RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780275|ref|YP_003064688.1| SsrA-binding protein
[Candidatus Liberibacter asiaticus str. psy62]
(159 letters)
>gnl|CDD|180069 PRK05422, smpB, SsrA-binding protein; Validated.
Length = 148
Score = 236 bits (604), Expect = 3e-63
Identities = 84/148 (56%), Positives = 107/148 (72%), Gaps = 1/148 (0%)
Query: 9 PPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNS 68
P KV++ N+KAR++Y I +FEAGIVLTGTEVKSLR K N+ DSY +N E WL N+
Sbjct: 1 PGSKVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNA 60
Query: 69 YIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLA 128
+I Y Q N FNH PRR RKLLL K+EI +L V R G TLVP+K+YF G AK+++
Sbjct: 61 HISPYEQGNHFNHDPRRTRKLLLHKKEIDKLIGKVERKGYTLVPLKLYFK-NGRAKVEIG 119
Query: 129 LAQGKKNYDKRETEKKRDWDRQKHRILR 156
LA+GKK +DKRET K+RDW R+K R ++
Sbjct: 120 LAKGKKLHDKRETIKERDWKREKARAMK 147
>gnl|CDD|129194 TIGR00086, smpB, SsrA-binding protein. This model describes the
SsrA-binding protein, also called tmRNA binding protein,
small protein B, and SmpB. The small, stable RNA SsrA
(also called tmRNA or 10Sa RNA) recognizes stalled
ribosomes such as occur during translation from message
that lacks a stop codon. It becomes charged with Ala
like a tRNA, then acts as mRNA to resume translation
started with the defective mRNA. The short C-terminal
peptide tag added by the SsrA system marks the
abortively translated protein for degradation. SmpB
binds SsrA after its aminoacylation but before the
coupling of the Ala to the nascent polypeptide chain and
is an essential part of the SsrA peptide tagging system.
SmpB has been associated with the survival of bacterial
pathogens in conditions of stress. It is universal in
the first 100 sequenced bacterial genomes.
Length = 144
Score = 190 bits (485), Expect = 1e-49
Identities = 73/144 (50%), Positives = 103/144 (71%)
Query: 13 VVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPE 72
+++ N+KA ++Y I+ ++EAGIVL G+EVKS+R KV++ DSY + E+WL N +I
Sbjct: 1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAP 60
Query: 73 YLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQG 132
Y N FNH PRR RKLLL K+EI +L V+ G+TLVP+K+YF KG K+++ALA+G
Sbjct: 61 YKFGNYFNHDPRRPRKLLLHKKEIDKLQGKVKEKGLTLVPLKLYFKNKGKVKVEIALAKG 120
Query: 133 KKNYDKRETEKKRDWDRQKHRILR 156
KK +DKRE+ KKRD R+ R L+
Sbjct: 121 KKLHDKRESIKKRDAKRELKRALK 144
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 33.1 bits (76), Expect = 0.033
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 67 NSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFN 118
+S+ +LQ FNHYP R++L + E L+ D L P+K +
Sbjct: 223 SSFGKPHLQ-AYFNHYPNEVREILDKQSETGILH----HDIYDLKPLKSFVY 269
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 29.3 bits (65), Expect = 0.44
Identities = 27/92 (29%), Positives = 38/92 (41%), Gaps = 19/92 (20%)
Query: 74 LQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDL------ 127
L NR +K LL ++ I R+ A+ +FN KID+
Sbjct: 410 LTDNRLYLMLNPKQKPLLQQKHIERISEALSE----------HFNRTITVKIDISNHQTE 459
Query: 128 ---ALAQGKKNYDKRETEKKRDWDRQKHRILR 156
ALAQ K + E EK+ DRQ RI++
Sbjct: 460 TPAALAQKKAQDRQTEAEKRMMNDRQVQRIMQ 491
>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
Length = 2435
Score = 28.7 bits (63), Expect = 0.81
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 16 DNRKARYNYHIVRSFEAGIVLTGTEVKSL--RVSKVNISDSYATFENDEIWLTNSYIPEY 73
D+ KA+Y H+ +F + E K R + +D+ EN+E W T S P
Sbjct: 1724 DSDKAKYWGHMPETFTNSKGV---EFKRPLLRAELSSTADTSGYTENNETWYTWSRYPNM 1780
Query: 74 LQ 75
Q
Sbjct: 1781 YQ 1782
>gnl|CDD|185080 PRK15126, PRK15126, thiamin pyrimidine pyrophosphate hydrolase;
Provisional.
Length = 272
Score = 28.1 bits (63), Expect = 0.95
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 60 NDEIWLTNSYIPEYLQANRFN--HY 82
ND+ W T IP LQA+ ++ Y
Sbjct: 106 NDDGWFTGKEIPALLQAHVYSGFRY 130
>gnl|CDD|173323 PTZ00024, PTZ00024, cyclin-dependent protein kinase; Provisional.
Length = 335
Score = 25.5 bits (56), Expect = 6.2
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 87 RKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKI-DLALAQGKKN------YDKR 139
++L +H+ Y + RD L P I+ N+KG+ KI D LA+ K
Sbjct: 126 LQILNGLNVLHKWYF-MHRD---LSPANIFINSKGICKIADFGLARRYGYPPYSDTLSKD 181
Query: 140 ETEKKR 145
ET ++R
Sbjct: 182 ETMQRR 187
>gnl|CDD|178188 PLN02576, PLN02576, protoporphyrinogen oxidase.
Length = 496
Score = 25.0 bits (55), Expect = 9.7
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 1 MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAG-IVLTGTEVKSLRVSKVNIS 52
+++ PK D R + V SF G L K L KV ++
Sbjct: 205 KAIQEAKKNPKPEPRDPRLPKPKGQTVGSFRGGLQTLPDALAKRLGKDKVKLN 257
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
0.319 0.134 0.387
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,612,607
Number of extensions: 155840
Number of successful extensions: 313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 312
Number of HSP's successfully gapped: 15
Length of query: 159
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,136,185
Effective search space: 301941505
Effective search space used: 301941505
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 (21.7 bits)
S2: 53 (24.3 bits)