RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9255
(127 letters)
>gnl|CDD|146221 pfam03465, eRF1_3, eRF1 domain 3. 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 = 100
Score = 68.0 bits (167), Expect = 4e-16
Identities = 19/48 (39%), Positives = 33/48 (68%)
Query: 39 NNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYV 86
+ ++ +E+++DTG +GVE+ L+ALE+G+VETL+ + L R V
Sbjct: 6 KLLEEFLEELAKDTGLAVYGVEEVLKALEMGAVETLLISDELLRSRDV 53
>gnl|CDD|224420 COG1503, eRF1, Peptide chain release factor 1 (eRF1) [Translation,
ribosomal structure and biogenesis].
Length = 411
Score = 51.6 bits (124), Expect = 1e-08
Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHL 100
+ ++F E+++D+G +G E+ ALE+G+V+TL+ E+L+ +R K +L
Sbjct: 282 MEEFFKELAKDSGLAVYGEEEVREALEMGAVDTLLVSEDLEKERVTYKC---PTCGYENL 338
Query: 101 TPEQEKDKSHFTDKE 115
++E ++ F E
Sbjct: 339 KSKREFEQKRFRCPE 353
>gnl|CDD|234307 TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and
eukaryotic forms. Directs the termination of nascent
peptide synthesis (translation) in response to the
termination codons UAA, UAG and UGA. This model
identifies both archaeal (aRF1) and eukaryotic (eRF1) of
the protein. Also known as translation termination
factor 1 [Protein synthesis, Translation factors].
Length = 357
Score = 43.8 bits (104), Expect = 5e-06
Identities = 15/38 (39%), Positives = 29/38 (76%)
Query: 43 KYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENL 80
++F E+++DTG +G E+ +ALE+G+V+TL+ E++
Sbjct: 277 RFFKELAKDTGLAAYGEEEVRKALEMGAVDTLLISEDI 314
>gnl|CDD|235198 PRK04011, PRK04011, peptide chain release factor 1; Provisional.
Length = 411
Score = 42.9 bits (102), Expect = 1e-05
Identities = 17/48 (35%), Positives = 31/48 (64%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLK 88
+ ++F E+++D G +G E+ +ALE+G+V+TL+ E+L R K
Sbjct: 283 MEEFFKELAKDGGLAVYGEEEVRKALEMGAVDTLLISEDLRKDRVTYK 330
>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
prediction only].
Length = 352
Score = 37.3 bits (87), Expect = 8e-04
Identities = 14/62 (22%), Positives = 32/62 (51%), Gaps = 7/62 (11%)
Query: 14 RYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVET 73
+ AV ++ + I ++ ++ + +++D K +G+E+ +A E G+VET
Sbjct: 239 KRGAVDKILSETRIAEEIELVE-------EFLERLAKDDDKVAYGLEEVEKAAEYGAVET 291
Query: 74 LI 75
L+
Sbjct: 292 LL 293
>gnl|CDD|151380 pfam10933, DUF2827, Protein of unknown function (DUF2827). This is
a family of uncharacterized proteins found in
Burkholderia.
Length = 364
Score = 30.8 bits (70), Expect = 0.16
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 2/46 (4%)
Query: 3 KYFKDKHKYLGRYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEI 48
Y K + + Y D V E + + R LF +DE+
Sbjct: 90 AYLKARGGKIVSYCCGNDYVIAIERMMFGRPSGHLFIGTP--YDEV 133
>gnl|CDD|224823 COG1911, RPL30, Ribosomal protein L30E [Translation, ribosomal
structure and biogenesis].
Length = 100
Score = 28.5 bits (64), Expect = 0.46
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 51 DTGKYCFGVEDTLRALELGSVETLICWENL------DIQRY 85
TGK G + T+++L+LG + +I N DI+ Y
Sbjct: 16 KTGKVILGSKRTIKSLKLGKAKLIIIASNCPKELKEDIEYY 56
>gnl|CDD|143588 cd07564, nitrilases_CHs, Nitrilases, cyanide hydratase (CH)s, and
similar proteins (class 1 nitrilases). Nitrilases
(nitrile aminohydrolases, EC:3.5.5.1) hydrolyze nitriles
(RCN) to ammonia and the corresponding carboxylic acid.
