases (HMT) such as CLLD8
and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and
a bifurcated SET domain, suggesting that CLLD8 might be
associated with methylation-mediated transcriptional
repression. SETDB1 and other proteins in this group
have a similar domain architecture. SETDB1 is a novel
KAP-1-associated histone H3, lysine 9-specific
methyltransferase that contributes to HP1-mediated
silencing of euchromatic genes by KRAB zinc-finger
proteins.
Length = 60
Score = 32.4 bits (74), Expect = 0.006
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 32 GWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIR 72
G+ R + G V K V Y +PCG+ LR SEV + +R
Sbjct: 9 GFQRMKYRARVG-KVKKH-VIYKAPCGRSLRNMSEVHRYLR 47
>gnl|CDD|181922 PRK09512, rbsC, ribose ABC transporter permease protein; Reviewed.
Length = 320
Score = 29.3 bits (66), Expect = 0.26
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 36 EEVTRNKGLSVGKVDVFYYSPCG 58
E TR G++V KV + Y+ CG
Sbjct: 205 EAATRLSGINVNKVKIIVYALCG 227
>gnl|CDD|132813 cd07280, PX_YPT35, The phosphoinositide binding Phox Homology
domain of the fungal protein YPT35. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions such as cell signaling,
vesicular trafficking, protein sorting, and lipid
modification, among others. This subfamily is composed
of YPT35 proteins from the fungal subkingdom Dikarya.
The PX domain is involved in targeting of proteins to
PI-enriched membranes, and may also be involved in
protein-protein interaction. The PX domain of YPT35
binds to phosphatidylinositol 3-phosphate (PI3P). It
also serves as a protein interaction domain, binding to
members of the Yip1p protein family, which localize to
the ER and Golgi. YPT35 is mainly associated with
endosomes and together with Yip1p proteins, may be
involved in a specific function in the endocytic
pathway.
Length = 120
Score = 28.8 bits (65), Expect = 0.28
Identities = 16/32 (50%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 13 NLLKMLPTKKRYECPQLPPG--WYREEVTRNK 42
LL P KR E PQLPP WY V NK
Sbjct: 54 ALLDEFPRHKRNEIPQLPPKVPWYDSRVNLNK 85
>gnl|CDD|180652 PRK06667, motB, flagellar motor protein MotB; Validated.
Length = 252
Score = 27.1 bits (60), Expect = 1.7
Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 21/93 (22%)
Query: 17 MLPTKKRYECPQLPPGW---YREEVTRNKGLSVGKVDVFY---YSPCGKKLRTRSEVLQV 70
+ KK +C Q P + Y + VT + F+ ++ VLQ+
Sbjct: 2 AMRKKKCPKCIQGAPEYMLTYGDMVTL--------LLCFFVMLFTTN----DVDENVLQI 49
Query: 71 IRGNIPGVSFDFRSGKLNSLQKHRNKQRGNQFE 103
I + G F F+ G+ +L K + + GN
Sbjct: 50 ISASFTGTGF-FKGGQ--TLSKGKLSELGNSIM 79
>gnl|CDD|143273 cd05865, Ig1_NCAM-1, First immunoglobulin (Ig)-like domain of
neural cell adhesion molecule NCAM-1. Ig1_NCAM-1:
first immunoglobulin (Ig)-like domain of neural cell
adhesion molecule NCAM-1. NCAM-1 plays important roles
in the development and regeneration of the central
nervous system, in synaptogenesis and neural migration.
NCAM mediates cell-cell and cell-substratum recognition
and adhesion via homophilic (NCAM-NCAM), and
heterophilic (NCAM-nonNCAM), interactions. NCAM is
expressed as three major isoforms having different
intracellular extensions. The extracellular portion of
NCAM has five N-terminal Ig-like domains and two
fibronectin type III domains. The double zipper
adhesion complex model for NCAM homophilic binding
involves the Ig1, Ig2, and Ig3 domains. By this model,
Ig1 and Ig2 mediate dimerization of NCAM molecules
situated on the same cell surface (cis interactions),
and Ig3 domains mediate interactions between NCAM
molecules expressed on the surface of opposing cells
(trans interactions), through binding to the Ig1 and
Ig2 domains. The adhesive ability of NCAM is modulated
by the addition of polysialic acid chains to the fifth
Ig-like domain.
Length = 96
Score = 25.8 bits (56), Expect = 3.5
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 50 DVFYYSPCGKKLRTRSEVLQVIRGN 74
D+ ++SP G+KL + + V+R +
Sbjct: 32 DISWFSPNGEKLTPNQQRISVVRND 56
>gnl|CDD|239288 cd02990, UAS_FAF1, UAS family, FAS-associated factor 1 (FAF1)
subfamily; FAF1 contains a UAS domain of unknown
function N-terminal to a ubiquitin-associated UBX
domain. FAF1 also contains ubiquitin-associated UBA and
nuclear targeting domains, N-terminal to the UAS domain.
FAF1 is an apoptotic signaling molecule that acts
downstream in the Fas signal transduction pathway. It
interacts with the cytoplasmic domain of Fas, but not to
a Fas mutant that is deficient in signal transduction.
It is widely expressed in adult and embryonic tissues,
and in tumor cell lines, and is localized not only in
the cytoplasm where it interacts with Fas, but also in
the nucleus. FAF1 contains phosphorylation sites for
protein kinase CK2 within the nuclear targeting domain.
Phosphorylation influences nuclear localization of FAF1
but does not affect its potentiation of Fas-induced
apoptosis. Other functions have also been attributed to
FAF1. It inhibits nuclear factor-kB (NF-kB) by
interfering with the nuclear translocation of the p65
subunit. FAF1 also interacts with valosin-containing
protein (VCP), which is involved in the
ubiquitin-proteosome pathway.
Length = 136
Score = 24.8 bits (54), Expect = 7.5
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 60 KLRTRSEVLQVIRGNI 75
R+ +EVL VI+GN
Sbjct: 105 GKRSSNEVLNVIQGNT 120
>gnl|CDD|150620 pfam09966, DUF2200, Uncharacterized protein conserved in bacteria
(DUF2200). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 111
Score = 24.5 bits (54), Expect = 9.9
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 43 GLSVGKVDVFYYSPCGKKLRTRSEVLQVIR 72
+S V Y + KK RT+ EV +VIR
Sbjct: 4 TMSFASVYPHYVAKAEKKGRTKEEVDEVIR 33
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.137 0.412
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,081,695
Number of extensions: 408965
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 17
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)