RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18
[Candidatus Liberibacter asiaticus str. psy62]
(83 letters)
>gnl|CDD|30587 COG0238, RpsR, Ribosomal protein S18 [Translation, ribosomal
structure and biogenesis].
Length = 75
Score = 77.6 bits (191), Expect = 8e-16
Identities = 38/68 (55%), Positives = 47/68 (69%)
Query: 11 RRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIK 70
R RRK C + +G IDYKD+ LL RF+S+RGKI+P RI+ S K QR LA+AIK
Sbjct: 8 RAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFISERGKILPRRITGTSAKHQRRLARAIK 67
Query: 71 RARYLGLI 78
RARYL L+
Sbjct: 68 RARYLALL 75
>gnl|CDD|144612 pfam01084, Ribosomal_S18, Ribosomal protein S18.
Length = 54
Score = 75.6 bits (187), Expect = 3e-15
Identities = 31/53 (58%), Positives = 40/53 (75%)
Query: 26 KGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLI 78
IDYKD+ LL RF+S+RGKI+P RI+ + K+QR+LAKAIKRAR L L+
Sbjct: 2 DKIEYIDYKDVELLRRFISERGKILPRRITGLCAKQQRKLAKAIKRARILALL 54
>gnl|CDD|177016 CHL00077, rps18, ribosomal protein S18.
Length = 86
Score = 65.4 bits (160), Expect = 3e-12
Identities = 31/75 (41%), Positives = 52/75 (69%), Gaps = 2/75 (2%)
Query: 8 PLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAK 67
P + S RR+ P+ + RIDYK++ LL+RF+S++GKI+ R++ ++ K+QR + K
Sbjct: 7 PFRKSKRSFRRRLPPI--QSGDRIDYKNMSLLSRFISEQGKILSRRVTRLTLKQQRLITK 64
Query: 68 AIKRARYLGLIAYVN 82
AIK+AR L L+ ++N
Sbjct: 65 AIKQARILSLLPFLN 79
>gnl|CDD|38372 KOG3162, KOG3162, KOG3162, Mitochondrial/chloroplast ribosomal
protein S18 [Translation, ribosomal structure and
biogenesis].
Length = 159
Score = 49.6 bits (118), Expect = 2e-07
Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 17 RRKSCPLSGKGAP-RIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYL 75
C L KG ++ YK++ LL++F+S+ G I+P +I+ + K QR++ +AIKRAR
Sbjct: 65 SEPQCILCTKGVDIKLSYKNVLLLSQFVSEDGGILPRKITGLCAKNQRKIERAIKRARAA 124
Query: 76 GLIAYVNL 83
GL+ N
Sbjct: 125 GLMPVTNT 132
>gnl|CDD|39224 KOG4021, KOG4021, KOG4021, Mitochondrial ribosomal protein S18b
[Translation, ribosomal structure and biogenesis].
Length = 239
Score = 30.0 bits (67), Expect = 0.16
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 10 LRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLS-QRGKIVPSRISSVSHKKQRELAKA 68
+R+N CP+ DY++ LL +FL+ G+ + + + K+ L A
Sbjct: 100 IRKNGRFLGNPCPICRDEYLYFDYRNPGLLEQFLADHTGQPIDYLKTGLCRKQHTRLRAA 159
Query: 69 IKRARYLGLIAY 80
+++AR G + Y
Sbjct: 160 LQKARDHGTLTY 171
>gnl|CDD|29457 cd02761, MopB_FmdB-FwdB, The MopB_FmdB-FwdB CD contains the
molybdenum/tungsten formylmethanofuran dehydrogenases,
subunit B (FmdB/FwdB), and other related proteins.
Formylmethanofuran dehydrogenase catalyzes the first
step in methane formation from CO2 in methanogenic
archaea and some eubacteria. Members of this CD belong
to the molybdopterin_binding (MopB) superfamily of
proteins..
