RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12
[Candidatus Liberibacter asiaticus str. psy62]
(124 letters)
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12.
Length = 123
Score = 186 bits (475), Expect = 1e-48
Identities = 82/124 (66%), Positives = 99/124 (79%), Gaps = 1/124 (0%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
MPT+ QLIR R+ R K ALRG PQ+RG C RVYT+TPKKPNSALRKV + RLTS
Sbjct: 1 MPTIKQLIRNTRQ-PIRNKTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTS 59
Query: 61 GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
G E+ AY+PG GHNLQEHSVV++ GGRVKDLPGV+Y ++RG LDA GVK+R+Q RS+YG
Sbjct: 60 GFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGV 119
Query: 121 ERPK 124
++PK
Sbjct: 120 KKPK 123
>gnl|CDD|30397 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 159 bits (404), Expect = 2e-40
Identities = 84/124 (67%), Positives = 100/124 (80%), Gaps = 1/124 (0%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
MPT+NQL+RK R+ S +K AL G PQ RGVC RVYTVTPKKPNSALRKV + RL +
Sbjct: 7 MPTINQLVRKKRR-SLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLIN 65
Query: 61 GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
G EV AY+PGEGHNLQEHS V++ GGRVKDLPGV+Y+V+RG LD+ GV +R Q RS+YGA
Sbjct: 66 GKEVTAYIPGEGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDSLGVLDRGQKRSKYGA 125
Query: 121 ERPK 124
+RPK
Sbjct: 126 KRPK 129
>gnl|CDD|143932 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 112
Score = 159 bits (403), Expect = 3e-40
Identities = 74/104 (71%), Positives = 87/104 (83%)
Query: 21 KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80
K AL G PQKRGVCL VYT+TPKKPNSALRKV + RL +G EV AY+PG+GHNLQEHS
Sbjct: 9 KSPALEGCPQKRGVCLEVYTITPKKPNSALRKVARVRLINGKEVTAYIPGDGHNLQEHSE 68
Query: 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124
V++ GGRVKDLPGV+Y+V+RG LD GV +RKQARS+YG E+PK
Sbjct: 69 VLIRGGRVKDLPGVRYKVVRGALDVAGVSDRKQARSKYGKEKPK 112
>gnl|CDD|48341 cd03368, Ribosomal_S12, S12-like family, 30S ribosomal protein S12
subfamily; S12 is located at the interface of the large
and small ribosomal subunits of prokaryotes,
chloroplasts and mitochondria, where it plays an
important role in both tRNA and ribosomal subunit
interactions. S12 is essential for maintenance of a
pretranslocation state and, together with S13, functions
as a control element for the rRNA- and tRNA-driven
movements of translocation. Antibiotics such as
streptomycin bind S12 and cause the ribosome to misread
the genetic code..
Length = 108
Score = 155 bits (393), Expect = 3e-39
Identities = 76/109 (69%), Positives = 90/109 (82%), Gaps = 1/109 (0%)
Query: 3 TVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGV 62
T+NQLIRK RK + +K AL G PQK+GVCL+VYT TPKKPNSALRKV + RL++G
Sbjct: 1 TINQLIRKGRK-KKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGK 59
Query: 63 EVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNR 111
EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGVLD GVKNR
Sbjct: 60 EVTAYIPGEGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGVLDLAGVKNR 108
>gnl|CDD|36961 KOG1750, KOG1750, KOG1750, Mitochondrial/chloroplast ribosomal
protein S12 [Translation, ribosomal structure and
biogenesis].
Length = 139
Score = 135 bits (341), Expect = 3e-33
Identities = 66/112 (58%), Positives = 80/112 (71%)
Query: 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
M T+NQLIR + R K AL G PQ++GV LRV+T PKKPNSA RK + RL++
Sbjct: 28 MATLNQLIRNGGRPPKRRPRKSPALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRLST 87
Query: 61 GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRK 112
G EV AY+PG GHNLQEHS+V++ GGRV+DLPGVKY V+RGV D GV R
Sbjct: 88 GREVTAYIPGIGHNLQEHSIVLVRGGRVQDLPGVKYHVVRGVYDLAGVVGRI 139
>gnl|CDD|48339 cd00319, Ribosomal_S12_like, Ribosomal protein S12-like family;
composed of prokaryotic 30S ribosomal protein S12,
eukaryotic 40S ribosomal protein S23 and similar
proteins. S12 and S23 are located at the interface of
the large and small ribosomal subunits, adjacent to the
decoding center. They play an important role in
translocation during the peptide elongation step of
protein synthesis. They are also involved in important
RNA and protein interactions. Ribosomal protein S12 is
essential for maintenance of a pretranslocation state
and, together with S13, functions as a control element
for the rRNA- and tRNA-driven movements of
translocation. S23 interacts with domain III of the
eukaryotic elongation factor 2 (eEF2), which catalyzes
translocation. Mutations in S12 and S23 have been found
to affect translational accuracy. Antibiotics such as
streptomycin may also bind S12/S23 and cause the
ribosome to misread the genetic code..
