RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2262
(137 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 = 159 bits (405), Expect = 6e-52
Identities = 62/108 (57%), Positives = 72/108 (66%), Gaps = 1/108 (0%)
Query: 24 TLWDMHMKGPHYKKRPPRQP-LLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKE 82
T+ + KG KK+ + P L G P KGV LKV PKKPNSA RK VRLS GKE
Sbjct: 1 TINQLIRKGRKKKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGKE 60
Query: 83 MVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 130
+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ VRGV DL V +
Sbjct: 61 VTAYIPGEGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGVLDLAGVKNR 108
>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 116 bits (293), Expect = 1e-34
Identities = 53/90 (58%), Positives = 61/90 (67%)
Query: 43 PLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGEGHNLQEHNIVLC 102
L G P A+GV +V PKKPNSA RK VRL GKE+ AYIPGEGHNLQEH+ VL
Sbjct: 29 ALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLINGKEVTAYIPGEGHNLQEHSEVLI 88
Query: 103 KVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 132
+ GRVKDLPGV+ K VRG D V+ + Q
Sbjct: 89 RGGRVKDLPGVRYKVVRGALDSLGVLDRGQ 118
>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 113 bits (286), Expect = 1e-33
Identities = 49/89 (55%), Positives = 58/89 (65%)
Query: 44 LLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGEGHNLQEHNIVLCK 103
L P +GV +V PKKPNSA RK VRL+ G E+ AYIPGEGHNLQEH++VL +
Sbjct: 24 LNACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSVVLIR 83
Query: 104 VGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 132
GRVKDLPGV+ VRG D V + Q
Sbjct: 84 GGRVKDLPGVRYHIVRGALDTAGVKDRKQ 112
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 112 bits (282), Expect = 4e-33
Identities = 51/90 (56%), Positives = 61/90 (67%)
Query: 43 PLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGEGHNLQEHNIVLC 102
L G P +G+ L+V PKKPNSA RK VRL GKE+ AYIPG+GHNLQEH+ VL
Sbjct: 22 ALEGCPQKRGICLEVYTITPKKPNSALRKVARVRLINGKEVTAYIPGDGHNLQEHSEVLI 81
Query: 103 KVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 132
+ GRVKDLPGV+ K VRG D+ V + Q
Sbjct: 82 RGGRVKDLPGVRYKVVRGALDVAGVSDRKQ 111
>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 = 111 bits (278), Expect = 2e-32
Identities = 54/103 (52%), Positives = 65/103 (63%), Gaps = 1/103 (0%)
Query: 31 KGPHYKKRPPRQPLLGK-PFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPG 89
KG KK+ + P L P +GV +V PKKPNSA RK VRL+ G E+ AYIPG
Sbjct: 10 KGRKKKKKKSKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPG 69
Query: 90 EGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 132
EGHNLQEH++VL + GRVKDLPGV+ VRG D V + Q
Sbjct: 70 EGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNRKQ 112
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12.
Length = 123
Score = 105 bits (264), Expect = 2e-30
Identities = 46/88 (52%), Positives = 57/88 (64%)
Query: 36 KKRPPRQPLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGEGHNLQ 95
+ + L G P +G +V PKKPNSA RK VRL++G E+ AYIPG GHNLQ
Sbjct: 16 RNKTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQ 75
Query: 96 EHNIVLCKVGRVKDLPGVKIKCVRGVYD 123
EH++VL + GRVKDLPGV+ VRG D
Sbjct: 76 EHSVVLVRGGRVKDLPGVRYHIVRGTLD 103
>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 101 bits (254), Expect = 3e-27
Identities = 48/93 (51%), Positives = 60/93 (64%), Gaps = 1/93 (1%)
Query: 33 PHYKKRPPRQPLL-GKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGEG 91
P K + R L G P KG+ +KV ++ P+KPNS RK VRLSTG+ + YIPG G
Sbjct: 108 PKLKPKNRRSKWLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIG 167
Query: 92 HNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDL 124
HNL H++VL + GR KD+PG K VRGVYDL
Sbjct: 168 HNLNTHSVVLVRGGRCKDVPGCNYKAVRGVYDL 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 = 72.0 bits (176), Expect = 1e-17
Identities = 49/79 (62%), Positives = 57/79 (72%)
Query: 43 PLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGEGHNLQEHNIVLC 102
L G PF +GV V PKKPNSA RK VRL++G E+ AYIPGEGHNLQEH++VL
Sbjct: 8 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLI 67
Query: 103 KVGRVKDLPGVKIKCVRGV 121
+ GRVKDLPGV+ VRGV
Sbjct: 68 RGGRVKDLPGVRYHIVRGV 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 = 58.8 bits (143), Expect = 3e-12
Identities = 42/99 (42%), Positives = 60/99 (60%), Gaps = 13/99 (13%)
