RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16455
(82 letters)
>gnl|CDD|239466 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 = 93.0 bits (232), Expect = 1e-26
Identities = 43/104 (41%), Positives = 52/104 (50%), Gaps = 29/104 (27%)
Query: 1 MHMKGPHYKKRPPRQP-LLGKPFAKG----------------------------KEMVAY 31
+ KG KK+ + P L G P KG KE+ AY
Sbjct: 5 LIRKGRKKKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGKEVTAY 64
Query: 32 IPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
IPGEGHNLQEH++VL + GRVKDLPGV+ VRGV DL V +
Sbjct: 65 IPGEGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGVLDLAGVKNR 108
>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 76.9 bits (190), Expect = 4e-20
Identities = 32/53 (60%), Positives = 38/53 (71%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ VRG D V + Q
Sbjct: 60 GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQ 112
>gnl|CDD|130054 TIGR00981, rpsL_bact, ribosomal protein S12, bacterial/organelle.
This model recognizes ribosomal protein S12 of Bacteria,
mitochondria, and chloroplasts. The homologous ribosomal
proteins of Archaea and Eukarya, termed S23 in Eukarya
and S12 or S23 in Archaea, score below the trusted
cutoff [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 124
Score = 71.0 bits (174), Expect = 1e-17
Identities = 32/53 (60%), Positives = 38/53 (71%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ VRG D V + Q
Sbjct: 60 GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNRKQ 112
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12.
Length = 123
Score = 69.3 bits (170), Expect = 5e-17
Identities = 29/44 (65%), Positives = 34/44 (77%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYD 68
G E+ AYIPG GHNLQEH++VL + GRVKDLPGV+ VRG D
Sbjct: 60 GFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLD 103
>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 68.8 bits (169), Expect = 8e-17
Identities = 34/53 (64%), Positives = 40/53 (75%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
GKE+ AYIPGEGHNLQEH+ VL + GRVKDLPGV+ K VRG D V+ + Q
Sbjct: 66 GKEVTAYIPGEGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDSLGVLDRGQ 118
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 65.4 bits (160), Expect = 1e-15
Identities = 33/53 (62%), Positives = 40/53 (75%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
GKE+ AYIPG+GHNLQEH+ VL + GRVKDLPGV+ K VRG D+ V + Q
Sbjct: 59 GKEVTAYIPGDGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDVAGVSDRKQ 111
>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 61.0 bits (148), Expect = 9e-13
Identities = 26/45 (57%), Positives = 32/45 (71%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDL 69
G+ + YIPG GHNL H++VL + GR KD+PG K VRGVYDL
Sbjct: 156 GRTVTVYIPGIGHNLNTHSVVLVRGGRCKDVPGCNYKAVRGVYDL 200
>gnl|CDD|238196 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 = 41.6 bits (97), Expect = 2e-06
Identities = 30/42 (71%), Positives = 35/42 (83%)
Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGV 66
G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ VRGV
Sbjct: 45 GYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGV 86
>gnl|CDD|239465 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 = 26.5 bits (59), Expect = 1.2
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 7/47 (14%)
Query: 25 GKEMVAYIPGEG--HNLQEHNIVL-CKVGR----VKDLPGVKIKCVR 64
GK++ A++PG+G + + E++ VL GR V D+PGV+ K V+
Sbjct: 53 GKKITAFVPGDGCLNFIDENDEVLVAGFGRKGRAVGDIPGVRFKVVK 99
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 26.6 bits (59), Expect = 1.2
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 9/51 (17%)
Query: 25 GKEMVAYIPGEG--HNLQEHNIVLCK-VGR----VKDLPGVKIK--CVRGV 66
GK++ A++P +G + + E++ VL GR V D+PGV+ K V GV
Sbjct: 78 GKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVKVAGV 128
>gnl|CDD|233425 TIGR01467, cobI_cbiL, precorrin-2 C20-methyltransferase. This
model represents precorrin-2 C20-methyltransferase, one
of several closely related
S-adenosylmethionine-dependent methyltransferases
involved in cobalamin (vitamin B12) biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 230
Score = 25.7 bits (57), Expect = 2.7
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 18 LGKPFAKGKEMVAYIPGEGHN------LQEHN-IVLCKVGRVKDLPGVK 59
G P +G E +A +P L E + +VL KVGR LP +K
Sbjct: 137 AGLPLVEGDESLAILPATAGEAELEKALAEFDTVVLMKVGRN--LPQIK 183
>gnl|CDD|218954 pfam06246, Isy1, Isy1-like splicing family. Isy1 protein is
important in the optimisation of splicing.
Length = 253
Score = 25.0 bits (55), Expect = 5.7
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 50 GRVKDLPGVK 59
GR K+LPGVK
Sbjct: 128 GRAKELPGVK 137
>gnl|CDD|216177 pfam00891, Methyltransf_2, O-methyltransferase. This family
includes a range of O-methyltransferases. These enzymes
utilise S-adenosyl methionine.
Length = 239
Score = 24.9 bits (55), Expect = 5.9
Identities = 8/14 (57%), Positives = 11/14 (78%), Gaps = 2/14 (14%)
Query: 60 IKCVRGVYDLPHVV 73
IK + V+DLPHV+
Sbjct: 126 IKGI--VFDLPHVI 137
>gnl|CDD|211968 TIGR04245, nodulat_NodA, N-acyltransferase NodA. Nodulation
factors are lipo-chitooligosaccharides made by bacterial
nitrogen-fixing bacteria as a signal to plant hosts. Nod
factors differ slightly from system to system are serve
as host range determinants. Because the N-acyl group
varies from one NodA to another, the family treated as a
subfamily, but all members of this family belong to
NodABC systems.
Length = 193
Score = 24.7 bits (54), Expect = 6.9
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 18 LGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIK-CVRGVY-DLP 70
LG PFA G H L+ H LC+ G + GV+++ + V+ DLP
Sbjct: 113 LGVPFAFGTVR--------HALRNHVERLCRNGLATIVSGVRVRSTLPDVHLDLP 159
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 24.4 bits (54), Expect = 8.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 25 GKEMVAYIPGEGHNLQEH 42
G +V +PG G NLQ+H
Sbjct: 282 GIPVVHDLPGVGENLQDH 299
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.143 0.451
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,169,242
Number of extensions: 320249
Number of successful extensions: 202
Number of sequences better than 10.0: 1
Number of HSP's gapped: 201
Number of HSP's successfully gapped: 15
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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: 53 (24.2 bits)