RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032641
(136 letters)
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 242 bits (620), Expect = 2e-84
Identities = 109/137 (79%), Positives = 121/137 (88%), Gaps = 1/137 (0%)
Query: 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAI 59
+ A RKL+ HRR RWADK YKK+HLG +K PF G+SHAKGIV+EKIGIEAKQPNSAI
Sbjct: 7 LRAARKLRRHRRVNRWADKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAI 66
Query: 60 RKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVS 119
RKC RVQLIKNGKKI AFVPNDGCLN+I ENDEVL++GFGR GHAVGDIPGVRFKVVKV+
Sbjct: 67 RKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVKVA 126
Query: 120 GVSLLALFKEKKEKPRS 136
GVSLLAL+K KKEKPR+
Sbjct: 127 GVSLLALYKGKKEKPRN 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 = 211 bits (540), Expect = 2e-72
Identities = 93/115 (80%), Positives = 102/115 (88%), Gaps = 1/115 (0%)
Query: 20 SYKKSHLGNEWKK-PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFV 78
YKK HLG ++K P G+ HAKGIVLEK+G+EAKQPNSAIRKC RVQLIKNGKKI AFV
Sbjct: 1 RYKKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV 60
Query: 79 PNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEK 133
P DGCLN+I+ENDEVL+AGFGRKG AVGDIPGVRFKVVKV+GVSLLALFK KKEK
Sbjct: 61 PGDGCLNFIDENDEVLVAGFGRKGRAVGDIPGVRFKVVKVNGVSLLALFKGKKEK 115
>gnl|CDD|235257 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
Length = 145
Score = 178 bits (455), Expect = 5e-59
Identities = 83/135 (61%), Positives = 104/135 (77%), Gaps = 2/135 (1%)
Query: 3 AGRKLKSHRRRQRWADKSYKKSHLG-NEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRK 61
A RKLK R++ RW+D+ YK+ LG E P G+ A+GIVLEK+G+EAKQPNSAIRK
Sbjct: 10 AARKLKLKRKKFRWSDRRYKRRMLGLKEKADPLEGAPMARGIVLEKVGVEAKQPNSAIRK 69
Query: 62 CARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF-GRKGHAVGDIPGVRFKVVKVSG 120
C RVQLIKNGK++ AF P DG +N+I+E+DEV+I G G KG ++GDIPGVR+KV+KV+G
Sbjct: 70 CVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNG 129
Query: 121 VSLLALFKEKKEKPR 135
VSL L K KKEKP
Sbjct: 130 VSLKELVKGKKEKPV 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 = 155 bits (394), Expect = 5e-50
Identities = 80/135 (59%), Positives = 103/135 (76%), Gaps = 2/135 (1%)
Query: 3 AGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRK 61
A RKLK R++ RW+D+ +K+ L + K P G+ A+GIVLEK+G+EA+QPNSAIRK
Sbjct: 4 AARKLKRKRKKFRWSDRRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRK 63
Query: 62 CARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF-GRKGHAVGDIPGVRFKVVKVSG 120
C RVQLIKNGK + AF P DG +N+I+E+DEV+I G G +G ++GDIPGVR+KVVKV+
Sbjct: 64 CVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNN 123
Query: 121 VSLLALFKEKKEKPR 135
VSL L K KKEKPR
Sbjct: 124 VSLKELVKGKKEKPR 138
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 132 bits (335), Expect = 3e-41
Identities = 58/140 (41%), Positives = 77/140 (55%), Gaps = 26/140 (18%)
Query: 3 AGRKLKSHRRRQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRK 61
R+L RRR LG + K G +GI LE I K+PNSA+RK
Sbjct: 2 TIRQLVRKRRR-----------KLGLKTKSPALEGCPQKRGICLEVYTITPKKPNSALRK 50
Query: 62 CARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVK---- 117
ARV+LI NGK++ A++P DG + ++E+ EVLI G V D+PGVR+KVV+
Sbjct: 51 VARVRLI-NGKEVTAYIPGDG--HNLQEHSEVLIRGGR-----VKDLPGVRYKVVRGALD 102
Query: 118 VSGVS--LLALFKEKKEKPR 135
V+GVS A K KEKP+
Sbjct: 103 VAGVSDRKQARSKYGKEKPK 122
>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 132 bits (335), Expect = 4e-41
Identities = 49/134 (36%), Positives = 75/134 (55%), Gaps = 14/134 (10%)
Query: 3 AGRKLKSHRRRQRWADKSYKKSHLGNEWKKP-FAGSSHAKGIVLEKIGIEAKQPNSAIRK 61
