RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 042342
(87 letters)
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 142 bits (361), Expect = 1e-45
Identities = 60/77 (77%), Positives = 66/77 (85%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
PF G SHAKGIV+EKIGIEAKQPN AIRKC RVQLIKNGKKI FVP+DGCLN+I END+
Sbjct: 40 PFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDE 99
Query: 61 VLIAGFGRKGHAVATSP 77
VL++GFGR GHAV P
Sbjct: 100 VLVSGFGRSGHAVGDIP 116
>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 = 140 bits (354), Expect = 5e-45
Identities = 58/77 (75%), Positives = 64/77 (83%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
P G HAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI FVP DGCLN+I+END+
Sbjct: 15 PLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDE 74
Query: 61 VLIAGFGRKGHAVATSP 77
VL+AGFGRKG AV P
Sbjct: 75 VLVAGFGRKGRAVGDIP 91
>gnl|CDD|235257 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
Length = 145
Score = 105 bits (264), Expect = 7e-31
Identities = 44/73 (60%), Positives = 56/73 (76%), Gaps = 1/73 (1%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
P G A+GIVLEK+G+EAKQPN AIRKC RVQLIKNGK++ F P DG +N+I+E+D+
Sbjct: 41 PLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDE 100
Query: 61 VLIAGF-GRKGHA 72
V+I G G KG +
Sbjct: 101 VVIEGIGGPKGRS 113
>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 = 96.5 bits (240), Expect = 2e-27
Identities = 43/80 (53%), Positives = 58/80 (72%), Gaps = 1/80 (1%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
P G A+GIVLEK+G+EA+QPN AIRKC RVQLIKNGK + F P DG +N+I+E+D+
Sbjct: 35 PLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDE 94
Query: 61 VLIAGF-GRKGHAVATSPPI 79
V+I G G +G ++ P +
Sbjct: 95 VIIEGIGGPRGRSMGDIPGV 114
>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 = 90.9 bits (225), Expect = 1e-25
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
G +G+ + K+PN A+RK ++V+L +G ++ ++P +G + ++E+
Sbjct: 8 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLT-SGYEVTAYIPGEG--HNLQEHSV 64
Query: 61 VLIAG 65
VLI G
Sbjct: 65 VLIRG 69
>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12.
Length = 122
Score = 86.6 bits (215), Expect = 9e-24
Identities = 28/69 (40%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
G +GI LE I K+PN A+RK +RV+LI NGK++ ++P DG + ++E+ +
Sbjct: 22 ALEGCPQKRGICLEVYTITPKKPNSALRKVARVRLI-NGKEVTAYIPGDG--HNLQEHSE 78
Query: 61 VLIAGFGRK 69
VLI G K
Sbjct: 79 VLIRGGRVK 87
>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 83.4 bits (207), Expect = 2e-22
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
G A+G+ + K+PN A+RK +RV+LI NGK++ ++P +G ++E+ +
Sbjct: 29 ALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIPGEGHN--LQEHSE 85
Query: 61 VLIAGFGRK 69
VLI G K
Sbjct: 86 VLIRGGRVK 94
>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 = 36.3 bits (85), Expect = 3e-04
Identities = 23/60 (38%), Positives = 39/60 (65%), Gaps = 4/60 (6%)
Query: 9 KGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
KG+ L+ K+PN A+RK +RV+L NGK++ ++P +G + ++E+ VL+ G GR
Sbjct: 29 KGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEG--HNLQEHSVVLVRG-GR 84
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12.
Length = 123
Score = 35.8 bits (83), Expect = 5e-04
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 9 KGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
+G I K+PN A+RK +RV+L +G +I ++P G + ++E+ VL+ G GR
Sbjct: 31 RGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIG--HNLQEHSVVLVRG-GR 86
>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 = 33.2 bits (76), Expect = 0.004
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 9 KGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
+G+ K+PN A+RK +RV+L NG ++ ++P +G + ++E+ VLI G GR
Sbjct: 31 RGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR 86
>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
Length = 124
Score = 31.4 bits (72), Expect = 0.020
Identities = 20/48 (41%), Positives = 33/48 (68%), Gaps = 4/48 (8%)
Query: 21 KQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
K+PN A+RK +RV+L NG ++ ++P +G + ++E+ VLI G GR
Sbjct: 43 KKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR 86
>gnl|CDD|235131 PRK03562, PRK03562, glutathione-regulated potassium-efflux system
protein KefC; Provisional.
