RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032383
(142 letters)
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 255 bits (652), Expect = 5e-89
Identities = 114/143 (79%), Positives = 126/143 (88%), Gaps = 1/143 (0%)
Query: 1 MGKTRGMGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAK 59
MGK RG+ A RKL+ HRR RWADK YKK+HLG +K PF G+SHAKGIV+EKIGIEAK
Sbjct: 1 MGKPRGLRAARKLRRHRRVNRWADKEYKKAHLGTRYKANPFGGASHAKGIVVEKIGIEAK 60
Query: 60 QPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRF 119
QPNSAIRKC RVQLIKNGKKI AFVPNDGCLN+I ENDEVL++GFGR GHAVGDIPGVRF
Sbjct: 61 QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVRF 120
Query: 120 KVVKVSGVSLLALFKEKKEKPRS 142
KVVKV+GVSLLAL+K KKEKPR+
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 = 212 bits (542), Expect = 1e-72
Identities = 93/115 (80%), Positives = 102/115 (88%), Gaps = 1/115 (0%)
Query: 26 SYKKSHLGNEWKK-PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFV 84
YKK HLG ++K P G+ HAKGIVLEK+G+EAKQPNSAIRKC RVQLIKNGKKI AFV
Sbjct: 1 RYKKRHLGTKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFV 60
Query: 85 PNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEK 139
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 = 180 bits (459), Expect = 1e-59
Identities = 84/139 (60%), Positives = 105/139 (75%), Gaps = 2/139 (1%)
Query: 5 RGMGAGRKLKTHRRTQRWADKSYKKSHLG-NEWKKPFAGSSHAKGIVLEKIGIEAKQPNS 63
G+ A RKLK R+ RW+D+ YK+ LG E P G+ A+GIVLEK+G+EAKQPNS
Sbjct: 6 NGLFAARKLKLKRKKFRWSDRRYKRRMLGLKEKADPLEGAPMARGIVLEKVGVEAKQPNS 65
Query: 64 AIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF-GRKGHAVGDIPGVRFKVV 122
AIRKC RVQLIKNGK++ AF P DG +N+I+E+DEV+I G G KG ++GDIPGVR+KV+
Sbjct: 66 AIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGVRYKVI 125
Query: 123 KVSGVSLLALFKEKKEKPR 141
KV+GVSL L K KKEKP
Sbjct: 126 KVNGVSLKELVKGKKEKPV 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 = 7e-50
Identities = 81/138 (58%), Positives = 104/138 (75%), Gaps = 2/138 (1%)
Query: 6 GMGAGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSA 64
G+ A RKLK R+ RW+D+ +K+ L + K P G+ A+GIVLEK+G+EA+QPNSA
Sbjct: 1 GLFAARKLKRKRKKFRWSDRRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSA 60
Query: 65 IRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF-GRKGHAVGDIPGVRFKVVK 123
IRKC RVQLIKNGK + AF P DG +N+I+E+DEV+I G G +G ++GDIPGVR+KVVK
Sbjct: 61 IRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVK 120
Query: 124 VSGVSLLALFKEKKEKPR 141
V+ VSL L K KKEKPR
Sbjct: 121 VNNVSLKELVKGKKEKPR 138
>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 135 bits (342), Expect = 5e-42
Identities = 50/134 (37%), Positives = 75/134 (55%), Gaps = 14/134 (10%)
Query: 9 AGRKLKTHRRTQRWADKSYKKSHLGNEWKKP-FAGSSHAKGIVLEKIGIEAKQPNSAIRK 67
A RK+ T + R K+ LG + K P G+ A+G+ + K+PNSA+RK
Sbjct: 3 AARKMPTINQLVR-----KKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRK 57
Query: 68 CARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGV 127
ARV+LI NGK++ A++P +G ++E+ EVLI G V D+PGVR+KVV+ +
Sbjct: 58 VARVRLI-NGKEVTAYIPGEGHN--LQEHSEVLIRGGR-----VKDLPGVRYKVVRGALD 109
Query: 128 SLLALFKEKKEKPR 141
SL L + +K
Sbjct: 110 SLGVLDRGQKRSKY 123
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 131 bits (332), Expect = 1e-40
Identities = 57/140 (40%), Positives = 76/140 (54%), Gaps = 26/140 (18%)
Query: 9 AGRKLKTHRRTQRWADKSYKKSHLGNEWK-KPFAGSSHAKGIVLEKIGIEAKQPNSAIRK 67
