RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17134
(89 letters)
>gnl|CDD|198188 cd09934, SH2_Tec_family, Src homology 2 (SH2) domain found in
Tec-like proteins. The Tec protein tyrosine kinase is
the founding member of a family that includes Btk, Itk,
Bmx, and Txk. The members have a PH domain, a
zinc-binding motif, a SH3 domain, a SH2 domain, and a
protein kinase catalytic domain. Btk is involved in
B-cell receptor signaling with mutations in Btk
responsible for X-linked agammaglobulinemia (XLA) in
humans and X-linked immunodeficiency (xid) in mice. Itk
is involved in T-cell receptor signaling. Tec is
expressed in both T and B cells, and is thought to
function in activated and effector T lymphocytes to
induce the expression of genes regulated by NFAT
transcription factors. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 104
Score = 27.0 bits (60), Expect = 0.70
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEY 60
VSL + P ++ Y + + LA + E +P L Y
Sbjct: 44 VSLFTKVPGSPHVKHYHIKQNARSEFYLAEKHCFETIPELINY 86
>gnl|CDD|219667 pfam07962, Swi3, Replication Fork Protection Component Swi3.
Replication fork pausing is required to initiate a
recombination events. More specifically, Swi1 is
required for recombination near the mat1 locus. Swi3
has been found to co-purify with Swi1 Swi3, together
with Swi1, define a fork protection complex that
coordinates leading- and lagging-strand synthesis and
stabilises stalled replication forks. The Swi1-Swi3
complex is required for accurate replication, fork
protection and replication checkpoint signalling.
Length = 84
Score = 26.8 bits (60), Expect = 0.70
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 1 MPLWAILLFPKRKRQLVVSLLERACVKPVLRPY 33
LWA LFPK K + ++L+E+ K ++ Y
Sbjct: 42 YQLWAHDLFPKAKFKDFLNLVEKLGHKKQVQTY 74
>gnl|CDD|222559 pfam14126, DUF4293, Domain of unknown function (DUF4293). This
family of integral membrane proteins is functionally
uncharacterized. This family of proteins is found in
bacteria. Proteins in this family are typically between
136 and 154 amino acids in length.
Length = 111
Score = 26.7 bits (60), Expect = 0.93
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 2 PLWAILLFPKRKRQLVVSLL 21
L AI LF RK Q+ + L
Sbjct: 29 ALVAIFLFKNRKLQIRLCRL 48
>gnl|CDD|234708 PRK00274, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Reviewed.
Length = 272
Score = 27.0 bits (61), Expect = 1.0
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 20 LLERACVKPVLRPYQLSVQEFGQICLAYRDM 50
LE A + P R LSV+EF ++ A +
Sbjct: 241 ALEAAGIDPNRRAETLSVEEFVRLANALAAL 271
>gnl|CDD|177087 CHL00185, ycf59, magnesium-protoporphyrin IX monomethyl ester
cyclase; Provisional.
Length = 351
Score = 26.6 bits (59), Expect = 1.6
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 9 FPKRKRQLVVSLLERAC 25
++ + L V LER+C
Sbjct: 72 LDEKTKSLFVEFLERSC 88
>gnl|CDD|87993 pfam09448, MmlI, Methylmuconolactone methyl-isomerase. MmlI is a
short, approx 115 residue, protein of two alpha helices
and four beta strands. It is involved in the catabolism
of methyl-substituted aromatics via a modified
oxo-adipate pathway in bacteria. The enzyme appears to
be monomeric in some species and tetrameric in others.
The known structure shows two copies of the protein
form a dimeric alpha beta barrel.
Length = 112
Score = 26.2 bits (57), Expect = 1.9
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 29 VLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPG 67
+++P +S + F CL + +M ++PGL++Y +
Sbjct: 7 LVKPAGMSDETFRAECLRHYEMSHDVPGLHKYEVRLVAE 45
>gnl|CDD|147079 pfam04737, Lant_dehyd_N, Lantibiotic dehydratase, N terminus.
Lantibiotics are ribosomally synthesised antimicrobial
agents derived from ribosomally synthesised peptides.
They are produced by bacteria of the Firmicutes phylum,
and include mutacin, subtilin, and nisin. Lantibiotic
peptides contain thioether bridges termed lanthionines
that are thought to be generated by dehydration of
serine and threonine residues followed by addition of
cysteine residues. This family constitutes the
N-terminus of the enzyme proposed to catalyze the
dehydration step.
Length = 97
Score = 25.3 bits (56), Expect = 3.5
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 10 PKRKRQLVVSL---LERACVKP 28
K+KR+L SL L+R C +
Sbjct: 27 RKKKRRLERSLYRYLQRMCTRN 48
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 25.6 bits (57), Expect = 3.8
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRD 49
+ +LE A + P R LS ++F ++ A +
Sbjct: 224 LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256
>gnl|CDD|173682 cd05591, STKc_nPKC_epsilon, Catalytic domain of the Protein
Serine/Threonine Kinase, Novel Protein Kinase C epsilon.
Serine/Threonine Kinases (STKs), Novel Protein Kinase C
(nPKC), epsilon isoform, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The nPKC subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PKCs are classified into three groups
(classical, atypical, and novel) depending on their mode
of activation and the structural characteristics of
their regulatory domain. nPKCs are calcium-independent,
but require DAG (1,2-diacylglycerol) and
phosphatidylserine (PS) for activity. There are four
nPKC isoforms, delta, epsilon, eta, and theta.