Query: 34 HYKKRPPRQ-----PLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRL-STGKEMVAYI 87
YKKR PL G P AKG+VL+ + + K+PNSA RKCV V+L GK++ A++
Sbjct: 1 RYKKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV 60
Query: 88 PGEG--HNLQEHNIVL-CKVGR----VKDLPGVKIKCVR 119
PG+G + + E++ VL GR V D+PGV+ K V+
Sbjct: 61 PGDGCLNFIDENDEVLVAGFGRKGRAVGDIPGVRFKVVK 99
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 54.4 bits (131), Expect = 2e-10
Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 10/105 (9%)
Query: 27 DMHMKGPHYKKRPPRQPLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRL-STGKEMVA 85
D K H R P G AKG+V++ + + K+PNSA RKCV V+L GK++ A
Sbjct: 24 DKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITA 83
Query: 86 YIPGEG--HNLQEHNIVLCK-VGR----VKDLPGVKIK--CVRGV 121
++P +G + + E++ VL GR V D+PGV+ K V GV
Sbjct: 84 FVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVKVAGV 128
>gnl|CDD|130055 TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12). This model
represents the eukaryotic and archaeal homologs of
bacterial ribosomal protein S12. This protein is known
typically as S23 in eukaryotes and as either S12 or S23
in the Archaea [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 139
Score = 52.2 bits (125), Expect = 2e-09
Identities = 36/100 (36%), Positives = 58/100 (58%), Gaps = 14/100 (14%)
Query: 34 HYKKRPPR-----QPLLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRL-STGKEMVAYI 87
+K+R R PL G P A+G+VL+ + + ++PNSA RKCV V+L GK + A+
Sbjct: 21 RFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFC 80
Query: 88 PGEG--HNLQEHNIVLC------KVGRVKDLPGVKIKCVR 119
PG+G + + EH+ V+ + + D+PGV+ K V+
Sbjct: 81 PGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVK 120
>gnl|CDD|235257 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
Length = 145
Score = 50.3 bits (121), Expect = 9e-09
Identities = 37/86 (43%), Positives = 54/86 (62%), Gaps = 11/86 (12%)
Query: 43 PLLGKPFAKGVVL-KVLIKKPKKPNSANRKCVLVRL-STGKEMVAYIPGEG--HNLQEHN 98
PL G P A+G+VL KV ++ K+PNSA RKCV V+L GK++ A+ PG+G + + EH+
Sbjct: 41 PLEGAPMARGIVLEKVGVEA-KQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHD 99
Query: 99 IVLC-----KVGRVK-DLPGVKIKCV 118
V+ GR D+PGV+ K +
Sbjct: 100 EVVIEGIGGPKGRSMGDIPGVRYKVI 125
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 28.4 bits (64), Expect = 1.3
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 44 LLGKPFAKGVVLKVLIKKPKKPNSANRKCVLVRL 77
L GKPF IKK + NS N+K +LV L
Sbjct: 51 LFGKPFRD-------IKKGQLINSINKKDLLVEL 77
>gnl|CDD|226810 COG4373, COG4373, Mu-like prophage FluMu protein gp28 [General
function prediction only].
Length = 509
Score = 28.0 bits (62), Expect = 1.7
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 2/77 (2%)
Query: 2 LNLVIDASLSDILPVWVREKTKTLWDMHMKGPHYK-KRPPRQPLLGKPFAKGVVLKVLIK 60
L + + DI P W+RE W + P + P + G FA+ L VL
Sbjct: 274 LIFELGSEFHDI-PAWLRESEVLTWCLPDLRPALQALNPGGRLYFGVDFARKRDLSVLWV 332
Query: 61 KPKKPNSANRKCVLVRL 77
K ++A R V + +
Sbjct: 333 WEKVGDTAWRAVVELEI 349
>gnl|CDD|164586 MTH00010, ND1, NADH dehydrogenase subunit 1; Validated.
Length = 311
Score = 27.1 bits (60), Expect = 3.6
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 34 HYKKRPPRQPLLG--KPFAKGVVLKVLIKKPKKPNSAN 69
+K P + L G +PFA +K+ K+ KP+ AN
Sbjct: 35 QLRKGPNKVGLAGIPQPFAD--AIKLFTKEQTKPSPAN 70
>gnl|CDD|227654 COG5351, COG5351, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 367
Score = 26.0 bits (57), Expect = 7.5
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 9 SLSDILPVWVREKTKTLWDMHMKGPHY 35
++ D E T TL +KGP Y
Sbjct: 326 TILDFSECDAGETTLTLTRARLKGPEY 352
>gnl|CDD|214409 MTH00040, ND1, NADH dehydrogenase subunit 1; Validated.
Length = 323
Score = 25.7 bits (57), Expect = 9.0
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 2/23 (8%)
Query: 47 KPFAKGVVLKVLIKKPKKPNSAN 69
+PFA G LK+ IK+ KP++A+
Sbjct: 51 QPFADG--LKLFIKETLKPSNAS 71
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 0.139 0.431
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: 6,841,907
Number of extensions: 587777
Number of successful extensions: 387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 383
Number of HSP's successfully gapped: 23
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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: 54 (24.6 bits)