RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5246
(119 letters)
>gnl|CDD|238246 cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18 (L5e) is a
ribosomal protein found in the central protuberance (CP)
of the large subunit. L18 binds 5S rRNA and induces a
conformational change that stimulates the binding of L5
to 5S rRNA. Association of 5S rRNA with 23S rRNA depends
on the binding of L18 and L5 to 5S rRNA. L18/L5e is
generally described as L18 in prokaryotes and archaea,
and as L5e (or L5) in eukaryotes. In bacteria, the CP
proteins L5, L18, and L25 are required for the ribosome
to incorporate 5S rRNA into the large subunit, one of
the last steps in ribosome assembly. In archaea, both
L18 and L5 bind 5S rRNA; in eukaryotes, only the L18
homolog (L5e) binds 5S rRNA but a homolog to L5 is also
identified.
Length = 103
Score = 85.3 bits (212), Expect = 6e-23
Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 42 YHLDRLGREYWHTLYFTTTKKHITGQIVH-NNGNVVVSASTNEWALKKHLYNTNDICAYS 100
RLG + L + KHI QI+ + +VSAST E A+K L + N++ A
Sbjct: 1 RRRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAY 60
Query: 101 NLARVLAQRCLETGISEI 118
+ R+LA+R LE GI ++
Sbjct: 61 LVGRLLAKRALEKGIKKV 78
>gnl|CDD|214373 CHL00139, rpl18, ribosomal protein L18; Validated.
Length = 109
Score = 34.6 bits (80), Expect = 0.002
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 62 KHITGQIVHN-NGNVVVSASTNEWALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118
KHI QI+ + NG +V+ ST E +K L +T+ A + + LA++ L+ GI+++
Sbjct: 25 KHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKV 82
>gnl|CDD|235524 PRK05593, rplR, 50S ribosomal protein L18; Reviewed.
Length = 117
Score = 34.7 bits (81), Expect = 0.003
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 62 KHITGQIVH-NNGNVVVSASTNEWALKKHLYNTN-DICAYSNLARVLAQRCLETGISEI 118
+HI Q++ G + SAST E ++ L N + + +++A+R GI ++
Sbjct: 34 RHIYAQVIDDVKGKTLASASTLEKDVRAGLKGGNKEAAKK--VGKLIAERAKAKGIKQV 90
>gnl|CDD|223334 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 31.8 bits (73), Expect = 0.033
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 60 TKKHITGQIV-HNNGNVVVSASTNEWALKKHLY--NTNDICAYSNLARVLAQRCLETGIS 116
+ +HI QI+ G + SAST L+K+ + A + +++A+R L GI
Sbjct: 37 SNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIE 96
Query: 117 EI 118
E+
Sbjct: 97 EV 98
>gnl|CDD|216159 pfam00861, Ribosomal_L18p, Ribosomal L18p/L5e family. This family
includes ribosomal proteins from the large subunit. This
family includes L18 from bacteria and L5 from
eukaryotes. It has been shown that the amino terminal 93
amino acids of rat Rpl5 are necessary and sufficient to
bind 5S rRNA in vitro. Suggesting that the entire family
has a function in rRNA binding.
Length = 119
Score = 30.7 bits (70), Expect = 0.073
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 60 TKKHITGQIVH-NNGNVVVSASTNEWALKKH--LYNTNDICAYSNLARVLAQRCLETGI 115
+ KHI QI+ G +VSAST LKK+ N+ A + +LA+R L+ GI
Sbjct: 31 SNKHIYAQIIDDTKGGTLVSASTLSKELKKYGLKGGGNNTAAAYLVGLLLAKRALKKGI 89
>gnl|CDD|213499 TIGR00060, L18_bact, ribosomal protein L18, bacterial type. The
archaeal and eukaryotic type rpL18 is not detectable
under this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 114
Score = 30.6 bits (69), Expect = 0.080
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 10/95 (10%)
Query: 25 KNPRNLERLRIARKPQGYHLDRLGREYWHTLYFTTTKKHITGQIVHNNGNVV-VSASTNE 83
K+ R RI RK + R L + +HI Q++ ++ + V SAST E
Sbjct: 2 KSARIRRHKRIRRKLRETGEANRPR-----LVVFRSNRHIYAQVIDDSKSEVLASASTLE 56
Query: 84 WALKKHLYNTNDICAYSNLARVLAQRCLETGISEI 118
LK T + A + +++A+R E GI ++
Sbjct: 57 KKLK----YTGNKDAAKKVGKLVAERLKEKGIKDV 87
>gnl|CDD|237379 PRK13412, fkp, bifunctional
fucokinase/L-fucose-1-P-guanylyltransferase;
Provisional.