Length = 95
Score = 70.5 bits (172), Expect = 1e-13
Identities = 62/82 (75%), Positives = 70/82 (85%)
Query: 21 KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80
KV AL+G P +RGVC V TVTPKKPNSALRKV K RLTSG EV AY+PGEGHNLQEHSV
Sbjct: 5 KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV 64
Query: 81 VMLCGGRVKDLPGVKYRVIRGV 102
V++ GGRVKDLPGV+Y ++RGV
Sbjct: 65 VLIRGGRVKDLPGVRYHIVRGV 86
>gnl|CDD|48340 cd03367, Ribosomal_S23, S12-like family, 40S ribosomal protein S23
subfamily; S23 is located at the interface of the large
and small ribosomal subunits of eukaryotes, adjacent to
the decoding center. It interacts with domain III of the
eukaryotic elongation factor 2 (eEF2), which catalyzes
the translocation of the growing peptidyl-tRNA to the P
site to make room for the next aminoacyl-tRNA at the A
(acceptor) site. Through its interaction with eEF2, S23
may play an important role in translocation. Also
members of this subfamily are the archaeal 30S ribosomal
S12 proteins. Prokaryotic S12 is essential for
maintenance of a pretranslocation state and, together
with S13, functions as control element for the rRNA- and
tRNA-driven movements of translocation. S12 and S23 are
also implicated in translation accuracy. Antibiotics
such as streptomycin bind S12/S23 and cause the ribosome
to misread the genetic code..
Length = 115
Score = 54.8 bits (132), Expect = 6e-09
Identities = 33/97 (34%), Positives = 57/97 (58%), Gaps = 8/97 (8%)
Query: 12 RKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPG 70
+K K L G P +G+ L V K+PNSA+RK ++ +L +G ++ A+VPG
Sbjct: 3 KKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPG 62
Query: 71 EG--HNLQEHSVVMLCG----GR-VKDLPGVKYRVIR 100
+G + + E+ V++ G GR V D+PGV+++V++
Sbjct: 63 DGCLNFIDENDEVLVAGFGRKGRAVGDIPGVRFKVVK 99
>gnl|CDD|36960 KOG1749, KOG1749, KOG1749, 40S ribosomal protein S23 [Translation,
ribosomal structure and biogenesis].
Length = 143
Score = 42.6 bits (100), Expect = 3e-05
Identities = 29/88 (32%), Positives = 54/88 (61%), Gaps = 8/88 (9%)
Query: 21 KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQE 77
K + G +G+ L V K+PNSA+RK ++ +L +G ++ A+VP +G + ++E
Sbjct: 37 KSSPFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEE 96
Query: 78 HSVVMLCG-GR----VKDLPGVKYRVIR 100
+ V++ G GR V D+PGV+++V++
Sbjct: 97 NDEVLVAGFGRKGHAVGDIPGVRFKVVK 124
>gnl|CDD|111238 pfam02324, Glyco_hydro_70, Glycosyl hydrolase family 70. Members
of this family belong to glycosyl hydrolase family 70
Glucosyltransferases or sucrose 6-glycosyl transferases
(GTF-S) catalyse the transfer of D-glucopyramnosyl units
from sucrose onto acceptor molecules, EC:2.4.1.5. This
family roughly corresponds to the N-terminal catalytic
domain of the enzyme. Members of this family also
contain the Putative cell wall binding domain pfam01473,
which corresponds with the C-terminal glucan-binding
domain.
Length = 808
Score = 29.3 bits (66), Expect = 0.31
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 42 TPKKPNSA--LRKVIKARLTSGVEVIA-YVPGEGHNLQEHSVV 81
K SA LR +KA G++ IA +VP + +NL VV
Sbjct: 638 KNNKYGSADDLRDALKALHAQGIQAIADWVPDQIYNLPGKEVV 680
>gnl|CDD|39046 KOG3842, KOG3842, KOG3842, Adaptor protein Pellino [Signal
transduction mechanisms].
