RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9115
(96 letters)
>gnl|CDD|238288 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling
factor dissociates the posttermination complex, composed
of the ribosome, deacylated tRNA, and mRNA, after
termination of translation. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis. RRF is believed to bind the ribosome at the
A-site in a manner that mimics tRNA, but the specific
mechanisms remain unclear. RRF is essential for
bacterial growth. It is not necessary for cell growth
in archaea or eukaryotes, but is found in mitochondria
or chloroplasts of some eukaryotic species.
Length = 179
Score = 44.2 bits (105), Expect = 8e-07
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 24 VTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQ 78
+T+E R+ L K+AK + + K IR+I+ +K EK + +S+D+V+ E
Sbjct: 101 LTEERRKELVKDAKKIAEEAKVAIRNIRRDANDKIKKLEKEKEISEDEVKKAEED 155
>gnl|CDD|216689 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling
factor (RRF / ribosome release factor) dissociates the
ribosome from the mRNA after termination of translation,
and is essential bacterial growth. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis.
Length = 165
Score = 42.9 bits (102), Expect = 2e-06
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 24 VTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQ 78
+T+E R+ L K AK L + K IR+I+ +K EK + +S+D+V+ ++
Sbjct: 87 LTEERRKELVKQAKKLAEEAKVAIRNIRRDANDKLKKLEKDKEISEDEVKRAEKE 141
>gnl|CDD|223311 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal
structure and biogenesis].
Length = 187
Score = 34.9 bits (81), Expect = 0.002
Identities = 17/54 (31%), Positives = 30/54 (55%)
Query: 25 TKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQ 78
T+E R+ L K AK + K +R+I+ +K EK + +S+D+V+ E+
Sbjct: 108 TEERRKELVKVAKKYAEEAKVAVRNIRRDANDKIKKLEKDKEISEDEVKKAEEE 161
>gnl|CDD|129587 TIGR00496, frr, ribosome recycling factor. This model finds only
eubacterial proteins. Mitochondrial and/or chloroplast
forms might be expected but are not currently known.
This protein was previously called ribosome releasing
factor. By releasing ribosomes from mRNA at the end of
protein biosynthesis, it prevents inappropriate
translation from 3-prime regions of the mRNA and frees
the ribosome for new rounds of translation.
EGAD|53116|YHR038W is part of the frr superfamily
[Protein synthesis, Translation factors].
Length = 176
Score = 29.3 bits (66), Expect = 0.19
Identities = 17/55 (30%), Positives = 33/55 (60%)
Query: 24 VTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQ 78
+T+E R+ L K+AK + + K +R+++ VK EK + +S+D+ R + E+
Sbjct: 96 LTEERRKELVKHAKKIAEQAKVAVRNVRRDANDKVKKLEKDKEISEDEERRLQEE 150
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 28.9 bits (66), Expect = 0.30
Identities = 15/54 (27%), Positives = 29/54 (53%)
Query: 25 TKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQ 78
T+E R+ L K K + K IR+I+ +K EK + +S+D+++ ++
Sbjct: 106 TEERRKELVKQVKKEAEEAKVAIRNIRRDANDKLKKLEKDKEISEDELKRAEDE 159
>gnl|CDD|227808 COG5521, COG5521, Predicted integral membrane protein [Function
unknown].
Length = 275
Score = 27.5 bits (61), Expect = 1.0
Identities = 19/97 (19%), Positives = 31/97 (31%), Gaps = 14/97 (14%)
Query: 8 GLECRRDKFQDQSSF----------VVTKEHRESLSKNAK-ALFVKCKENIRDIQNKYTK 56
G + DK +SS V K E+L +N + + + E + Q+
Sbjct: 81 GFQIENDKLTGKSSERIEDSQNVMVVDMKHEYETLGENFENQIIFQPDELVITDQSGTGF 140
Query: 57 TV---KNKEKSEGLSQDDVRSVSEQSAFESYHGFISG 90
V K + K E S V + + I
Sbjct: 141 RVSYRKMQTKLEKTSVHSVEDLISTQWYAQNKAMIML 177
>gnl|CDD|172564 PRK14074, rpsF, 30S ribosomal protein S6; Provisional.
