RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13859
(108 letters)
>gnl|CDD|219729 pfam08148, DSHCT, DSHCT (NUC185) domain. This C terminal domain is
found in DOB1/SK12/helY-like DEAD box helicases.
Length = 178
Score = 90.0 bits (224), Expect = 3e-24
Identities = 41/103 (39%), Positives = 66/103 (64%), Gaps = 15/103 (14%)
Query: 4 EVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWA--------MQK----EGIIVRCIQQ 51
++ +E++HG++ + E +FGL++VVYEWA ++ EG IVR I++
Sbjct: 79 KLAKVEREHGLDEPEYVER---FDFGLMEVVYEWARGASFSEICEETDLFEGDIVRVIRR 135
Query: 52 LSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDIVFAPSLWT 94
L ELLR + + AKI G+ +L K ++AI++I+RDIVFA SL+
Sbjct: 136 LDELLRQLANAAKIIGDPELAEKAEEAIELIRRDIVFAASLYL 178
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 57.0 bits (138), Expect = 8e-11
Identities = 34/101 (33%), Positives = 52/101 (51%), Gaps = 15/101 (14%)
Query: 4 EVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWA--MQK----------EGIIVRCIQQ 51
++ + +E E ++ + GL++VVYEWA + EG VR ++
Sbjct: 942 KLNKDQNSSQIE---IYPELNDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRR 998
Query: 52 LSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDIVFAPSL 92
L ELLR ++ A + G +L K +AIQ I+RDIVF SL
Sbjct: 999 LRELLRQLRKAASVIGNPELEEKAYRAIQEIRRDIVFVDSL 1039
>gnl|CDD|223514 COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1
[Energy production and conversion].
Length = 203
Score = 28.2 bits (63), Expect = 0.82
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 62 GAKIFGERDLPLKMDQAIQVIKRDIVFAPSLWTKLLVGGQPHYYHV 107
GA IFG+ D P A + + TK +GG+PH Y+V
Sbjct: 151 GALIFGDIDDPKSKRVAELKPEGNAGL-----TKPNLGGKPHVYYV 191
>gnl|CDD|241302 cd01272, PTB1_Fe65, Fe65 N-terminal Phosphotyrosine-binding (PTB)
domain. The neuronal adaptor protein Fe65 is involved
in brain development, Alzheimer disease amyloid
precursor protein (APP) signaling, and proteolytic
processing of APP. It contains three protein-protein
interaction domains, one WW domain, and a unique tandem
array of phosphotyrosine-binding (PTB) domains. The
N-terminal PTB domain was shown to interact with a
variety of proteins, including the low density
lipoprotein receptor-related protein (LRP-1), the
ApoEr2 receptor, and the histone acetyltransferase
Tip60. PTB domains have a common PH-like fold and are
found in various eukaryotic signaling molecules. This
domain was initially shown to binds peptides with a
NPXY motif with differing requirements for
phosphorylation of the tyrosine, although more recent
studies have found that some types of PTB domains can
bind to peptides lack tyrosine residues altogether. In
contrast to SH2 domains, which recognize
phosphotyrosine and adjacent carboxy-terminal residues,
PTB-domain binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 138
Score = 26.9 bits (60), Expect = 1.7
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 47 RCIQQLSELLRSIKDGAKIFGE-RDLPLKMDQ 77
CI+QLS I+D I+GE +D+ + ++
Sbjct: 30 NCIRQLSYGRNDIRDTVGIWGEGKDMLMILED 61
>gnl|CDD|176168 cd08479, PBP2_CrgA_like_9, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 9. The LTTRs are acting as
both auto-repressors and activators of target promoters,
controlling operons involved in a wide variety of
cellular processes such as amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of nitrogen-fixing bacteria,
and synthesis of virulence factors, to name a few. In
contrast to the tetrameric form of other LTTRs, CrgA
from Neisseria meningitides assembles into an octameric
ring, which can bind up to four 63-bp DNA
oligonucleotides. Phylogenetic cluster analysis showed
that the CrgA-like regulators form a subclass of the
LTTRs that function as octamers. The CrgA is an
auto-repressor of its own gene and activates the
expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 198
Score = 25.6 bits (57), Expect = 4.9
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 33 VVYEWAMQKEGIIVRCIQQLSELLRS 58
VV +WA+ GII+R ++ LRS
Sbjct: 135 VVLQWALDGHGIILRSEWDVAPYLRS 160
>gnl|CDD|218883 pfam06075, DUF936, Plant protein of unknown function (DUF936).
This family consists of several hypothetical proteins
from Arabidopsis thaliana and Oryza sativa. The
function of this family is unknown.
Length = 564
Score = 25.9 bits (57), Expect = 5.2
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 52 LSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDIVFAPSL 92
L +LL+++ K+ GE L +QV IV P+L
Sbjct: 6 LLKLLQAMNTDVKVAGEHRSSL-----LQVT--SIV--PAL 37
>gnl|CDD|218969 pfam06277, EutA, Ethanolamine utilisation protein EutA. This
family consists of several bacterial EutA ethanolamine
utilisation proteins. The EutA protein is thought to
protect the lyase (EutBC) from inhibition by CNB12.
Length = 473
Score = 25.6 bits (57), Expect = 6.2
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 50 QQLSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDI 86
Q + L +I +G ER LPL I V+++D+
Sbjct: 388 QAVQALAEAIAEGMADLIERGLPL-----IIVVEQDM 419
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 25.0 bits (55), Expect = 9.1
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 58 SIKDGAKIFGERDLPLKMDQAIQVIKRDIVFA 89
++ D A+ +G+R LPL +D V R VFA
Sbjct: 39 TLADLAEKYGDRLLPLALD----VTDRAAVFA 66
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
0.319 0.137 0.398
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,496,642
Number of extensions: 465830
Number of successful extensions: 411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 409
Number of HSP's successfully gapped: 15
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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 (24.1 bits)