Length = 429
Score = 25.3 bits (55), Expect = 4.6
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 67 YVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124
V E + LQ+ S++ LCG + +R G+ + +K+ + R A RP+
Sbjct: 241 LVEEETNVLQDGSLIDLCGAT------LLWRTADGLEHSPTMKHLEALRQEINAARPQ 292
>gnl|CDD|132931 cd07020, Clp_protease_NfeD_1, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin
operon partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair,
causing NfeD to be previously named STOPP (stomatin
operon partner protein). NfeD homologs can be divided
into two groups: long and short forms. Long-form
homologs have a putative ClpP-class serine protease
domain while the short form homologs do not. Downstream
from the ClpP-class domain is the so-called NfeD or
DUF107 domain. N-terminal region of the NfeD homolog
PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii
has been shown to possess serine protease activity and
has a Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 187
Score = 25.2 bits (56), Expect = 4.7
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 48 SALRKVIKARLTSGVEVIAYV-PGEGH 73
+ R++++A L S V V+ YV P
Sbjct: 45 DSTREIVQAILASPVPVVVYVYPSGAR 71
>gnl|CDD|31208 COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 414
Score = 25.2 bits (55), Expect = 5.3
Identities = 13/31 (41%), Positives = 14/31 (45%), Gaps = 6/31 (19%)
Query: 45 KPN------SALRKVIKARLTSGVEVIAYVP 69
KPN S +IK G EVIAY P
Sbjct: 321 KPNTDDMRESPALDIIKRLQEKGAEVIAYDP 351
>gnl|CDD|29309 cd00231, ZipA, ZipA C-terminal domain. ZipA, a membrane-anchored
protein, is one of at least nine essential gene products
necessary for assembly of the septal ring which mediates
cell division in E.coli. ZipA and FtsA directly bind
FtsZ, a homolog of eukaryotic tubulins, at the
prospective division site, followed by the sequential
addition of FtsK, FtsQ, FtsL, FtsW, FtsI, and FtsN.
ZipA contains three domains: a short N-terminal
membrane-anchored domain, a central P/Q domain that is
rich in proline and glutamine and a C-terminal domain,
which comprises almost half the protein..
Length = 130
Score = 24.9 bits (54), Expect = 5.6
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 59 TSGVEVIAYVPGEGHNLQEHSVVMLCGGRV-KDLPGVKYRVIRGVLDAQGVKNRKQ 113
T G+ +P G LQ +++ R+ DL GV R ++ Q ++ +
Sbjct: 73 TPGISFFMQLPSPGDALQNFKLMLQAAQRIADDLGGVVLDDQRRMMTPQKLRAYRD 128
>gnl|CDD|163668 cd07425, MPP_Shelphs, Shewanella-like phosphatases,
metallophosphatase domain. This family includes
bacterial, eukaryotic, and archeal proteins orthologous
to the Shewanella cold-active protein-tyrosine
phosphatase, CAPTPase. CAPTPase is an uncharacterized
protein that belongs to the Shelph (Shewanella-like
phosphatase) family of PPP (phosphoprotein
phosphatases). The PPP family is one of two known
protein phosphatase families specific for serine and
threonine. In addition to Shelps, the PPP family also
includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6,
PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase.
The PPP catalytic domain is defined by three conserved
motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme
family is ancient with members found in all eukaryotes,
and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 208
Score = 24.9 bits (55), Expect = 6.2
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 72 GHNLQEHSVVMLCGGRV 88
GH QE +V CGG+V
Sbjct: 174 GHTPQEGGIVTFCGGKV 190
>gnl|CDD|36452 KOG1238, KOG1238, KOG1238, Glucose dehydrogenase/choline
dehydrogenase/mandelonitrile lyase (GMC oxidoreductase
family) [General function prediction only].
Length = 623
Score = 24.5 bits (53), Expect = 6.9
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 7/33 (21%)
Query: 46 PNSALRKVIKARLTSGVEVIAYVPGEGHNLQEH 78
P L+K+ G+ V+ +PG G NLQ+H
Sbjct: 330 PADHLKKL-------GIPVVLDLPGVGQNLQDH 355
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
0.320 0.136 0.400
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,420,485
Number of extensions: 66127
Number of successful extensions: 151
Number of sequences better than 10.0: 1
Number of HSP's gapped: 146
Number of HSP's successfully gapped: 26
Length of query: 124
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,491,799
Effective search space: 188655558
Effective search space used: 188655558
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: 51 (23.5 bits)