RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4801
(143 letters)
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 270 bits (692), Expect = 3e-95
Identities = 122/143 (85%), Positives = 133/143 (93%)
Query: 1 MGKPRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAK 60
MGKPRG+R ARK +RRV RWADK+YKKAHLGTR+KANPFGGASHAKGIV+EK+G+EAK
Sbjct: 1 MGKPRGLRAARKLRRHRRVNRWADKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAK 60
Query: 61 QPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRF 120
QPNSAIRKCVRVQLIKNGKKITAFVP DGCLN+I ENDEVLV+GFGR GHAVGDIPGVRF
Sbjct: 61 QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRF 120
Query: 121 KVVKVANVSLLALYKEKKERPRS 143
KVVKVA VSLLALYK KKE+PR+
Sbjct: 121 KVVKVAGVSLLALYKGKKEKPRN 143
>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 = 227 bits (580), Expect = 2e-78
Identities = 99/115 (86%), Positives = 106/115 (92%)
Query: 26 DYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV 85
YKK HLGT++KA+P GGA HAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV
Sbjct: 1 RYKKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV 60
Query: 86 PRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKER 140
P DGCLN+I+ENDEVLVAGFGRKG AVGDIPGVRFKVVKV VSLLAL+K KKE+
Sbjct: 61 PGDGCLNFIDENDEVLVAGFGRKGRAVGDIPGVRFKVVKVNGVSLLALFKGKKEK 115
>gnl|CDD|235257 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
Length = 145
Score = 190 bits (484), Expect = 2e-63
Identities = 86/140 (61%), Positives = 107/140 (76%), Gaps = 1/140 (0%)
Query: 4 PRGIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPN 63
P G+ ARK R+ RW+D+ YK+ LG + KA+P GA A+GIVLEKVGVEAKQPN
Sbjct: 5 PNGLFAARKLKLKRKKFRWSDRRYKRRMLGLKEKADPLEGAPMARGIVLEKVGVEAKQPN 64
Query: 64 SAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGF-GRKGHAVGDIPGVRFKV 122
SAIRKCVRVQLIKNGK++TAF P DG +N+I+E+DEV++ G G KG ++GDIPGVR+KV
Sbjct: 65 SAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGVRYKV 124
Query: 123 VKVANVSLLALYKEKKERPR 142
+KV VSL L K KKE+P
Sbjct: 125 IKVNGVSLKELVKGKKEKPV 144
>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 = 160 bits (405), Expect = 2e-51
Identities = 84/138 (60%), Positives = 106/138 (76%), Gaps = 1/138 (0%)
Query: 6 GIRTARKHVNNRRVQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSA 65
G+ ARK R+ RW+D+ +K+ L + KA+P GA A+GIVLEKVGVEA+QPNSA
Sbjct: 1 GLFAARKLKRKRKKFRWSDRRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSA 60
Query: 66 IRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGF-GRKGHAVGDIPGVRFKVVK 124
IRKCVRVQLIKNGK +TAF P DG +N+I+E+DEV++ G G +G ++GDIPGVR+KVVK
Sbjct: 61 IRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVK 120
Query: 125 VANVSLLALYKEKKERPR 142
V NVSL L K KKE+PR
Sbjct: 121 VNNVSLKELVKGKKEKPR 138
>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 134 bits (339), Expect = 2e-41
Identities = 46/116 (39%), Positives = 68/116 (58%), Gaps = 8/116 (6%)
Query: 27 YKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVP 86
K+ LG + K+ GA A+G+ V K+PNSA+RK RV+LI NGK++TA++P
Sbjct: 16 KKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIP 74
Query: 87 RDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPR 142
+G ++E+ EVL+ G V D+PGVR+KVV+ A SL L + +K
Sbjct: 75 GEGHN--LQEHSEVLIRGGR-----VKDLPGVRYKVVRGALDSLGVLDRGQKRSKY 123
>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 = 129 bits (325), Expect = 5e-40
Identities = 33/105 (31%), Positives = 57/105 (54%), Gaps = 10/105 (9%)
Query: 33 GTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLN 92
+ K GA +G+ V K+PNSA+RK +V+L +G ++TA++P +G +
Sbjct: 1 RKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLT-SGYEVTAYIPGEG--H 57
Query: 93 YIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEK 137
++E+ VL+ G K D+PGVR+ +V+ V A K++
Sbjct: 58 NLQEHSVVLIRGGRVK-----DLPGVRYHIVR--GVYDAAGVKDR 95
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 128 bits (325), Expect = 1e-39
Identities = 50/121 (41%), Positives = 73/121 (60%), Gaps = 14/121 (11%)
Query: 28 KKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPR 87
++ LG + K+ G +GI LE + K+PNSA+RK RV+LI NGK++TA++P
Sbjct: 10 RRRKLGLKTKSPALEGCPQKRGICLEVYTITPKKPNSALRKVARVRLI-NGKEVTAYIPG 68
Query: 88 DGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVK----VANVS--LLALYKEKKERP 141
DG + ++E+ EVL+ G V D+PGVR+KVV+ VA VS A K KE+P
Sbjct: 69 DG--HNLQEHSEVLIRGGR-----VKDLPGVRYKVVRGALDVAGVSDRKQARSKYGKEKP 121
Query: 142 R 142
+
Sbjct: 122 K 122
>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 = 57.5 bits (140), Expect = 8e-12
Identities = 36/98 (36%), Positives = 57/98 (58%), Gaps = 8/98 (8%)
Query: 27 YKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVP 86
+ + K+ G KG+ L+ K+PNSA+RK RV+L NGK++TA++P
Sbjct: 8 KGRKKKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIP 66
Query: 87 RDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVK 124
+G + ++E+ VLV G GR V D+PGVR+ +V+
Sbjct: 67 GEG--HNLQEHSVVLVRG-GR----VKDLPGVRYHIVR 97
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12.