R+L RR LG + K G +GI LE I K+PNSA+RK
Sbjct: 2 TIRQLVRKRR-----------RKLGLKTKSPALEGCPQKRGICLEVYTITPKKPNSALRK 50
Query: 68 CARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVK---- 123
ARV+LI NGK++ A++P DG + ++E+ EVLI G V D+PGVR+KVV+
Sbjct: 51 VARVRLI-NGKEVTAYIPGDG--HNLQEHSEVLIRGGR-----VKDLPGVRYKVVRGALD 102
Query: 124 VSGVS--LLALFKEKKEKPR 141
V+GVS A K KEKP+
Sbjct: 103 VAGVSDRKQARSKYGKEKPK 122
>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 = 5e-37
Identities = 32/98 (32%), Positives = 56/98 (57%), Gaps = 10/98 (10%)
Query: 39 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98
G+ +G+ + K+PNSA+RK A+V+L +G ++ A++P +G + ++E+
Sbjct: 8 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLT-SGYEVTAYIPGEG--HNLQEHSV 64
Query: 99 VLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEK 136
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: 42 GSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLI 101
G KG+ L+ K+PNSA+RK ARV+L NGK++ A++P +G + ++E+ VL+
Sbjct: 24 GCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEG--HNLQEHSVVLV 80
Query: 102 AGFGRKGHAVGDIPGVRFKVVK 123
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 = 3e-10
Identities = 31/77 (40%), Positives = 48/77 (62%), Gaps = 8/77 (10%)
Query: 47 KGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGR 106
+G I K+PNSA+RK ARV+L +G +I A++P G + ++E+ VL+ G GR
Sbjct: 31 RGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIG--HNLQEHSVVLVRG-GR 86
Query: 107 KGHAVGDIPGVRFKVVK 123
V D+PGVR+ +V+
Sbjct: 87 ----VKDLPGVRYHIVR 99
>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 49.5 bits (119), Expect = 1e-08
Identities = 30/65 (46%), Positives = 46/65 (70%), Gaps = 8/65 (12%)
Query: 59 KQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVR 118
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: 119 FKVVK 123
+ +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 = 6e-08
Identities = 31/77 (40%), Positives = 49/77 (63%), Gaps = 8/77 (10%)
Query: 47 KGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGR 106
+G+ K+PNSA+RK ARV+L NG ++ A++P +G + ++E+ VLI G GR
Sbjct: 31 RGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR 86
Query: 107 KGHAVGDIPGVRFKVVK 123
V D+PGVR+ +V+
Sbjct: 87 ----VKDLPGVRYHIVR 99
>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 36.7 bits (85), Expect = 0.002
Identities = 28/97 (28%), Positives = 49/97 (50%), Gaps = 11/97 (11%)
Query: 27 YKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPN 86
K + ++W G+ KGI ++ ++PNS +RK ARV+L G+ + ++P
Sbjct: 110 LKPKNRRSKW---LEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPG 165
Query: 87 DGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVK 123
G + + + VL+ G GR D+PG +K V+
Sbjct: 166 IG--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 = 0.26
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 94 EENDEVLIAGFGRKGHAVG 112
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 = 0.60
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 10/33 (30%)
Query: 90 LNYIEENDE----------VLIAGFGRKGHAVG 112
LN EE DE V+I GFGR G +G
Sbjct: 384 LNGPEEEDEKPWVEDDKPQVIIVGFGRFGQVIG 416
>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 = 25.7 bits (57), Expect = 5.2
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 14/73 (19%)
Query: 39 PFAGSSHAKGIVLEKIGIEAKQPNSA---------IRKCARVQLIKNGKKIAAFVPNDGC 89
