RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15112
(73 letters)
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 47.8 bits (114), Expect = 3e-08
Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 25 HAARIHRMIKLGLGIEDDDEPAPSEEVKSEELPAADADTEDASRMEEVD 73
A+RI+RMIKLGL I++D+E +E E + + S+MEEVD
Sbjct: 481 FASRIYRMIKLGLSIDEDEEVEEEDEEAEVETTEPAEEDAEDSKMEEVD 529
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 37.7 bits (87), Expect = 1e-04
Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 5/50 (10%)
Query: 25 HAARIHRMIKLGLGIEDDDEPAPSEEVKSEELPAADAD-TEDASRMEEVD 73
+A RI+RMIKLGL +++++E E ++ A A+ T S ME+VD
Sbjct: 656 YAERINRMIKLGLSLDEEEE----EAAEAPVAETAPAEVTAGTSSMEQVD 701
>gnl|CDD|133086 cd06228, M14-like_3, Peptidase M14-like domain; uncharacterized
subfamily. A functionally uncharacterized subgroup of
the M14 family of metallocarboxypeptidases (MCPs). The
M14 family are zinc-binding carboxypeptidases (CPs)
which hydrolyze single, C-terminal amino acids from
polypeptide chains, and have a recognition site for the
free C-terminal carboxyl group, which is a key
determinant of specificity. Two major subfamilies of
the M14 family, defined based on sequence and
structural homology, are the A/B and N/E subfamilies.
Enzymes belonging to the A/B subfamily are normally
synthesized as inactive precursors containing preceding
signal peptide, followed by an N-terminal pro-region
linked to the enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues
lysine or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate
cleavages. They contain an extra C-terminal
transthyretin-like domain, thought to be involved in
folding or formation of oligomers. MCPs can also be
classified based on their involvement in specific
physiological processes; the pancreatic MCPs
participate only in alimentary digestion and include
carboxypeptidase A and B (A/B subfamily), while others,
namely regulatory MCPs or the N/E subfamily, are
involved in more selective reactions, mainly in
non-digestive tissues and fluids, acting on blood
coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity
in the MCP family, that of dipeptidyl-peptidase
activity of gamma-glutamyl-(L)-meso-diaminopimelate
peptidase I which is involved in bacterial cell wall
metabolism.
Length = 332
Score = 27.0 bits (60), Expect = 0.70
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 2 ERGSVDLAIGKSQELDFWLENLIHAARIHRMIKLG 36
ERGS D I +++ +L++A + R IK G
Sbjct: 41 ERGSPDNLI-------YFVSDLLNARKAGRGIKYG 68
>gnl|CDD|146336 pfam03643, Vps26, Vacuolar protein sorting-associated protein 26.
Vacuolar protein sorting-associated protein (Vps) 26 is
one of around 50 proteins involved in protein
trafficking. In particular, Vps26 assembles into a
retromer complex with at least four other proteins Vps5,
Vps17, Vps29 and Vps35. This family also contains Down
syndrome critical region 3/A.
Length = 275
Score = 27.0 bits (60), Expect = 0.81
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 1 MERGSVDLAIGKSQELDFWLENLIHAARIHRMIKLGLGIED 41
+ R D+ ++E DFW+ N + IK+ +GIED
Sbjct: 128 VVRRLTDI----TKEKDFWVHNFTTYPETNNSIKMEVGIED 164
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 26.6 bits (59), Expect = 1.2
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 7/46 (15%)
Query: 24 IHAARIHRMIKLG-------LGIEDDDEPAPSEEVKSEELPAADAD 62
AARIH+ +K G E+D++ + P DAD
Sbjct: 133 WKAARIHKALKEGEDPNPGPPLDEEDEDADVATTNSDNSFPGEDAD 178
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 25.7 bits (56), Expect = 2.3
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 36 GLGIEDDDEPAPSEEVKSEELPAADADTEDASRMEEV 72
L + DDE SEE SE A+ D D + +E
Sbjct: 922 FLMVGSDDESDESEEEVSEYE-ASSDDESDETDEDEE 957
>gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate
binding domain of LysR-type transcriptional regulators
that are involved in the catabolism of dinitrotoluene,
naphthalene and gamma-hexachlorohexane; contains the
type 2 periplasmic binding fold. This CD includes
LysR-like bacterial transcriptional regulators, DntR,
NahR, and LinR, which are involved in the degradation
of aromatic compounds. The transcription of the genes
encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced
by inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. DntR
from Burkholderia species controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The active form of DntR is
homotetrameric, consisting of a dimer of dimers. NahR
is a salicylate-dependent transcription activator of
the nah and sal operons for naphthalene degradation.
Salicylic acid is an intermediate of the oxidative
degradation of the aromatic ring in soil bacteria.
