RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18
[Candidatus Liberibacter asiaticus str. psy62]
(83 letters)
>gnl|CDD|178997 PRK00391, rpsR, 30S ribosomal protein S18; Reviewed.
Length = 79
Score = 94.9 bits (237), Expect = 4e-21
Identities = 37/72 (51%), Positives = 49/72 (68%)
Query: 11 RRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIK 70
RR R+K C + IDYKD+ LL +F+S+RGKI+P RI+ S K QR+LA AIK
Sbjct: 7 RRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQLATAIK 66
Query: 71 RARYLGLIAYVN 82
RAR+L L+ YV+
Sbjct: 67 RARFLALLPYVD 78
>gnl|CDD|161738 TIGR00165, S18, ribosomal protein S18. This ribosomal small
subunit protein is found in all eubacteria so far, as
well as in chloroplasts. YER050C from Saccharomyces
cerevisiae and a related protein from Caenorhabditis
elegans appear to be homologous and may represent
mitochondrial forms. The trusted cutoff is set high
enough that these two candidate S18 proteins are not
categorized automatically.
Length = 70
Score = 76.3 bits (188), Expect = 2e-15
Identities = 37/66 (56%), Positives = 48/66 (72%)
Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76
R+K C + +G IDYKD+ LL +F+S+RGKI+P RI+ S K QR LA+AIKRARYL
Sbjct: 4 RKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILPRRITGTSAKYQRRLARAIKRARYLA 63
Query: 77 LIAYVN 82
L+ YV
Sbjct: 64 LLPYVK 69
>gnl|CDD|184031 PRK13401, PRK13401, 30S ribosomal protein S18; Provisional.
Length = 82
Score = 66.3 bits (162), Expect = 1e-12
Identities = 27/77 (35%), Positives = 40/77 (51%)
Query: 6 PTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQREL 65
R + K L G +DYKD LL F+S RGKI R++ ++ ++QR++
Sbjct: 1 MAAKPARKGPTKAKKNLLDSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLTVQQQRQV 60
Query: 66 AKAIKRARYLGLIAYVN 82
A AIK AR + L+ Y
Sbjct: 61 ATAIKNAREMALLPYPG 77
>gnl|CDD|184030 PRK13400, PRK13400, 30S ribosomal protein S18; Provisional.
Length = 147
Score = 58.5 bits (141), Expect = 4e-10
Identities = 30/65 (46%), Positives = 40/65 (61%)
Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76
+RK C + RIDYKD L R++S RGKI P R + + QR LA AIKRAR++
Sbjct: 21 KRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTCARHQRALANAIKRARFIA 80
Query: 77 LIAYV 81
L+ +V
Sbjct: 81 LMPFV 85
>gnl|CDD|162733 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
type 2. Isopentenyl-diphosphate delta-isomerase (IPP
isomerase) interconverts isopentenyl diphosphate and
dimethylallyl diphosphate. This model represents the
type 2 enzyme. FMN, NADPH, and Mg2+ are required by
this form, which lacks homology to the type 1 enzyme
(TIGR02150). IPP is precursor to many compounds,
including enzyme cofactors, sterols, and isoprenoids.
Length = 333
Score = 28.4 bits (64), Expect = 0.42
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVS--HKK----QRELAKAIKRARYLGL 77
P I+ DI L FL +R K P I++++ ++ R LA+A AR LG+
Sbjct: 34 PEINLDDIDLTTEFLGKRLK-APFYINAMTGGSEEAGKINRNLARA---ARELGI 84
>gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA;
Provisional.