Length = 415
Score = 26.0 bits (57), Expect = 2.1
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 15 SHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARY 74
S K + + P DY+ + L R L + +VP ++ + + ELA+ +K A++
Sbjct: 179 SDTAKLADIHLQIDPGSDYELLAAL-RALLRGAGLVPDEVAGIPAETILELAERLKNAKF 237
>gnl|CDD|143377 cd07872, STKc_PCTAIRE2, Catalytic domain of the Serine/Threonine
Kinase, PCTAIRE-2 kinase. Serine/Threonine Kinases
(STKs), PCTAIRE-2 subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The PCTAIRE-2 subfamily is part of a larger superfamily
that includes the catalytic domains of other protein
STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. PCTAIRE-2 shares sequence
similarity with Cyclin-Dependent Kinases (CDKs), which
belong to a large family of STKs that are regulated by
their cognate cyclins. Together, CDKs and cyclins are
involved in the control of cell-cycle progression,
transcription, and neuronal function. PCTAIRE-2 is
specifically expressed in neurons in the central nervous
system, mainly in terminally differentiated neurons. It
associates with Trap (Tudor repeat associator with
PCTAIRE-2) and could play a role in regulating
mitochondrial function in neurons.
Length = 309
Score = 26.1 bits (57), Expect = 2.3
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 28 APRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAI 69
APR+D + I LL +FL K S ++ H R L I
Sbjct: 255 APRLDTEGIELLTKFLQYESKKRISAEEAMKHAYFRSLGTRI 296
>gnl|CDD|145922 pfam03031, NIF, NLI interacting factor-like phosphatase. This
family contains a number of NLI interacting factor
isoforms and also an N-terminal regions of RNA
polymerase II CTC phosphatase and FCP1 serine
phosphatase. This region has been identified as the
minimal phosphatase domain.
Length = 151
Score = 25.3 bits (56), Expect = 3.9
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 11 RRNVSHR--RKSCPLSGKGAPRIDYKDIRLLNRFLSQ 45
++ HR R+SC L+G KD+ LL R LS+
Sbjct: 68 KKYFKHRLYRESCTLTGGNYYV---KDLSLLGRDLSR 101
>gnl|CDD|146045 pfam03219, TLC, TLC ATP/ADP transporter.
Length = 491
Score = 25.3 bits (56), Expect = 3.9
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 37 RLLNRFLSQRGKIVPSRISSVSHKKQR----ELAKAIKRARYLGLIA 79
R +N+ + ++ S KK + E K + +RYL LIA
Sbjct: 241 RWINKNVLTDPRLYAS-AKKKKKKKPKMSLKESFKYLLSSRYLLLIA 286
>gnl|CDD|33015 COG3202, COG3202, ATP/ADP translocase [Energy production and
conversion].
Length = 509
Score = 24.8 bits (54), Expect = 5.2
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 37 RLLNRFLSQRGKIVPSRISSVSHKKQR----ELAKAIKRARYLGLIA 79
R +NR + KK + E K I R++YLG IA
Sbjct: 242 RYINRNVLTDPLFYLRAKKKKKKKKLKLGLIESFKMILRSKYLGAIA 288
>gnl|CDD|132871 cd07044, CofD_YvcK, Family of CofD-like proteins and proteins
related to YvcK. CofD is a 2-phospho-L-lactate
transferase that catalyzes the last step in the
biosynthesis of coenzyme F(420)-0 (F(420) without
polyglutamate) by transferring the lactyl phosphate
moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to
7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0).
F420 is a hydride carrier, important for energy
metabolism of methanogenic archaea, as well as for the
biosynthesis of other natural products, like
tetracycline in Streptomyces. F420 and some of its
precursors are also utilized as cofactors for enzymes,
like DNA photolyase in Mycobacterium tuberculosis. YvcK
from Bacillus subtilis is a member of a family of mostly
uncharacterized proteins and has been proposed to play a
role in carbon metabolism, since its function is
essential for growth on intermediates of the Krebs cycle
and pentose phosphate pathway. Both families appear to
have a conserved phosphate binding site, but have
different substrate binding residues conserved within
each family.
Length = 309
Score = 24.5 bits (53), Expect = 7.5
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 32 DYKDIRLLNRFLSQRGKIVPSRISSVS 58
I L++ + +G I+PS VS
Sbjct: 101 FTDAIVELSKVFNIKGNILPSSDDPVS 127
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
0.323 0.136 0.386
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 986,251
Number of extensions: 42358
Number of successful extensions: 132
Number of sequences better than 10.0: 1
Number of HSP's gapped: 132
Number of HSP's successfully gapped: 18
Length of query: 83
Length of database: 6,263,737
Length adjustment: 53
Effective length of query: 30
Effective length of database: 5,118,460
Effective search space: 153553800
Effective search space used: 153553800
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 (23.5 bits)