Length = 257
Score = 27.2 bits (60), Expect = 1.2
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 12/85 (14%)
Query: 9 LECRRDKFQDQSSFVVTKEHRESL-------SKNAKALFVKCKE---NIRDIQNKYTKTV 58
LE DK Q V ++ +ESL K L+V+ +E N++++++K K +
Sbjct: 46 LEKGNDKLTKQELEVRAEDIKESLIAYSDFLEDLTKILWVELEEDLSNLKEVKSKIDKEL 105
Query: 59 KNKEKSEGLSQD--DVRSVSEQSAF 81
K+ K G++QD + S +SAF
Sbjct: 106 KDDLKDLGITQDFTKLPGGSTKSAF 130
>gnl|CDD|213276 cd05908, A_NRPS_MycA_like, The adenylation domain of nonribosomal
peptide synthetases (NRPS) similar to mycosubtilin
synthase subunit A (MycA). The adenylation (A) domain
of NRPS recognizes a specific amino acid or hydroxy acid
and activates it as (amino)-acyl adenylate by hydrolysis
of ATP. The activated acyl moiety then forms thioester
to the enzyme-bound cofactor phosphopantetheine of a
peptidyl carrier protein domain. This family includes
NRPS similar to mycosubtilin synthase subunit A (MycA).
Mycosubtilin, which is characterized by a beta-amino
fatty acid moiety linked to the circular heptapeptide
Asn-Tyr-Asn-Gln-Pro-Ser-Asn, belongs to the iturin
family of lipopeptide antibiotics. The mycosubtilin
synthase subunit A (MycA) combines functional domains
derived from peptide synthetases, amino transferases,
and fatty acid synthases. Nonribosomal peptide
synthetases are large multifunction enzymes that
synthesize many therapeutically useful peptides. NRPS
has a distinct modular structure in which each module is
responsible for the recognition, activation, and, in
some cases, modification of a single amino acid residue
of the final peptide product. The modules can be
subdivided into domains that catalyze specific
biochemical reactions.
Length = 499
Score = 27.2 bits (61), Expect = 1.2
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 26 KEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSE 77
KE E + +FV+ ++++ D K ++ K GL+ D V V
Sbjct: 430 KEQSEEV-----VIFVEYRQSLDDFTPLALKIKRHVNKKMGLNIDHVIPVRS 476
>gnl|CDD|239940 cd04494, BRCA2DBD_OB2, BRCA2DBD_OB2: A subfamily of OB folds
corresponding to the second OB fold (OB2) of the
800-amino acid C-terminal ssDNA binding domain (DBD) of
BRCA2 (breast cancer susceptibility gene 2) protein,
called BRCA2DBD. BRCA2 participates in homologous
recombination-mediated repair of double-strand DNA
breaks. It stimulates the displacement of Replication
protein A (RPA), the most abundant eukaryotic ssDNA
binding protein. It also facilitates filament formation.
Mutations that map throughout the BRCA2 protein are
associated with breast cancer susceptibility. BRCA2 is a
large nuclear protein and its most conserved region is
the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro,
and is composed of five structural domains, three of
which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and
OB3 are arranged in tandem, and their mode of binding
can be considered qualitatively similar to two OB folds
of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Length = 251
Score = 26.3 bits (58), Expect = 2.4
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 22 FVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQDDVRSV 75
+++E E+LS N + L + K+ +Q ++ K V+ K EGLS+ DV V
Sbjct: 116 AELSEEQLEALS-NYQQLQNEKKQ--ARLQEEFRKAVEEALKEEGLSKRDVTPV 166
>gnl|CDD|177876 PLN02231, PLN02231, alanine transaminase.
Length = 534
Score = 24.9 bits (54), Expect = 8.1
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 44 KENIRDIQNKYTKTVKNKEKSEGLSQDDVRSVSEQSAFESYHG 86
+EN+ + +K + K +S G + D+ VS QS + Y+G
Sbjct: 314 QENVY-VPDKKFHSFKKVARSMGYGEKDISLVSFQSVSKGYYG 355
>gnl|CDD|218313 pfam04890, DUF648, Family of unknown function (DUF648). Family of
hypothetical Chlamydia proteins. This family may well
comprise of two domains, as some members only match the
N-terminus.
Length = 288
Score = 24.7 bits (54), Expect = 8.7
Identities = 12/84 (14%), Positives = 29/84 (34%), Gaps = 4/84 (4%)
Query: 11 CRRDKFQDQSSFVVTKEHRESLSKNAKALFVKCKENIRDIQNKYTKTVKNKEKSEGLSQD 70
QS+ + E + +++ +R++ +K K E+ + L D
Sbjct: 175 VLDTYDLSQSTLNLISEMDFCGKADKRSIE----NKLRELLGIESKISKLPEQLKQLFFD 230
Query: 71 DVRSVSEQSAFESYHGFISGEPLD 94
+ +S + E ++ D
Sbjct: 231 GICQLSPEFIEELVREYLCELSDD 254
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
0.312 0.128 0.358
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,371,173
Number of extensions: 318703
Number of successful extensions: 295
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 25
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)