Length = 362
Score = 26.8 bits (59), Expect = 1.4
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 1 MAEVAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHK 60
E+ P L + +R + P K R++ D RLL RFL++ I P + S+V ++
Sbjct: 282 EQELFACPDLAVRIRYRSRPIPCRVK---RLE--DGRLLVRFLAEASAIAPGQ-SAVFYE 335
Query: 61 KQRELAKA-IKRARYLGLIAYVN 82
+R L A I R +GL+ N
Sbjct: 336 GRRVLGGAFIASQRGIGLVIEQN 358
>gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 25.3 bits (56), Expect = 3.6
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 34 KDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRA 72
D + FL ++ I SS Q E KA+ A
Sbjct: 482 DDALEIKEFLQEQFGIKAVTESSAKLINQPE-VKALIEA 519
>gnl|CDD|162863 TIGR02456, treS_nterm, trehalose synthase. Trehalose synthase
interconverts maltose and alpha, alpha-trehalose by
transglucosylation. This is one of at least three
mechanisms for biosynthesis of trehalose, an important
and widespread compatible solute. However, it is not
driven by phosphate activation of sugars and its
physiological role may tend toward trehalose
degradation. This view is accentuated by numerous
examples of fusion to a probable maltokinase domain. The
sequence region described by this model is found both as
the whole of a trehalose synthase and as the N-terminal
region of a larger fusion protein that includes
trehalose synthase activity. Several of these fused
trehalose synthases have a domain homologous to proteins
with maltokinase activity from Actinoplanes
missouriensis and Streptomyces coelicolor
(PubMed:15378530).
Length = 539
Score = 25.1 bits (55), Expect = 3.7
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 2 AEVAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFL 43
A AP P +R N+ RR+ PL D + I LL L
Sbjct: 324 AAYAPDPRMRINLGIRRRLAPLLDN-----DRRRIELLTALL 360
>gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional.
Length = 343
Score = 25.1 bits (55), Expect = 4.1
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 49 IVPSRISSVSHKKQRELAKAIKRA 72
IVP+ IS+ + +E AKAI RA
Sbjct: 259 IVPADISAEERSRVQETAKAIYRA 282
>gnl|CDD|180527 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 24.8 bits (54), Expect = 5.0
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 31 IDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR 71
+ YK +L+R L +R + R+ SV+ K + KAI+
Sbjct: 145 VGYKISPILSRKLQRRSGVSAGRVQSVALKLVVDREKAIEA 185
>gnl|CDD|132173 TIGR03129, one_C_dehyd_B, formylmethanofuran dehydrogenase subunit
B. Members of this largely archaeal protein family are
subunit B of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit C. Note
that this model does not distinguish tungsten (FwdB)
from molybdenum-containing (FmdB) forms of this enzyme.
Length = 421
Score = 24.6 bits (54), Expect = 6.6
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 34 KDIRLLNRFLSQ-RGK-IVPSRISSVSHKKQRELAKAIKRARY 74
D L++ + RGK P ++ + +K ELA+ +K A++
Sbjct: 201 SDYELISALRAVLRGKEPQPEEVAGIPKEKILELAEILKNAKF 243
>gnl|CDD|132362 TIGR03319, YmdA_YtgF, conserved hypothetical protein YmdA/YtgF.
Length = 514
Score = 24.1 bits (53), Expect = 9.3
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 42 FLSQRGKIVPSRISSVSHKKQRELAKAIKRA 72
L Q G+I P+RI + K +E+ AI+
Sbjct: 266 KLIQDGRIHPARIEEMVEKATKEVDNAIREE 296
>gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 715
Score = 24.1 bits (53), Expect = 9.8
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 6/27 (22%)
Query: 60 KKQRELAKAIKRARYLGL------IAY 80
KK + AK +K+A LG IAY
Sbjct: 304 KKLAKDAKPVKQAAVLGAGIMGGGIAY 330
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.323 0.136 0.386
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,379,710
Number of extensions: 73446
Number of successful extensions: 172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 172
Number of HSP's successfully gapped: 27
Length of query: 83
Length of database: 5,994,473
Length adjustment: 52
Effective length of query: 31
Effective length of database: 4,870,857
Effective search space: 150996567
Effective search space used: 150996567
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: 50 (23.0 bits)