RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17076
(71 letters)
>gnl|CDD|224173 COG1253, TlyC, Hemolysins and related proteins containing CBS
domains [General function prediction only].
Length = 429
Score = 33.8 bits (78), Expect = 0.002
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 19 ALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFTVISEIVRTG 70
L+++E +I+ L++ + V EIMT D LD+ + +I I+ +G
Sbjct: 188 VLEEEEREMINNVLDLDDRTVREIMTPRTDIVALDLTDTVE-ELIELILESG 238
>gnl|CDD|133134 cd06603, GH31_GANC_GANAB_alpha, This family includes the closely
related glycosyl hydrolase family 31 (GH31) isozymes,
neutral alpha-glucosidase C (GANC) and the alpha
subunit of heterodimeric neutral alpha-glucosidase AB
(GANAB). Initially distinguished on the basis of
differences in electrophoretic mobility in starch gel,
GANC and GANAB have been shown to have other
differences, including those of substrate specificity.
GANC and GANAB are key enzymes in glycogen metabolism
that hydrolyze terminal, non-reducing 1,4-linked
alpha-D-glucose residues from glycogen in the
endoplasmic reticulum. The GANC/GANAB family includes
the alpha-glucosidase II (ModA) from Dictyostelium
discoideum as well as the alpha-glucosidase II (GLS2,
or ROT2 - Reversal of TOR2 lethality protein 2) from
Saccharomyces cerevisiae.
Length = 339
Score = 27.9 bits (63), Expect = 0.31
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 34 MTQKKVEEIMTKLD------DCYMLDIE 55
Q+ V+E+ D D LDIE
Sbjct: 21 KDQEDVKEVDAGFDEHDIPYDVIWLDIE 48
>gnl|CDD|226256 COG3733, TynA, Cu2+-containing amine oxidase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 654
Score = 26.3 bits (58), Expect = 1.2
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 3/64 (4%)
Query: 8 GIPMEATSNLVALKKDEVNIISGALEMTQKKVEEIMTKLDDCYMLDIETILNFTVISEIV 67
P+E + V + D I +++ KV D M+ ++ F + IV
Sbjct: 79 NKPIERKALAVVYELDGKGIYEAVVDLDNNKVLSWQPIKDAHPMITLD---EFASVENIV 135
Query: 68 RTGE 71
R
Sbjct: 136 RNDP 139
>gnl|CDD|119346 cd06554, ASCH_ASC-1_like, ASC-1 homology domain, ASC-1-like
subfamily. The ASCH domain, a small beta-barrel domain
found in all three kingdoms of life, resembles the
RNA-binding PUA domain and may also interact with RNA.
ASCH has been proposed to function as an RNA-binding
domain during coactivation, RNA-processing and the
regulation of prokaryotic translation. The domain has
been named after the ASC-1 protein, the activating
signal cointegrator 1 or thyroid hormone receptor
interactor protein 4 (TRIP4). ASC-1 is conserved in
many eukaryotes and has been suggested to participate
in a protein complex that interacts with RNA. It has
been shown that ASC-1 mediates the interaction between
various transciption factors and the basal
transcriptional machinery.
Length = 113
Score = 25.8 bits (57), Expect = 1.4
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 27 IISGALEMTQKKVEEIMTKLDDCYMLDIE 55
I + A T+ +EE+ Y LDIE
Sbjct: 36 IHASAKLPTKLDIEEVEEFYRILYKLDIE 64
>gnl|CDD|217347 pfam03063, Prismane, Prismane/CO dehydrogenase family. This family
includes both hybrid-cluster proteins and the beta chain
of carbon monoxide dehydrogenase. The hybrid-cluster
proteins contain two Fe/S centres - a [4Fe-4S] cubane
cluster, and a hybrid [4Fe-2S-2O] cluster. The
physiological role of this protein is as yet unknown,
although a role in nitrate/nitrite respiration has been
suggested. The prismane protein from Escherichia coli
was shown to contain hydroxylamine reductase activity
(NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is
rather low. Hydroxylamine reductase activity was also
found in CO-dehydrogenase in which the active site Ni
was replaced by Fe. The CO dehydrogenase contains a
Ni-3Fe-2S-3O centre.