A RK+ + + R K+ LG + K P G+ A+G+ + K+PNSA+RK
Sbjct: 3 AARKMPTINQLVR-----KKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRK 57
Query: 62 CARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGV 121
ARV+LI NGK++ A++P +G ++E+ EVLI G V D+PGVR+KVV+ +
Sbjct: 58 VARVRLI-NGKEVTAYIPGEGHN--LQEHSEVLIRGGR-----VKDLPGVRYKVVRGALD 109
Query: 122 SLLALFKEKKEKPR 135
SL L + +K
Sbjct: 110 SLGVLDRGQKRSKY 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 = 121 bits (305), Expect = 4e-37
Identities = 32/98 (32%), Positives = 56/98 (57%), Gaps = 10/98 (10%)
Query: 33 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 92
G+ +G+ + K+PNSA+RK A+V+L +G ++ A++P +G + ++E+
Sbjct: 8 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLT-SGYEVTAYIPGEG--HNLQEHSV 64
Query: 93 VLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEK 130
VLI G K D+PGVR+ +V+ GV A K++
Sbjct: 65 VLIRGGRVK-----DLPGVRYHIVR--GVYDAAGVKDR 95
>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 = 7e-12
Identities = 34/82 (41%), Positives = 53/82 (64%), Gaps = 8/82 (9%)
Query: 36 GSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLI 95
G KG+ L+ K+PNSA+RK ARV+L NGK++ A++P +G + ++E+ VL+
Sbjct: 24 GCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEG--HNLQEHSVVLV 80
Query: 96 AGFGRKGHAVGDIPGVRFKVVK 117
G GR V D+PGVR+ +V+
Sbjct: 81 RG-GR----VKDLPGVRYHIVR 97
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12.
Length = 123
Score = 53.9 bits (130), Expect = 2e-10
Identities = 31/77 (40%), Positives = 48/77 (62%), Gaps = 8/77 (10%)
Query: 41 KGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGR 100
+G I K+PNSA+RK ARV+L +G +I A++P G + ++E+ VL+ G GR
Sbjct: 31 RGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIG--HNLQEHSVVLVRG-GR 86
Query: 101 KGHAVGDIPGVRFKVVK 117
V D+PGVR+ +V+
Sbjct: 87 ----VKDLPGVRYHIVR 99
>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 49.9 bits (120), Expect = 8e-09
Identities = 30/65 (46%), Positives = 46/65 (70%), Gaps = 8/65 (12%)
Query: 53 KQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVR 112
K+PNSA+RK ARV+L NG ++ A++P +G + ++E+ VLI G GR V D+PGVR
Sbjct: 43 KKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR----VKDLPGVR 94
Query: 113 FKVVK 117
+ +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 = 47.9 bits (114), Expect = 5e-08
Identities = 31/77 (40%), Positives = 49/77 (63%), Gaps = 8/77 (10%)
Query: 41 KGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGR 100
+G+ K+PNSA+RK ARV+L NG ++ A++P +G + ++E+ VLI G GR
Sbjct: 31 RGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR 86
Query: 101 KGHAVGDIPGVRFKVVK 117
V D+PGVR+ +V+
Sbjct: 87 ----VKDLPGVRYHIVR 99
>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 37.5 bits (87), Expect = 8e-04
Identities = 31/108 (28%), Positives = 55/108 (50%), Gaps = 12/108 (11%)
Query: 10 HRRRQRWADKSYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIK 69
++RR + K K + ++W G+ KGI ++ ++PNS +RK ARV+L
Sbjct: 100 YKRRPKQVPK-LKPKNRRSKW---LEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-S 154
Query: 70 NGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVK 117
G+ + ++P G + + + VL+ G GR D+PG +K V+
Sbjct: 155 TGRTVTVYIPGIG--HNLNTHSVVLVRG-GR----CKDVPGCNYKAVR 195
>gnl|CDD|235131 PRK03562, PRK03562, glutathione-regulated potassium-efflux system
protein KefC; Provisional.
Length = 621
Score = 30.7 bits (70), Expect = 0.23
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 88 EENDEVLIAGFGRKGHAVG 106
E+ V+IAGFGR G VG
Sbjct: 398 EQQPRVIIAGFGRFGQIVG 416
>gnl|CDD|179625 PRK03659, PRK03659, glutathione-regulated potassium-efflux system
protein KefB; Provisional.