Length = 974
Score = 26.7 bits (59), Expect = 3.5
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 79 ASTNEWALKKHLYNTNDICAYSNLARVLAQR 109
W + L + ++I AY+NLAR+ AQR
Sbjct: 475 EGKEIWLRSEKL-SADEISAYANLARLYAQR 504
>gnl|CDD|224788 COG1876, VanY, D-alanyl-D-alanine carboxypeptidase [Cell envelope
biogenesis, outer membrane].
Length = 241
Score = 25.9 bits (57), Expect = 5.0
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 36 ARKPQGYHLDRLGREYWHTLYFTTTKKHITG 66
G L +Y L + K+ TG
Sbjct: 184 LPTAAGKWLQENAPKYGFILRYPKGKEASTG 214
>gnl|CDD|131404 TIGR02351, thiH, thiazole biosynthesis protein ThiH. Members this
protein family are the ThiH protein of thiamine
biosynthesis, a homolog of the BioB protein of biotin
biosynthesis. Genes for the this protein generally are
found in operons with other thiamin biosynthesis genes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 366
Score = 26.2 bits (58), Expect = 5.7
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 41 GYHLDRLGREYWHTLY 56
YHL L ++YW T
Sbjct: 237 AYHLRYLQKKYWKTEI 252
>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 = 5.8
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 5/27 (18%)
Query: 63 HITGQIVHNNGNVVVSASTNEWALKKH 89
+ G + N+G VV+ +WAL H
Sbjct: 123 RVRGALSSNDGEVVL-----QWALDGH 144
>gnl|CDD|188576 TIGR04061, AZL_007950_fam, AZL_007950 family protein. This set
of proteins includes PP_3335 from Pseudomonas putida, a
protein of unknown function, and AZL_007950, a member
of a putative biosynthetic cluster from Azospirillum
sp. B510.
Length = 164
Score = 25.9 bits (57), Expect = 5.8
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 43 HLDRLGREYWHTLY 56
LD YWHTL+
Sbjct: 13 RLDARLLPYWHTLF 26
>gnl|CDD|216125 pfam00797, Acetyltransf_2, N-acetyltransferase. Arylamine
N-acetyltransferase (NAT) is a cytosolic enzyme of
approximately 30kDa. It facilitates the transfer of an
acetyl group from Acetyl Coenzyme A on to a wide range
of arylamine, N-hydroxyarylamines and hydrazines.
Acetylation of these compounds generally results in
inactivation. NAT is found in many species from
Mycobacteria (M. tuberculosis, M. smegmatis etc) to man.
It was the first enzyme to be observed to have
polymorphic activity amongst human individuals. NAT is
responsible for the inactivation of Isoniazid (a drug
used to treat Tuberculosis) in humans. The NAT protein
has also been shown to be involved in the breakdown of
folic acid.
Length = 240
Score = 25.7 bits (57), Expect = 6.3
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 34 RIARKPQGYH-LDRLGREYWHTLY-FTTTKKHI 64
R+ + G L + R+ W LY FT + I
Sbjct: 131 RLVEEGGGIWVLQKDRRDGWVPLYRFTLEPRDI 163
>gnl|CDD|143608 cd07584, nitrilase_6, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as
1-13). Class 13 represents proteins that at the time
were difficult to place in a distinct similarity group;
this subgroup represents either a new class or one that
was included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 258
Score = 25.8 bits (57), Expect = 6.6
Identities = 6/13 (46%), Positives = 7/13 (53%)
Query: 41 GYHLDRLGREYWH 53
GY D LG + W
Sbjct: 45 GYRPDLLGPKLWE 57
>gnl|CDD|236425 PRK09240, thiH, thiamine biosynthesis protein ThiH; Reviewed.
Length = 371
Score = 25.5 bits (57), Expect = 7.8
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 41 GYHLDRLGREYWHTLY 56
HL L R+YW Y
Sbjct: 238 ALHLRYLQRKYWQAEY 253
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 25.7 bits (57), Expect = 8.1
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 61 KKHITGQIVHNNGNVVVSASTNEW 84
K ITG + +VV A E+
Sbjct: 100 KNMITGASQADVAVLVVDARDGEF 123
>gnl|CDD|220923 pfam10980, DUF2787, Protein of unknown function (DUF2787). This
bacterial family of proteins has no known function.
Length = 128
Score = 24.9 bits (55), Expect = 9.6
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 5/24 (20%)
Query: 40 QGYH-----LDRLGREYWHTLYFT 58
G+H L+R E W +Y T
Sbjct: 38 GGFHPVEIRLERENSEQWQIVYIT 61
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 0.131 0.401
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,906,836
Number of extensions: 489828
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 25
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
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 (24.2 bits)