Length = 123
Score = 51.2 bits (123), Expect = 4e-09
Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 8/65 (12%)
Query: 60 KQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVR 119
K+PNSA+RK RV+L +G +ITA++P G + ++E+ VLV G GR V D+PGVR
Sbjct: 43 KKPNSALRKVARVRL-TSGFEITAYIPGIG--HNLQEHSVVLVRG-GR----VKDLPGVR 94
Query: 120 FKVVK 124
+ +V+
Sbjct: 95 YHIVR 99
>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 = 46.3 bits (110), Expect = 2e-07
Identities = 33/95 (34%), Positives = 56/95 (58%), Gaps = 9/95 (9%)
Query: 48 KGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGR 107
+G+ K+PNSA+RK RV+L NG ++TA++P +G + ++E+ VL+ G GR
Sbjct: 31 RGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR 86
Query: 108 KGHAVGDIPGVRFKVVKVANVSLLALYKEKKERPR 142
V D+PGVR+ +V+ A + + K+ R +
Sbjct: 87 ----VKDLPGVRYHIVRGA-LDTAGVKNRKQGRSK 116
>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 46.4 bits (111), Expect = 2e-07
Identities = 29/65 (44%), Positives = 46/65 (70%), Gaps = 8/65 (12%)
Query: 60 KQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVR 119
K+PNSA+RK RV+L NG ++TA++P +G + ++E+ VL+ G GR V D+PGVR
Sbjct: 43 KKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR----VKDLPGVR 94
Query: 120 FKVVK 124
+ +V+
Sbjct: 95 YHIVR 99
>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 38.7 bits (90), Expect = 4e-04
Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 12/98 (12%)
Query: 27 YKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVP 86
K + ++W GA KGI ++ ++PNS +RK RV+L G+ +T ++P
Sbjct: 110 LKPKNRRSKW----LEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIP 164
Query: 87 RDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVK 124
G + + + VLV G GR D+PG +K V+
Sbjct: 165 GIG--HNLNTHSVVLVRG-GR----CKDVPGCNYKAVR 195
>gnl|CDD|179625 PRK03659, PRK03659, glutathione-regulated potassium-efflux system
protein KefB; Provisional.
Length = 601
Score = 29.2 bits (66), Expect = 0.83
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 10/33 (30%)
Query: 91 LNYIEENDE----------VLVAGFGRKGHAVG 113
LN EE DE V++ GFGR G +G
Sbjct: 384 LNGPEEEDEKPWVEDDKPQVIIVGFGRFGQVIG 416
>gnl|CDD|235131 PRK03562, PRK03562, glutathione-regulated potassium-efflux system
protein KefC; Provisional.
Length = 621
Score = 28.8 bits (65), Expect = 0.98
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 95 EENDEVLVAGFGRKGHAVG 113
E+ V++AGFGR G VG
Sbjct: 398 EQQPRVIIAGFGRFGQIVG 416
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 27.5 bits (61), Expect = 3.2
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 20 QRWADKDYKKAHLGTRWKANPFGGASH 46
QRW +D+ A LG RW+ H
Sbjct: 360 QRWV-EDFAHAALGRRWRHADLADLEH 385
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 26.5 bits (59), Expect = 6.1
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 96 ENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKEKKE 139
+ +VLV G G G A+ +F A V L EK+E
Sbjct: 4 KGKKVLVVGAGVSGLAL-----AKFLKKLGAKV---ILTDEKEE 39
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 26.1 bits (58), Expect = 7.3
Identities = 15/56 (26%), Positives = 18/56 (32%), Gaps = 8/56 (14%)
Query: 72 VQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVAN 127
IK G K L IE V V G A+G+I K +V
Sbjct: 223 ANAIKYGAK--------PGLLDIELGGLVRVYTAKGLGIALGEIDEEGLKPKRVFM 270
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
0.319 0.137 0.409
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,365,311
Number of extensions: 654189
Number of successful extensions: 512
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 28
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 54 (24.5 bits)