Length = 601
Score = 29.6 bits (67), Expect = 0.55
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 10/33 (30%)
Query: 84 LNYIEENDE----------VLIAGFGRKGHAVG 106
LN EE DE V+I GFGR G +G
Sbjct: 384 LNGPEEEDEKPWVEDDKPQVIIVGFGRFGQVIG 416
>gnl|CDD|226567 COG4081, COG4081, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 148
Score = 25.9 bits (57), Expect = 5.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 67 LIKNGKKIAAFVPNDGCLNY 86
I+ G +AAFV ND L Y
Sbjct: 70 PIEGGILLAAFVHNDAGLQY 89
>gnl|CDD|132669 TIGR03630, arch_S17P, archaeal ribosomal protein S17P. This
model describes exclusively the archaeal ribosomal
protein S17P. It excludes the homologous ribosomal
protein S17 from bacteria, and is not intended for use
on eukaryotic sequences, where some instances of
ribosomal proteins S11 score above the trusted cutoff
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 102
Score = 25.3 bits (56), Expect = 6.4
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 14/73 (19%)
Query: 33 PFAGSSHAKGIVLEKIGIEAKQPNSA---------IRKCARVQLIKNGKKIAAFVPNDGC 83
PF G +G +LE + + K + RK R + + KI A P C
Sbjct: 18 PFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYE--RRRSKIHAHNP--PC 73
Query: 84 LNYIEENDEVLIA 96
++ ++E D V+I
Sbjct: 74 ID-VKEGDIVIIG 85
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 26.1 bits (58), Expect = 7.5
Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 8/54 (14%)
Query: 65 VQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKV 118
IK G K L IE V + G A+G+I K +V
Sbjct: 223 ANAIKYGAK--------PGLLDIELGGLVRVYTAKGLGIALGEIDEEGLKPKRV 268
>gnl|CDD|181707 PRK09221, PRK09221, beta alanine--pyruvate transaminase;
Provisional.
Length = 445
Score = 26.0 bits (58), Expect = 7.7
Identities = 13/26 (50%), Positives = 13/26 (50%), Gaps = 4/26 (15%)
Query: 91 DEVLIAGFGRKGHAVGDIPGVRFKVV 116
DEV I GFGR G A RF V
Sbjct: 258 DEV-ITGFGRLGAAFA---AERFGVT 279
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 26.1 bits (57), Expect = 8.0
Identities = 19/72 (26%), Positives = 27/72 (37%)
Query: 44 VLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGH 103
V E I I VQ I++ A + L + + L G +
Sbjct: 73 VFEGILPADGPYRLRIVWPDVVQEIEDPYAFAPTLDESLLLQIAAGDGQALRRALGAQHV 132
Query: 104 AVGDIPGVRFKV 115
VG++PGVRF V
Sbjct: 133 QVGEVPGVRFAV 144
>gnl|CDD|215020 smart01091, CorC_HlyC, Transporter associated domain. This small
domain is found in a family of proteins with the DUF21
domain and two CBS domains with this domain found at the
C-terminus of the proteins, the domain is also found at
the C terminus of some Na+/H+ antiporters. This domain
is also found in CorC that is involved in Magnesium and
cobalt efflux. The function of this domain is uncertain
but might be involved in modulating transport of ion
substrates.
Length = 78
Score = 24.7 bits (55), Expect = 8.6
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 87 IEENDEVLIAGF--GRKGH--AVGD---IPGVRFKVVKVSG 120
+ E + + G G VGD I G+RF+V++V G
Sbjct: 27 LPEEEYDTLGGLVLEELGRIPEVGDSVEIGGLRFEVLEVDG 67
>gnl|CDD|119366 cd06549, GH18_trifunctional, GH18 domain of an uncharacterized
family of bacterial proteins, which share a common
three-domain architecture: an N-terminal glycosyl
hydrolase family 18 (GH18) domain, a glycosyl
transferase family 2 domain, and a C-terminal
polysaccharide deacetylase domain.
Length = 298
Score = 25.8 bits (57), Expect = 9.3
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 17 ADKSYKKSHLGNEWKKPFAGSSHAKGIVL--EKIGIEAKQPNSAIRKCARVQLIKNGKKI 74
AD S + + N + + A GIVL E++ + A R +L GK++
Sbjct: 84 ADPSARAKFIANIAA--YLERNQADGIVLDFEELPADDLPKYVAFLSELRRRLPAQGKQL 141
Query: 75 AAFVPNDG 82
VP D
Sbjct: 142 TVTVPADE 149
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
0.317 0.135 0.400
Gapped
Lambda K H
0.267 0.0870 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,066,844
Number of extensions: 626692
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 498
Number of HSP's successfully gapped: 34
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.3 bits)