PKC-epsilon has been shown to behave as an oncoprotein.
Its overexpression contributes to neoplastic
transformation depending on the cell type. It
contributes to oncogenesis by inducing disordered cell
growth and inhibiting cell death. It also plays a role
in tumor invasion and metastasis. PKC-epsilon has also
been found to confer cardioprotection against ischemia
and reperfusion-mediated damage. Other cellular
functions include the regulation of gene expression,
cell adhesion, and cell motility.
Length = 321
Score = 25.6 bits (56), Expect = 3.9
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 41 GQICLAYRDMCEE--MPGLYEYTLEDTPGDIEPEAVAEQE 78
G LA MC+E + G+ T TP I PE + E E
Sbjct: 133 GHCKLADFGMCKEGILNGVTTTTFCGTPDYIAPEILQELE 172
>gnl|CDD|182536 PRK10546, PRK10546, pyrimidine (deoxy)nucleoside triphosphate
pyrophosphohydrolase; Provisional.
Length = 135
Score = 25.5 bits (56), Expect = 3.9
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 41 GQICLAYRDMCEEMPGLYEYT---LEDTPGDIEPEAVA 75
G+I LA R + GL+E+ +E PG+ +P+A+
Sbjct: 15 GKILLAQRPAHSDQAGLWEFAGGKVE--PGESQPQALI 50
>gnl|CDD|225221 COG2344, COG2344, AT-rich DNA-binding protein [General function
prediction only].
Length = 211
Score = 25.3 bits (56), Expect = 4.1
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 5 AILLFPKRKRQLVVSLLERACVKPVLR--PYQLSVQE 39
AIL P Q V L +A VK +L P +L V E
Sbjct: 150 AILTVPAEHAQEVADRLVKAGVKGILNFTPVRLQVPE 186
>gnl|CDD|151780 pfam11339, DUF3141, Protein of unknown function (DUF3141). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 581
Score = 25.3 bits (56), Expect = 4.7
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 55 PGLYEYTLEDTPGD 68
PGLYE T++D P +
Sbjct: 376 PGLYEATIDDIPPE 389
>gnl|CDD|107207 cd06446, Trp-synth_B, Tryptophan synthase-beta: Trptophan synthase
is a bifunctional enzyme that catalyses the last two
steps in the biosynthesis of L-tryptophan via its alpha
and beta reactions. In the alpha reaction, indole
3-glycerol phosphate is cleaved reversibly to
glyceraldehyde 3-phosphate and indole at the active site
of the alpha subunit. In the beta reaction, indole
undergoes a PLP-dependent reaction with L-serine to form
L-tryptophan at the active site of the beta subunit.
Members of this CD, Trp-synth_B, are found in all three
major phylogenetic divisions.
Length = 365
Score = 25.2 bits (56), Expect = 6.1
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 54 MPGLYEYTLEDTPGDIEP 71
+ GL YTL+D G I P
Sbjct: 258 LHGLKMYTLQDEDGQIVP 275
>gnl|CDD|221913 pfam13087, AAA_12, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 195
Score = 24.8 bits (55), Expect = 6.3
Identities = 9/36 (25%), Positives = 10/36 (27%), Gaps = 9/36 (25%)
Query: 18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE 53
SL ER L Q YR M +
Sbjct: 3 RSLFERLQEAGPEAVVMLDTQ--------YR-MHPD 29
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been
linked to a number of Rab proteins through their
association with mutual effectors, suggesting a
coordinate role in endocytic regulation. Eukaryotic EHDs
comprise four members (EHD1-4) in mammals and single
members in Caenorhabditis elegans (Rme-1), Drosophila
melanogaster (Past1) as well as several eukaryotic
parasites. EHD1 regulates trafficking of multiple
receptors from the endocytic recycling compartment (ERC)
to the plasma membrane; EHD2 regulates trafficking from
the plasma membrane by controlling Rac1 activity; EHD3
regulates endosome-to-Golgi transport, and preserves
Golgi morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from
the endocytic recycling compartment to the plasma
membrane. In D. melanogaster, deletion of the Past1 gene
leads to infertility as well as premature death of adult
flies. Arabidopsis thaliana also has homologs of EHD
proteins (AtEHD1 and AtEHD2), possibly involved in
regulating endocytosis and signaling.
Length = 241
Score = 24.9 bits (55), Expect = 6.5
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 31 RPYQLSVQEFGQICLAYRDMCEEMPG--LYEYTLEDTPGDIEPEAVAEQEGEGDEIDFN 87
+P++ + +FG L + +P L T+ DTPG + E + G DFN
Sbjct: 61 KPFR-GLSKFGNGFLN-KFEGSTLPHPLLESVTIVDTPGILSGEKQRQSRG----YDFN 113
>gnl|CDD|215852 pfam00311, PEPcase, Phosphoenolpyruvate carboxylase.
Length = 794
Score = 24.4 bits (54), Expect = 9.2
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 8/45 (17%)
Query: 30 LRPYQLSVQEFGQI--------CLAYRDMCEEMPGLYEYTLEDTP 66
L P + E+ +I AYR + E P +Y + TP
Sbjct: 548 LPPPPPKIPEWREIMEELSERSRKAYRALVYETPDFVDYFRQATP 592
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
0.320 0.141 0.428
Gapped
Lambda K H
0.267 0.0832 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,704,370
Number of extensions: 380721
Number of successful extensions: 292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 20
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.0 bits)