RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780245|ref|YP_003064658.1| 50S ribosomal protein L18
[Candidatus Liberibacter asiaticus str. psy62]
(120 letters)
>gnl|CDD|177061 CHL00139, rpl18, ribosomal protein L18; Validated.
Length = 109
Score = 105 bits (264), Expect = 3e-24
Identities = 51/108 (47%), Positives = 72/108 (66%), Gaps = 1/108 (0%)
Query: 13 SRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIV 72
R+R+ +K + R RLSV RS+KHIY QIIDD+ G TLV+ S+L ++SSL + +
Sbjct: 3 ERVRKKIKGTAE-RPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCD 61
Query: 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
A+ VG L ++++K G+ V FDRG LY GRI ALA+A R+ G+ F
Sbjct: 62 ASKLVGQKLAKKSLKKGITKVVFDRGGKLYHGRIKALAEAAREAGLQF 109
>gnl|CDD|144453 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 the rat 60S ribosomal protein L5 are
necessary and sufficient to bind 5S rRNA in vitro.
Suggesting that the entire family has a function in rRNA
binding.
Length = 119
Score = 100 bits (252), Expect = 8e-23
Identities = 57/120 (47%), Positives = 76/120 (63%), Gaps = 3/120 (2%)
Query: 3 TKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLR 62
K++ R+ R+RR LK + R RL V RS+KHIY QIIDD+ G TLVSAS+L++ L+
Sbjct: 1 GKRRRRRRKRLRVRRKLKGTA-ERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELK 59
Query: 63 SS--LKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGVSF 120
G N AA VG LL +RA+K G+ V FDRG + Y GR+ ALA R+ G++F
Sbjct: 60 KYGLKGGGNNTAAAYLVGLLLAKRALKKGIAVVVFDRGGYTYHGRVFALAKGAREAGLNF 119
>gnl|CDD|30605 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 100 bits (250), Expect = 1e-22
Identities = 57/122 (46%), Positives = 76/122 (62%), Gaps = 3/122 (2%)
Query: 1 MATKKKVLARRISRIRRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEP 60
+ +++ +R RIR+ L S GR RL V RS++HIY QIIDD G TL SAS+L++
Sbjct: 5 VKFRRRRRGKRAYRIRKKLLGTS-GRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKE 63
Query: 61 LRS--SLKTGANIVAATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118
LR G N AA VG L+ ERA+ G++ V FDRG + Y GR+AALAD R+ G+
Sbjct: 64 LRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGGYKYHGRVAALADGAREAGL 123
Query: 119 SF 120
F
Sbjct: 124 EF 125
>gnl|CDD|88603 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 = 95.6 bits (238), Expect = 3e-21
Identities = 51/103 (49%), Positives = 69/103 (66%)
Query: 16 RRHLKSVSRGRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAAT 75
RR + ++ R RL V +S+KHIY QIIDDS TLVSAS+L ++ L +G N+ AA
Sbjct: 1 RRRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAY 60
Query: 76 AVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGGV 118
VG LL +RA++ G+K V FDRG + Y GR+ ALA R+GG+
Sbjct: 61 LVGRLLAKRALEKGIKKVVFDRGGYRYHGRVKALAKGAREGGL 103
>gnl|CDD|133279 cd01878, HflX, HflX subfamily. A distinct conserved domain with
a glycine-rich segment N-terminal of the GTPase domain
characterizes the HflX subfamily. The E. coli HflX has
been implicated in the control of the lambda cII
repressor proteolysis, but the actual biological
functions of these GTPases remain unclear. HflX is
widespread, but not universally represented in all
three superkingdoms.
Length = 204
Score = 25.9 bits (58), Expect = 2.9
Identities = 7/22 (31%), Positives = 16/22 (72%)
Query: 5 KKVLARRISRIRRHLKSVSRGR 26
++++ RI+++RR L+ V + R
Sbjct: 8 RRLIRERIAKLRRELEKVKKQR 29
>gnl|CDD|143458 cd07140, ALDH_F1L_FTFDH, 10-formyltetrahydrofolate dehydrogenase,
ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase
(FTHFDH, EC=1.5.1.6), also known as aldehyde
dehydrogenase family 1 member L1 (ALDH1L1) in humans, is
a multi-domain homotetramer with an N-terminal formyl
transferase domain and a C-terminal ALDH domain. FTHFDH
catalyzes an NADP+-dependent dehydrogenase reaction
resulting in the conversion of 10-formyltetrahydrofolate
to tetrahydrofolate and CO2. The ALDH domain is also
capable of the oxidation of short chain aldehydes to
their corresponding acids.