PF G +G +LE + + K + RK R + + KI A P C
Sbjct: 18 PFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYE--RRRSKIHAHNP--PC 73
Query: 90 LNYIEENDEVLIA 102
++ ++E D V+I
Sbjct: 74 ID-VKEGDIVIIG 85
>gnl|CDD|226567 COG4081, COG4081, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 148
Score = 25.9 bits (57), Expect = 5.6
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 73 LIKNGKKIAAFVPNDGCLNY 92
I+ G +AAFV ND L Y
Sbjct: 70 PIEGGILLAAFVHNDAGLQY 89
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 26.1 bits (58), Expect = 8.0
Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 8/54 (14%)
Query: 71 VQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKV 124
IK G K L IE V + G A+G+I K +V
Sbjct: 223 ANAIKYGAK--------PGLLDIELGGLVRVYTAKGLGIALGEIDEEGLKPKRV 268
>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 = 8.2
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 23 ADKSYKKSHLGNEWKKPFAGSSHAKGIVL--EKIGIEAKQPNSAIRKCARVQLIKNGKKI 80
AD S + + N + + A GIVL E++ + A R +L GK++
Sbjct: 84 ADPSARAKFIANIAA--YLERNQADGIVLDFEELPADDLPKYVAFLSELRRRLPAQGKQL 141
Query: 81 AAFVPNDG 88
VP D
Sbjct: 142 TVTVPADE 149
>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
Provisional.
Length = 474
Score = 26.2 bits (57), Expect = 8.6
Identities = 3/22 (13%), Positives = 10/22 (45%)
Query: 16 HRRTQRWADKSYKKSHLGNEWK 37
R++ + ++ +K H +
Sbjct: 131 ERKSPKSYNQQSRKKHRDESLR 152
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 26.1 bits (57), Expect = 8.6
Identities = 19/72 (26%), Positives = 27/72 (37%)
Query: 50 VLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGH 109
V E I I VQ I++ A + L + + L G +
Sbjct: 73 VFEGILPADGPYRLRIVWPDVVQEIEDPYAFAPTLDESLLLQIAAGDGQALRRALGAQHV 132
Query: 110 AVGDIPGVRFKV 121
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 = 9.2
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 93 IEENDEVLIAGF--GRKGH--AVGD---IPGVRFKVVKVSG 126
+ E + + G G VGD I G+RF+V++V G
Sbjct: 27 LPEEEYDTLGGLVLEELGRIPEVGDSVEIGGLRFEVLEVDG 67
>gnl|CDD|181707 PRK09221, PRK09221, beta alanine--pyruvate transaminase;
Provisional.
Length = 445
Score = 26.0 bits (58), Expect = 9.3
Identities = 13/26 (50%), Positives = 13/26 (50%), Gaps = 4/26 (15%)
Query: 97 DEVLIAGFGRKGHAVGDIPGVRFKVV 122
DEV I GFGR G A RF V
Sbjct: 258 DEV-ITGFGRLGAAFA---AERFGVT 279
>gnl|CDD|220014 pfam08780, NTase_sub_bind, Nucleotidyltransferase substrate
binding protein like. Nucleotidyltransferases (EC
2.7.7) comprise a large enzyme family with diverse
roles in polynucleotide synthesis and modification.
This domain is structurally related to kanamycin
nucleotidyltransferase (KNTase) and forms a complex
with HI0073, a sequence homolog of the
nucleotide-binding domain of this
nucleotidyltransferase superfamily.
Length = 122
Score = 25.3 bits (56), Expect = 9.7
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 50 VLEKIGI-EAKQPNSAIRKCARVQLIKNG 77
LE GI + P IR+ LI +G
Sbjct: 49 YLEYQGIVDVVSPRDVIREAFENGLIDDG 77
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 0.399
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: 7,278,526
Number of extensions: 644152
Number of successful extensions: 527
Number of sequences better than 10.0: 1
Number of HSP's gapped: 504
Number of HSP's successfully gapped: 33
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
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)