RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2490
(64 letters)
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 59.9 bits (146), Expect = 9e-14
Identities = 21/44 (47%), Positives = 26/44 (59%)
Query: 19 DLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
LD +I E D++ R SGPGGQ V KT + V LTH+PT
Sbjct: 1 PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPT 44
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 54.9 bits (133), Expect = 5e-11
Identities = 27/61 (44%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 2 SIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIP 61
S RRH S AS +LD S +I + D++ R SG GGQ V KT++ V LTH+P
Sbjct: 82 SNGRRHTSFASV-EVFPELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLP 140
Query: 62 T 62
T
Sbjct: 141 T 141
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 48.6 bits (116), Expect = 1e-08
Identities = 25/58 (43%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S AS +F ++D +I +D++ R SG GGQ V KT++ V +THIPT
Sbjct: 210 RRHTSFAS-VFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPT 266
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 47.2 bits (113), Expect = 4e-08
Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 17/66 (25%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKID--------EKDIQERFVRGSGPGGQAVAKTNNCVV 56
RRH S AS P++D KD++ R SG GGQ V KT++ V
Sbjct: 210 RRHTSFASV---------EVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVR 260
Query: 57 LTHIPT 62
+THIPT
Sbjct: 261 ITHIPT 266
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 45.1 bits (107), Expect = 2e-07
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 26 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
I+ D++ R SG GGQ V T++ V +TH+PT
Sbjct: 216 VDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPT 252
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 44.3 bits (106), Expect = 3e-07
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 26 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+I+ KD++ R SG GGQ V T++ V +TH+PT
Sbjct: 216 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPT 252
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 44.1 bits (105), Expect = 4e-07
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 26 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+I+ KD++ R SG GGQ V T++ V +TH+PT
Sbjct: 218 IEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPT 254
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 42.8 bits (102), Expect = 5e-07
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVL 57
I E +++ RF+R SGPGGQ V K + V L
Sbjct: 10 IPENELEWRFIRASGPGGQNVNKVSTAVEL 39
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 42.7 bits (100), Expect = 1e-06
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTD 63
RRH S +S+F ++D + I+ D++ R SG GGQ V KT + V +THIPT+
Sbjct: 151 RRHTSF-TSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTN 208
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 42.0 bits (99), Expect = 2e-06
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 22 YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+S + +I+ +R SGPGGQ V KT++ V TH+ +
Sbjct: 98 FSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLAS 138
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 41.7 bits (98), Expect = 3e-06
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 22 YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+S + E +I+ +R SGPGGQ V KT + V TH+ +
Sbjct: 97 FSASEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLAS 137
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 39.5 bits (92), Expect = 2e-05
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S AS D +V ++E D++ R SG GGQ V T++ V +THIPT
Sbjct: 174 RRHTSFASIWVYPVIDDNIEV-DVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPT 230
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 36.7 bits (85), Expect = 2e-04
Identities = 16/35 (45%), Positives = 21/35 (60%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
I +D++ R G GGQ V KT + V +THIPT
Sbjct: 193 IRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPT 227
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 33.2 bits (75), Expect = 0.003
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
RRH S S D ++ ++ +D++ R SG GGQ V T++ V +TH PT++
Sbjct: 172 RRHTSFVSCEVVPEFNDEVEI-EVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNT 230
>gnl|CDD|236812 PRK10992, PRK10992, iron-sulfur cluster repair di-iron protein;
Provisional.
Length = 220
Score = 27.3 bits (61), Expect = 0.42
Identities = 8/12 (66%), Positives = 12/12 (100%)
Query: 11 ASSLFRKYDLDY 22
A++LFR+YDLD+
Sbjct: 18 ATALFREYDLDF 29
>gnl|CDD|177880 PLN02236, PLN02236, choline kinase.
Length = 344
Score = 26.5 bits (59), Expect = 0.81
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 3/20 (15%)
Query: 20 LDYSKVPKIDEKDIQERFVR 39
LDYSK P +E + RF+R
Sbjct: 257 LDYSKYPGEEE---RRRFIR 273
>gnl|CDD|237330 PRK13279, arnT, 4-amino-4-deoxy-L-arabinose transferase;
Provisional.
Length = 552
Score = 26.0 bits (58), Expect = 1.1
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 9 SLASSLFRKYDLDYSKVPKIDEKDIQERFV 38
SL L R DL +P D+ Q R V
Sbjct: 517 SLVLRLDRDEDLPELALPPADKVYRQGRLV 546
>gnl|CDD|223582 COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide acyltransferase (E2) component, and
related enzymes [Energy production and conversion].