Length = 486
Score = 25.5 bits (56), Expect = 3.2
Identities = 9/26 (34%), Positives = 22/26 (84%), Gaps = 1/26 (3%)
Query: 82 VERAVKVGVKSVYFDRGKH-LYCGRI 106
+++AV++G+ SV+F++G++ + GR+
Sbjct: 272 MDKAVRMGMSSVFFNKGENCIAAGRL 297
>gnl|CDD|113840 pfam05085, DUF685, Protein of unknown function (DUF685). This
family consists of several uncharacterized proteins from
Borrelia burgdorferi (Lyme disease spirochete). There is
some evidence to suggest that the proteins may be outer
surface proteins.
Length = 265
Score = 25.2 bits (55), Expect = 4.5
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 36 KHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAAT 75
+ IY +IID I + + S+L ++S L I +AT
Sbjct: 81 EKIYTKIIDKLINNDSTNLSNLFSKIKSRLTDS--ISSAT 118
>gnl|CDD|37663 KOG2452, KOG2452, KOG2452, Formyltetrahydrofolate dehydrogenase
[Nucleotide transport and metabolism].
Length = 881
Score = 25.0 bits (54), Expect = 5.4
Identities = 15/64 (23%), Positives = 36/64 (56%), Gaps = 8/64 (12%)
Query: 47 IGHTLVSASSLNEPLRSSLKTGAN---IVAATAVGNLLVERAVKVGVKSVYFDRGKH-LY 102
+G ++ + +++ + SL+ G I+ A + +AV++G+ SV+F +G++ +
Sbjct: 633 VGKHIMKSCAISNVKKVSLELGGESPFIIFADCD----LNKAVQMGMSSVFFSKGENCIA 688
Query: 103 CGRI 106
GR+
Sbjct: 689 AGRL 692
>gnl|CDD|38742 KOG3534, KOG3534, KOG3534, p53 inducible protein PIR121 [General
function prediction only].
Length = 1253
Score = 25.0 bits (54), Expect = 5.9
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 25 GRLRLSVCRSSKHIYGQIIDDSIGHTLVSASSLNEPLRSSLKTGANIVAA 74
GR+ + + + D I TL EPLR ++K +++A+
Sbjct: 461 GRMESVFNNAIRKTVYAELQDFIQVTL------REPLRKAVKKKKDLLAS 504
>gnl|CDD|153090 cd08025, RNR_PFL_like_DUF711, Uncharacterized proteins with
similarity to Ribonucleotide reductase and Pyruvate
formate lyase. This subfamily contains Streptococcus
pneumoniae Sp0239 and similar uncharacterized proteins.
Sp0239 is structurally similar to ribonucleotide
reductase (RNR) and pyruvate formate lyase (PFL), which
are believed to have diverged from a common ancestor.
RNR and PFL possess a ten-stranded alpha-beta barrel
domain that hosts the active site, and are radical
enzymes. RNRs are found in all organisms and provide the
only mechanism by which nucleotides are converted to
deoxynucleotides. PFL is an essential enzyme in
anaerobic bacteria that catalyzes the conversion of
pyruvate and CoA to acteylCoA and formate.
Length = 400
Score = 24.6 bits (54), Expect = 7.5
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 3/18 (16%)
Query: 104 GRIAALA---DAVRKGGV 118
G AALA DAV+KGG
Sbjct: 296 GTTAALALLNDAVKKGGA 313
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 24.3 bits (53), Expect = 8.9
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 8/45 (17%)
Query: 73 AATAVGNLLVERAVKVGVKSVYFDRGKHLYCGRIAALADAVRKGG 117
AA +G+LLV+ A G V G A VR G
Sbjct: 151 AAGGLGSLLVQLAKAAGATVVGAAGG--------PAKTALVRALG 187
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.134 0.371
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,270,015
Number of extensions: 55578
Number of successful extensions: 169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 21
Length of query: 120
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,491,799
Effective search space: 170688362
Effective search space used: 170688362
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 (22.0 bits)
S2: 51 (23.7 bits)