RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037036
(87 letters)
>gnl|CDD|176997 CHL00057, rpl14, ribosomal protein L14.
Length = 122
Score = 73.8 bits (182), Expect = 1e-18
Identities = 37/71 (52%), Positives = 50/71 (70%), Gaps = 5/71 (7%)
Query: 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTA 60
ASNR+YAHI +V + V+K+A+P MPL+ S+V +IV TC L+RDNG+II +DD+
Sbjct: 27 ASNRKYAHI-GDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRDNGMIIRFDDNAAV 85
Query: 61 VIHQKEKFEGN 71
VI Q EGN
Sbjct: 86 VIDQ----EGN 92
>gnl|CDD|201105 pfam00238, Ribosomal_L14, Ribosomal protein L14p/L23e.
Length = 122
Score = 52.5 bits (127), Expect = 2e-10
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 2 SNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAV 61
S ++YA + ++ VV +KKAIPK ++ DV +IV T +RR +G I +DD+ +
Sbjct: 28 SRKKYAKV-GDIIVVSVKKAIPKGKVKKGDVVKAVIVRTKKEVRRKDGSYIRFDDNAVVL 86
Query: 62 IHQKEKFEGNSSF 74
I+ K + +G F
Sbjct: 87 INNKGEPKGTRIF 99
>gnl|CDD|130139 TIGR01067, rplN_bact, ribosomal protein L14, bacterial/organelle.
This model distinguishes bacterial and most organellar
examples of ribosomal protein L14 from all archaeal and
eukaryotic forms [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 122
Score = 50.0 bits (120), Expect = 2e-09
Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTA 60
S RRYA + +V VVV+K AIP ++ DV +IV T +RR +G I +DD+
Sbjct: 27 GSRRRYATV-GDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRKDGSYIRFDDNACV 85
Query: 61 VIHQK 65
+I++
Sbjct: 86 LINKN 90
>gnl|CDD|180117 PRK05483, rplN, 50S ribosomal protein L14; Validated.
Length = 122
Score = 46.3 bits (111), Expect = 5e-08
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 2 SNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDD 56
S RRYA I +V VV +K+AIP+ ++ DV ++V T +RR +G I +DD
Sbjct: 28 SKRRYASI-GDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRPDGSYIRFDD 81
>gnl|CDD|223171 COG0093, RplN, Ribosomal protein L14 [Translation, ribosomal
structure and biogenesis].
Length = 122
Score = 45.3 bits (108), Expect = 1e-07
Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTA 60
S RRYA + ++ VV +KKAIP+ ++ DV ++V T +RR +G I +DD A
Sbjct: 27 GSRRRYAGV-GDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRPDGSYIKFDD-NAA 84
Query: 61 VIHQKEK 67
VI +
Sbjct: 85 VIINPDG 91
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, 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 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 = 468
Score = 26.9 bits (60), Expect = 1.4
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 63 HQKEKFEGNSSFWCGRPEIDKVEF 86
+E N +W G+P++ ++EF
Sbjct: 172 QGTYLYEANEDYWGGKPKVKRLEF 195
>gnl|CDD|173879 cd08514, PBP2_AppA_like, The substrate-binding component of the
oligopeptide-binding protein, AppA, from Bacillus
subtilis contains the type 2 periplasmic-binding fold.
This family represents the substrate-binding domain of
the oligopeptide-binding protein, AppA, from Bacillus
subtilis and its closest homologs from other bacteria
and archaea. Bacillus subtilis has three ABC-type
peptide transport systems, a dipeptide-binding protein
(DppA) and two oligopeptide-binding proteins (OppA and
AppA) with overlapping specificity. The dipeptide (DppA)
and oligopeptide (OppA) binding proteins differ in
several ways. The DppA binds dipeptides and some
tripeptides and also 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 = 483
Score = 26.0 bits (58), Expect = 2.8
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 64 QKEKFEGNSSFWCGRPEIDKVEFY 87
Q E N ++ GRP IDK+ F
Sbjct: 174 QYIVLEANPDYFLGRPYIDKIVFR 197
>gnl|CDD|173878 cd08513, PBP2_thermophilic_Hb8_like, The substrate-binding
component of ABC-type thermophilic oligopeptide-binding
protein Hb8-like import systems, contains the type 2
periplasmic binding fold. This family includes the
substrate-binding domain of an ABC-type
oligopeptide-binding protein Hb8 from Thermus
thermophilius and its closest homologs from other
bacteria. The structural topology of this
substrate-binding domain is similar to those of DppA
from Escherichia coli and OppA from Salmonella
typhimurium, and thus belongs to the type 2 periplasmic
binding fold protein (PBP2) superfamily. 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.
The type 2 periplasmic binding proteins are soluble
ligand-binding components of ABC or tripartite
ATP-independent transporters and chemotaxis systems.
Members of the PBP2 superfamily function in uptake of a
variety of metabolites in bacteria such as amino acids,
carbohydrate, ions, and polyamines. Ligands are then
transported across the cytoplasmic membrane energized by
ATP hydrolysis or electrochemical ion gradient. 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 = 482
Score = 24.9 bits (55), Expect = 6.4
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 67 KFEGNSSFWCGRPEIDKVEFY 87
+ N ++W G+P ID+V
Sbjct: 176 ELVRNPNYWGGKPYIDRVVLK 196
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
0.325 0.138 0.422
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,406,411
Number of extensions: 343989
Number of successful extensions: 368
Number of sequences better than 10.0: 1
Number of HSP's gapped: 365
Number of HSP's successfully gapped: 12
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)