Length = 621
Score = 28.4 bits (64), Expect = 0.37
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 56 EENDKVLIAGFGRKGHAVA 74
E+ +V+IAGFGR G V
Sbjct: 398 EQQPRVIIAGFGRFGQIVG 416
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 26.4 bits (59), Expect = 1.7
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 23 PNFAIRKCSRVQLIKNGK 40
N A R + L+K+GK
Sbjct: 199 LNLAARYADHLILLKDGK 216
>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
Length = 290
Score = 26.0 bits (57), Expect = 2.3
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 4 GPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDG 50
G KGI ++ ++PN +RK +RV+L G+ + ++P G
Sbjct: 122 GAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPGIG 167
>gnl|CDD|179625 PRK03659, PRK03659, glutathione-regulated potassium-efflux system
protein KefB; Provisional.
Length = 601
Score = 26.1 bits (58), Expect = 2.4
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 10/33 (30%)
Query: 52 LNYIEEND----------KVLIAGFGRKGHAVA 74
LN EE D +V+I GFGR G +
Sbjct: 384 LNGPEEEDEKPWVEDDKPQVIIVGFGRFGQVIG 416
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 26.1 bits (58), Expect = 2.6
Identities = 16/63 (25%), Positives = 21/63 (33%), Gaps = 15/63 (23%)
Query: 13 LEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHA 72
L I + P R + I+ L+ +E D VLIAG KGH
Sbjct: 406 LADILAGIEAPEKYEIIEDREEAIRKA------------LDLAKEGDVVLIAG---KGHE 450
Query: 73 VAT 75
Sbjct: 451 TYQ 453
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 24.9 bits (55), Expect = 6.2
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 57 ENDKVLIAGFGRKGHAVA 74
+ KVL+ G G G A+A
Sbjct: 4 KGKKVLVVGAGVSGLALA 21
>gnl|CDD|149912 pfam08994, T4_Gp59_C, T4 gene Gp59 loader of gp41 DNA helicase
C-term. Bacteriophage T4 gene-59 helicase assembly
protein is required for recombination-dependent DNA
replication, which is the predominant mode of DNA
replication in the late stage of T4 infection. T4
gene-59 helicase assembly protein accelerates the
loading of the T4 gene-41 helicase during DNA synthesis
by the T4 replication system in vitro. T4 gene-59
helicase assembly protein binds to both T4 gene-41
helicase and T4 gene-32 single-stranded DNA binding
protein, and to single and double-stranded DNA. The
structure of T4 gene-59 helicase assembly protein
reveals a novel alpha-helical bundle fold with two
domains of similar size, this being the C-terminal
domain that consists of seven alpha-helices with short
intervening loops and turns. The surface of the domain
contains large regions of exposed hydrophobic residues
and clusters of acidic and basic residues. The
hydrophobic region on the 'bottom' surface of the
domain near the C-terminal helix binds the leading
strand DNA, whilst the hydrophobic region on the 'top'
surface of the domain lies between the two arms of the
fork DNA, allowing for T4 gene 41 helicase binding and
assembly into a hexameric complex around the lagging
strand.
Length = 103
Score = 24.6 bits (54), Expect = 6.7
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 44 TFVPSDGCLNYIEENDKVL 62
TFV D L ++++D+VL
Sbjct: 47 TFVVLDSFLGIVDKHDEVL 65
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 24.7 bits (55), Expect = 7.0
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 23 PNFAIRKCSRVQLIKNGK 40
N A R RV L+K+G+
Sbjct: 158 LNLAARYADRVILLKDGR 175
>gnl|CDD|235792 PRK06390, PRK06390, adenylosuccinate lyase; Provisional.
Length = 451
Score = 24.9 bits (54), Expect = 7.2
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 27 IRKCSRVQLIKNGKKIVTFVPSDGCLNYIEEND 59
+R+ S ++ NGK + + + G L YI+E
Sbjct: 386 VRRAS-MEARSNGKSLKSSLIEAGILKYIDEKT 417
>gnl|CDD|235041 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 447
Score = 24.8 bits (55), Expect = 7.5
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 57 ENDKVLIAGFGRKGHAVAT 75
+N KVL+ G + G+A A
Sbjct: 4 QNKKVLVLGLAKSGYAAAK 22
>gnl|CDD|215681 pfam00054, Laminin_G_1, Laminin G domain.
Length = 131
Score = 24.2 bits (53), Expect = 8.9
Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 13/67 (19%)
Query: 32 RVQLIKNGKKIVTFVPSDGC-----------LNYIEENDKVLIAGFGRKGHAVATSPPII 80
V+L +NG+ V DG ++ + + + G +
Sbjct: 57 SVELERNGRSGTLSV--DGEARVTGESPLGATTDLDVDGPLYVGGLPSLAVKLRRLAISP 114
Query: 81 SLKGCMR 87
S GC+R
Sbjct: 115 SFDGCIR 121
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
0.321 0.140 0.421
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,410,448
Number of extensions: 358875
Number of successful extensions: 405
Number of sequences better than 10.0: 1
Number of HSP's gapped: 399
Number of HSP's successfully gapped: 25
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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)