LinR positively regulates expression of the genes (linD
and linE) encoding enzymes for
gamma-hexachlorocyclohexane (a haloorganic insecticide)
degradation. Expression of linD and linE are induced by
their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ)
and chlorohydroquinone (CHQ). 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 = 201
Score = 25.2 bits (56), Expect = 2.7
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 1 MERGSVDLAIG 11
+E G +DLAIG
Sbjct: 45 LESGEIDLAIG 55
>gnl|CDD|225470 COG2918, GshA, Gamma-glutamylcysteine synthetase [Coenzyme
metabolism].
Length = 518
Score = 24.7 bits (54), Expect = 5.1
Identities = 15/44 (34%), Positives = 19/44 (43%)
Query: 13 SQELDFWLENLIHAARIHRMIKLGLGIEDDDEPAPSEEVKSEEL 56
EL+ +N A R L LGI D+E P +EV E
Sbjct: 367 ESELELTRDNWNRVALEGRKPGLTLGIGCDNEQLPLQEVGKELF 410
>gnl|CDD|225256 COG2382, Fes, Enterochelin esterase and related enzymes [Inorganic
ion transport and metabolism].
Length = 299
Score = 24.3 bits (53), Expect = 6.6
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 20 LENLIHAARIHRMIKLGLGIEDDDE 44
L++LI A I I +G+ D +
Sbjct: 119 LDSLIAAGEIPPAILVGIDYIDVKK 143
>gnl|CDD|181580 PRK08912, PRK08912, hypothetical protein; Provisional.
Length = 387
Score = 24.2 bits (53), Expect = 6.8
Identities = 14/35 (40%), Positives = 14/35 (40%), Gaps = 6/35 (17%)
Query: 27 ARIHRMIKLGLGIEDDDEPAPSEEVKSEELPAADA 61
AR H I LG G DD P AADA
Sbjct: 23 AREHGAINLGQGFPDDPGPEDVRRA------AADA 51
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 24.1 bits (52), Expect = 9.1
Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 17/66 (25%)
Query: 2 ERGSVDLAIGKSQELD-----------------FWLENLIHAARIHRMIKLGLGIEDDDE 44
ERG+VDL + ++L + EN+ + I + LG E D
Sbjct: 366 ERGAVDLGLEWFKQLTGILIMRLLLPPTTIRICGFGENIDFGEVEVKKILVKLGTEQHDV 425
Query: 45 PAPSEE 50
+E
Sbjct: 426 KGVDKE 431
>gnl|CDD|235370 PRK05244, PRK05244, Der GTPase activator; Provisional.
Length = 177
Score = 23.7 bits (52), Expect = 9.6
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 27 ARIHRMIKLGLGIEDDDEPAPSEEVKSEE 55
RI +++ LGI DDD+ SEE +S++
Sbjct: 135 DRIDELMEK-LGISDDDDEEESEEEESDD 162
>gnl|CDD|143612 cd07304, Chorismate_synthase, Chorismase synthase, the enzyme
catalyzing the final step of the shikimate pathway.
Chorismate synthase (CS;
5-enolpyruvylshikimate-3-phosphate phospholyase;
1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C.
4.2.3.5) catalyzes the seventh and final step in the
shikimate pathway: the conversion of 5-
enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a
precursor for the biosynthesis of aromatic compounds.
This process has an absolute requirement for reduced FMN
as a co-factor which is thought to facilitate cleavage
of C-O bonds by transiently donating an electron to the
substrate, having no overall change its redox state.
Depending on the capacity of these enzymes to regenerate
the reduced form of FMN, chorismate synthases are
divided into two classes: Enzymes, mostly from plants
and eubacteria, that sequester CS from the cellular
environment, are monofunctiona,l while those that can
generate reduced FMN at the expense of NADPH, such as
found in fungi and the ciliated protozoan Euglena
gracilis, are bifunctional, having an additional
NADPH:FMN oxidoreductase activity. Recently,
bifunctionality of the Mycobacterium tuberculosis enzyme
(MtCS) was determined by measurements of both chorismate
synthase and NADH:FMN oxidoreductase activities. Since
shikimate pathway enzymes are present in bacteria, fungi
and apicomplexan parasites (such as Toxoplasma gondii,
Plasmodium falciparum, and Cryptosporidium parvum) but
absent in mammals, they are potentially attractive
targets for the development of new therapy against
infectious diseases such as tuberculosis (TB).
Length = 344
Score = 23.9 bits (53), Expect = 9.7
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 40 EDDDEPAPSEEVKSEELPAADADTEDASRMEEV 72
D DE EE + + D + E+ +M+E+
Sbjct: 159 FDLDEEELLEEAEESPVRCPDPEAEE--KMKEL 189
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
0.310 0.131 0.360
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,880,592
Number of extensions: 312753
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 280
Number of HSP's successfully gapped: 26
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.3 bits)