Length = 505
Score = 25.5 bits (57), Expect = 2.1
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 5 FKTGIPMEATSNLVALKKDEVNI-ISG----ALEMTQKKVEE 41
F T P+ NL LKKD VNI +SG LEM ++ E
Sbjct: 151 FGTPEPVLTEVNLGVLKKDYVNILVSGHDPKDLEMLLEQTEG 192
>gnl|CDD|219444 pfam07516, SecA_SW, SecA Wing and Scaffold domain. SecA protein
binds to the plasma membrane where it interacts with
proOmpA to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This family is composed of two C-terminal alpha
helical subdomains: the wing and scaffold subdomains.
Length = 213
Score = 24.1 bits (53), Expect = 6.7
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 27 IISGALEMTQKKVEE 41
+++ A+E QKKVE
Sbjct: 6 MVTKAIENAQKKVEG 20
>gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type
nickel import system contains the type 2 periplasmic
binding fold. This family represents the periplasmic
substrate-binding domain of nickel transport system,
which functions in the import of nickel and in the
control of chemotactic response away from nickel. The
ATP-binding cassette (ABC) type nickel transport system
is comprised of five subunits NikABCDE: the two
pore-forming integral inner membrane proteins NikB and
NikC; the two inner membrane-associated proteins with
ATPase activity NikD and NikE; and the periplasmic
nickel binding NikA, the initial nickel receptor. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA. The DppA binds dipeptides and some
tripeptides and is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which precludes
any involvement in chemotaxis. Most of other periplasmic
binding proteins are comprised of only two globular
subdomains corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains 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. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 488
Score = 24.1 bits (53), Expect = 7.3
Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 9 IPMEATSNLVALKKDEVNIISGAL 32
IP +A + L+AL+ E+++I GA
Sbjct: 194 IP-DAQTRLLALQSGEIDLIYGAD 216
>gnl|CDD|224074 COG1152, CdhA, CO dehydrogenase/acetyl-CoA synthase alpha subunit
[Energy production and conversion].
Length = 772
Score = 24.0 bits (52), Expect = 7.4
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 13/54 (24%)
Query: 6 KTGIPMEATSNLVALKKDEVNIISGALEMTQKKVEEIMTKL----DDCYMLDIE 55
K GIP+ AT+ L G ++T + V+EI+ L +LD
Sbjct: 322 KLGIPVIATNEKGML---------GLPDVTDEDVDEIVESLVSGEPGVVLLDPL 366
>gnl|CDD|238896 cd01915, CODH, Carbon monoxide dehydrogenase (CODH) is found in
acetogenic and methanogenic organisms and is responsible
for the synthesis and breakdown of acetyl-CoA,
respectively. CODH has two types of metal clusters, a
cubane [Fe4-S4] center (B-cluster) similar to that of
hybrid cluster protein (HCP) and a Ni-Fe-S center
(C-cluster) where carbon monoxide oxidation occurs.
Bifunctional CODH forms a heterotetramer with acetyl-CoA
synthase (ACS) consisting of two CODH and two ACS
subunits while monofunctional CODH forms a homodimer.
Bifunctional CODH reduces carbon dioxide to carbon
monoxide and ACS then synthesizes acetyl-CoA from carbon
monoxide, CoA, and a methyl group donated by another
protein (CoFeSP), while monofunctional CODH oxidizes
carbon monoxide to carbon dioxide. CODH and ACS each
have a metal cluster referred to as the C- and
A-clusters, respectively.
Length = 613
Score = 23.8 bits (52), Expect = 8.9
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 5 FKTGIPMEATSNLVALKKDEVNII 28
F T P+ + +NL L D VNI
Sbjct: 225 FGTPKPVVSEANLGVLDPDYVNIA 248
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
0.316 0.132 0.345
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,443,871
Number of extensions: 263038
Number of successful extensions: 367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 20
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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 (21.6 bits)
S2: 53 (24.2 bits)