RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12608
(65 letters)
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 50.7 bits (122), Expect = 2e-10
Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 15/62 (24%)
Query: 6 AGASAGVVVDVVLYPLDTIKTRLQSQYGF---------------WRSGGFKAIYKGLGPA 50
AG AG + V YPLD +KTRLQS ++ G + +YKGL P
Sbjct: 11 AGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGIRGLYKGLLPN 70
Query: 51 AI 52
+
Sbjct: 71 LL 72
>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
Length = 259
Score = 40.3 bits (94), Expect = 1e-05
Identities = 21/48 (43%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 7 GASAGVVVDVVLYPLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAAISS 54
GA +GV+VD VLYP+D+IKT +Q++ F S K +Y G+ P + +
Sbjct: 10 GALSGVIVDAVLYPIDSIKTNIQAKKSFSFS-DIKKLYSGILPTLVGT 56
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 30.9 bits (70), Expect = 0.024
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 16/59 (27%)
Query: 6 AGASAGVVVDVVLYPLDTIKTRLQSQYG----------------FWRSGGFKAIYKGLG 48
+G AG +++YPLD +TRL S G + GF ++Y+G G
Sbjct: 119 SGGLAGASSLLIVYPLDFARTRLASDIGKGGDREFTGLFDCLMKISKQTGFLSLYQGFG 177
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 29.2 bits (66), Expect = 0.085
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 17 VLYPLDTIKTRLQSQYGFWRSGGFKAI 43
VLYP D+ + RL+ +Y F S G + I
Sbjct: 227 VLYPGDSKELRLKQEY-FLGSAGVQDI 252
>gnl|CDD|222850 PHA02126, PHA02126, hypothetical protein.
Length = 153
Score = 28.8 bits (64), Expect = 0.14
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 12 VVVDVVLYPLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAAISSPIQEY 59
V++ PL I+ L S+ GF +S F A Y + + + + +
Sbjct: 98 VIIFNTQTPLTDIRIALYSKTGFSKSTEFTAYYVRYKESTMRNLVNRF 145
>gnl|CDD|222340 pfam13718, GNAT_acetyltr_2, GNAT acetyltransferase 2. This domain
has N-acetyltransferase activity. It has a GCN5-related
N-acetyltransferase (GNAT) fold.
Length = 169
Score = 27.4 bits (62), Expect = 0.34
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 34 FWRSGGFKAIYKGLGPAAISSPIQEYTVIVV 64
FW+ GF +Y G A S E++ I++
Sbjct: 138 FWQKNGFVPVYLGQTRNASSG---EHSAIML 165
>gnl|CDD|237172 PRK12683, PRK12683, transcriptional regulator CysB-like protein;
Reviewed.
Length = 309
Score = 25.0 bits (55), Expect = 3.1
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 4 DDAGASAGVVVDVVLYPLDT--IKT 26
D A A AG+V D+VL LD IKT
Sbjct: 208 DQAFAEAGLVPDIVLTALDADVIKT 232
>gnl|CDD|173861 cd08496, PBP2_NikA_DppA_OppA_like_9, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA can bind 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 = 454
Score = 24.6 bits (54), Expect = 3.6
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 12 VVVDVVLYPLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAA 51
+++++ P D K R Y R A+ GLG A
Sbjct: 238 LLLNITGAPFDDPKVRQAINYAIDRKAFVDALLFGLGEPA 277
>gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of
LysR-type transcriptional regulators CysB-like contains
type 2 periplasmic binding fold. CysB is a
transcriptional activator of genes involved in sulfate
and thiosulfate transport, sulfate reduction, and
cysteine synthesis. In Escherichia coli, the regulation
of transcription in response to sulfur source is
attributed to two transcriptional regulators, CysB and
Cbl. CysB, in association with Cbl, downregulates the
expression of ssuEADCB operon which is required for the
utilization of sulfur from aliphatic sulfonates, in the
presence of cysteine. Also, Cbl and CysB together
directly function as transcriptional activators of
tauABCD genes, which are required for utilization of
taurine as sulfur source for growth. Like many other
members of the LTTR family, CysB is composed of two
functional domains joined by a linker helix involved in
oligomerization: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal substrate-binding domain,
which is structurally homologous to the type 2
periplasmic binding proteins. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcriptional repressor undergoes a
conformational change upon substrate binding which in
turn changes the DNA binding affinity of the repressor.
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. Besides transport proteins, the PBP2
superfamily includes the substrate-binding domains from
ionotropic glutamate receptors, LysR-like
transcriptional regulators, and unorthodox sensor
proteins involved in signal transduction.
Length = 198
Score = 23.7 bits (52), Expect = 9.1
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 4 DDAGASAGVVVDVVLYPLDT--IKT 26
D A A AG+ ++VL LD IKT
Sbjct: 115 DRAFARAGLEPNIVLTALDADVIKT 139
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 0.137 0.402
Gapped
Lambda K H
0.267 0.0852 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,327,594
Number of extensions: 239360
Number of successful extensions: 187
Number of sequences better than 10.0: 1
Number of HSP's gapped: 186
Number of HSP's successfully gapped: 10
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
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)