Length = 404
Score = 25.0 bits (55), Expect = 2.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 30 EKDIQERFVRGSGPGGQAVAK 50
E I V+G+GPGG+ K
Sbjct: 125 EAGIDLSKVKGTGPGGRITKK 145
>gnl|CDD|233367 TIGR01349, PDHac_trf_mito, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model represents one of several closely related clades
of the dihydrolipoamide acetyltransferase subunit of the
pyruvate dehydrogenase complex. It includes sequences
from mitochondria and from alpha and beta branches of
the proteobacteria, as well as from some other bacteria.
Sequences from Gram-positive bacteria are not included.
The non-enzymatic homolog protein X, which serves as an
E3 component binding protein, falls within the clade
phylogenetically but is rejected by its low score
[Energy metabolism, Pyruvate dehydrogenase].
Length = 436
Score = 25.1 bits (55), Expect = 2.7
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 30 EKDIQERFVRGSGPGGQAVAK 50
EK I V GSGP G+ V K
Sbjct: 152 EKGIDLSAVAGSGPNGRIVKK 172
>gnl|CDD|234493 TIGR04189, surface_SprA, cell surface protein SprA. SprA is a cell
surface protein widely distributed in the Bacteroidetes
lineage. In Flavobacterium johnsoniae, a species that
shows gliding motility, mutation disrupts gliding.
Length = 2315
Score = 25.0 bits (55), Expect = 3.1
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 30 EKDIQERFVRGSGPGG---QAVAKTNNCVVLTHIP 61
I ER+ +G G AV TN T IP
Sbjct: 1052 PGSILERYKNYNGTEGNSPVAVQGTNYNRGNTTIP 1086
>gnl|CDD|225402 COG2846, COG2846, Regulator of cell morphogenesis and NO
signaling [Cell division and chromosome partitioning].
Length = 221
Score = 24.7 bits (54), Expect = 3.3
Identities = 6/12 (50%), Positives = 10/12 (83%)
Query: 11 ASSLFRKYDLDY 22
A+ +FR YD+D+
Sbjct: 18 AAEIFRSYDIDF 29
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 24.6 bits (54), Expect = 3.4
Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 3/18 (16%)
Query: 1 MSIFRRHLSLASS---LF 15
M+IF RHLS S LF
Sbjct: 230 MNIFHRHLSPDGSGPVLF 247
>gnl|CDD|188530 TIGR04015, WcaC, colanic acid biosynthesis glycosyl transferase
WcaC. This gene is one of the glycosyl transferases
involved in the biosynthesis of colanic acid, an
exopolysaccharide expressed in Enterobacteraceae
species.
Length = 405
Score = 24.9 bits (54), Expect = 3.7
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 30 EKDIQERFVRGSGPGG-QAVAKTNNCVVLTHIP 61
+K + FV G G GG ++V+ N V+ P
Sbjct: 28 QKGLTSHFVYGYGKGGKKSVSHDNYPQVIKQTP 60
>gnl|CDD|182255 PRK10125, PRK10125, putative glycosyl transferase; Provisional.
Length = 405
Score = 24.5 bits (53), Expect = 4.0
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 30 EKDIQERFVRGSGPGGQ-AVAKTNNCVVLTHIP 61
++ + FV G G GG+ +V+ N V+ H P
Sbjct: 28 QQGLASHFVYGYGKGGKESVSHQNYPQVIKHTP 60
>gnl|CDD|224132 COG1211, IspD, 4-diphosphocytidyl-2-methyl-D-erithritol synthase
[Lipid metabolism].
Length = 230
Score = 24.5 bits (54), Expect = 4.4
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 44 GGQAVAKTNNCVVLTH 59
G QA++K ++ VL H
Sbjct: 91 GLQALSKYDSDWVLVH 106
>gnl|CDD|235373 PRK05249, PRK05249, soluble pyridine nucleotide transhydrogenase;
Provisional.
Length = 461
Score = 24.0 bits (53), Expect = 6.4
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 38 VRGSGPGGQAVA 49
V GSGP G+ A
Sbjct: 10 VIGSGPAGEGAA 21
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
0.320 0.136 0.392
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,208,379
Number of extensions: 221879
Number of successful extensions: 233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 233
Number of HSP's successfully gapped: 27
Length of query: 64
Length of database: 10,937,602
Length adjustment: 35
Effective length of query: 29
Effective length of database: 9,385,212
Effective search space: 272171148
Effective search space used: 272171148
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 (24.1 bits)