Most nitrilases prefer aromatic nitriles, some prefer
arylacetonitriles and others aliphatic nitriles. This
group includes the nitrilase cyanide dihydratase (CDH),
which hydrolyzes inorganic cyanide (HCN) to produce
formate. It also includes cyanide hydratase (CH), which
hydrolyzes HCN to formamide. This group includes four
Arabidopsis thaliana nitrilases (Ath)NIT1-4. AthNIT1-3
have a strong substrate preference for
phenylpropionitrile (PPN) and other nitriles which may
originate from the breakdown of glucosinolates. The
product of PPN hydrolysis, phenylacetic acid has auxin
activity. AthNIT1-3 can also convert indoacetonitrile to
indole-3-acetic acid (IAA, auxin), but with a lower
affinity and velocity. From their expression patterns,
it has been speculated that NIT3 may produce IAA during
the early stages of germination, and that NIT3 may
produce IAA during embryo development and maturation.
AthNIT4 has a strong substrate specificity for the
nitrile, beta-cyano-L-alanine (Ala(CN)), an intermediate
of cyanide detoxification. AthNIT4 has both a nitrilase
activity and a nitrile hydratase (NHase) activity, which
generate aspartic acid and asparagine respectively from
Ala(CN). NHase catalyzes the hydration of nitriles to
their corresponding amides. This subgroup belongs to a
larger nitrilase superfamily comprised of belong to a
larger nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13),
this subgroup corresponds to class 1.
Length = 297
Score = 27.8 bits (63), Expect = 1.5
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 61 DTLRA--LELGSVETLICWENL 80
LR +G + LICWEN
Sbjct: 140 SGLRVVDTPIGRLGALICWENY 161
>gnl|CDD|184174 PRK13602, PRK13602, putative ribosomal protein L7Ae-like;
Provisional.
Length = 82
Score = 26.7 bits (59), Expect = 1.6
Identities = 11/37 (29%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 45 FDEISQDTGKYCFGVEDTLRALELGSVETLICWENLD 81
++++SQ G + T++AL+ GSV+ ++ E+ D
Sbjct: 3 YEKVSQ-AKSIVIGTKQTVKALKRGSVKEVVVAEDAD 38
>gnl|CDD|224855 COG1944, COG1944, Uncharacterized conserved protein [Function
unknown].
Length = 398
Score = 27.7 bits (62), Expect = 1.7
Identities = 10/49 (20%), Positives = 15/49 (30%), Gaps = 11/49 (22%)
Query: 12 LGRYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVE 60
L YP V +L+ K E + +D + D G
Sbjct: 211 LAGYPGVLELIEKLE----AEGFPVTL------WD-ATSDGGVPVVAAV 248
>gnl|CDD|179205 PRK01018, PRK01018, 50S ribosomal protein L30e; Reviewed.
Length = 99
Score = 26.9 bits (60), Expect = 1.9
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 51 DTGKYCFGVEDTLRALELGSVETLICWENL------DIQRY 85
DTGK G + T++A++LG + +I N DI+ Y
Sbjct: 13 DTGKVILGSKRTIKAIKLGKAKLVIVASNCPKDIKEDIEYY 53
>gnl|CDD|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III
synthetase/uroporphyrin-III C-methyltransferase;
Reviewed.
Length = 656
Score = 27.4 bits (61), Expect = 2.1
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 41 IGKYFDEISQDTGKYCFGVEDTLRALELGSV 71
+ +YFD S+DT V+D L+ ++ S+
Sbjct: 610 LARYFDTASKDTQ----TVQDLLKQVDAASL 636
>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 = 27.1 bits (60), Expect = 2.9
Identities = 11/45 (24%), Positives = 28/45 (62%)
Query: 40 NIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQR 84
I ++ + +++D K +G ++ ++A E G++E L+ + + +QR
Sbjct: 263 VIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVLVQR 307
>gnl|CDD|184103 PRK13512, PRK13512, coenzyme A disulfide reductase; Provisional.
Length = 438
Score = 26.3 bits (58), Expect = 6.1
Identities = 8/30 (26%), Positives = 11/30 (36%)
Query: 85 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDK 114
Y + L TPE+ D+ T K
Sbjct: 47 YYIGEVVEDRKYALAYTPEKFYDRKQITVK 76
>gnl|CDD|236170 PRK08166, PRK08166, NADH dehydrogenase subunit G; Validated.
Length = 791
Score = 26.1 bits (58), Expect = 6.6
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 58 GVEDTLRALELGSVETLICWENLDIQRY 85
+E+ L LE G + +I EN D+ R+
Sbjct: 492 SLEEALEELESGRADAVIVLEN-DLYRH 518
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
0.319 0.138 0.403
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,511,480
Number of extensions: 578795
Number of successful extensions: 540
Number of sequences better than 10.0: 1
Number of HSP's gapped: 540
Number of HSP's successfully gapped: 37
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
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 (21.7 bits)
S2: 53 (24.2 bits)