RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14161
(91 letters)
>gnl|CDD|217574 pfam03463, eRF1_1, eRF1 domain 1. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif
at an exposed tip of domain 2 suggests that the Gln
residue coordinates a water molecule to mediate the
hydrolytic activity at the peptidyl transferase centre.
A conserved groove on domain 1, 80 A from the GGQ
motif, is proposed to form the codon recognition site.
This family also includes other proteins for which the
precise molecular function is unknown. Many of them are
from Archaebacteria. These proteins may also be
involved in translation termination but this awaits
experimental verification.
Length = 133
Score = 92.3 bits (230), Expect = 8e-26
Identities = 37/88 (42%), Positives = 53/88 (60%), Gaps = 3/88 (3%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSE--SNTGSST 58
MKL+ KNI +K G++ L+PE D+WH +LI GD V + T RK+Q E + T
Sbjct: 1 MKLLEKNI-EKYGKGLIKLLPETLGDLWHLISLIIPGDRVISDTTRKLQDEYSNIKSKVT 59
Query: 59 SSRVRTMLTISVESIDFDTQACVLRLKG 86
RV++ LTI+VE + FD + +LR G
Sbjct: 60 RERVQSALTIAVERLKFDPENGLLRFCG 87
>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
prediction only].
Length = 352
Score = 83.9 bits (208), Expect = 7e-21
Identities = 35/86 (40%), Positives = 50/86 (58%), Gaps = 4/86 (4%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSS 60
M+++ ++ K GV+ LVPE +D+WH YN+I +GD V A T R+ +S S
Sbjct: 1 MRILEEDK----KRGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRSKKGE 56
Query: 61 RVRTMLTISVESIDFDTQACVLRLKG 86
R+ L I VE I+FD A LR+KG
Sbjct: 57 RIPMTLGIKVEKIEFDKFANRLRIKG 82
>gnl|CDD|129217 TIGR00111, pelota, mRNA surveillance protein pelota. This model
describes the Drosophila protein Pelota, the budding
yeast protein DOM34 which it can replace, and a set of
closely related archaeal proteins. Members contain a
proposed RNA binding motif. The meiotic defect in
pelota mutants may be a complex result of a protein
translation defect, as suggested in yeast by ribosomal
protein RPS30A being a multicopy suppressor and by an
altered polyribosome profile in DOM34 mutants rescued
by RPS30A. This family is homologous to a family of
peptide chain release factors. Pelota is proposed to
act in protein translation [Protein synthesis,
Translation factors].
Length = 351
Score = 63.3 bits (154), Expect = 2e-13
Identities = 31/86 (36%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSS 60
M +V ++ N V+ L+PE +D+WH Y +I +GD A T R+ Q S S
Sbjct: 1 MSIVEESFNKGG--AVIKLLPETLDDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDKSK 58
Query: 61 RVRTMLTISVESIDFDTQACVLRLKG 86
L I VES++FD + LR KG
Sbjct: 59 DT-VKLGIEVESVEFDMKTERLRYKG 83
>gnl|CDD|192254 pfam09333, ATG_C, ATG C terminal domain. ATG2 (also known as
Apg2) is a peripheral membrane protein. It functions in
both cytoplasm to vacuole targeting and autophagy.
Length = 98
Score = 26.4 bits (59), Expect = 1.5
Identities = 9/42 (21%), Positives = 16/42 (38%)
Query: 25 EDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTML 66
E + AY+ + G + A + SE + V +L
Sbjct: 15 EGLKKAYSSLGRGLLIAADALIAAPSEVHESKGAQGAVGAVL 56
>gnl|CDD|181113 PRK07775, PRK07775, short chain dehydrogenase; Provisional.
Length = 274
Score = 26.6 bits (59), Expect = 1.6
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 13 KSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRV 62
K+G+ A+V + EG VRAS + + + G S + V
Sbjct: 163 KAGLEAMV--------TNLQMELEGTGVRASIVHPGPTLTGMGWSLPAEV 204
>gnl|CDD|223766 COG0694, COG0694, Thioredoxin-like proteins and domains
[Posttranslational modification, protein turnover,
chaperones].
Length = 93
Score = 24.6 bits (54), Expect = 6.3
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 5/37 (13%)
Query: 60 SRVRTML-----TISVESIDFDTQACVLRLKGNCGNC 91
++R L + + ID + LRL G C C
Sbjct: 20 EKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGC 56
>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit
(sigma70/sigma32) [Transcription].
Length = 342
Score = 24.6 bits (54), Expect = 8.3
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 58 TSSRVRTMLTISVESIDFDTQ 78
+ +VR ML + E I DT
Sbjct: 218 SPDKVREMLKRASEPISLDTP 238
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 0.126 0.353
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,006,794
Number of extensions: 282528
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 9
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
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)