RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045445
(128 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 = 61.0 bits (149), Expect = 3e-13
Identities = 21/35 (60%), Positives = 27/35 (77%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
+ +DT++SSGPGGQ+ NK ESAVRL H+PT V
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVV 48
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 63.0 bits (154), Expect = 4e-13
Identities = 20/36 (55%), Positives = 26/36 (72%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
+ +DTY++SG GGQH NK +SAVRL H+PT V
Sbjct: 111 DLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVL 146
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 62.2 bits (152), Expect = 2e-12
Identities = 19/31 (61%), Positives = 25/31 (80%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
+ +DTY+SSG GGQH NK +SAVR+ H+PT
Sbjct: 236 DLRIDTYRSSGAGGQHVNKTDSAVRITHIPT 266
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 59.7 bits (146), Expect = 1e-11
Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 36 EMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
+DT++SSG GGQH N +SAVR+ H+PT
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPT 252
>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 = 57.1 bits (138), Expect = 4e-11
Identities = 27/60 (45%), Positives = 34/60 (56%), Gaps = 14/60 (23%)
Query: 20 KKNYF----------ELTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVN 69
+KN+F E T+DE R +T +SSGPGGQH NK ESAVR H+ + SV
Sbjct: 87 RKNWFIGVQRFSASEEATEDE-IR---FETLRSSGPGGQHVNKTESAVRATHLASGISVK 142
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 57.0 bits (138), Expect = 5e-11
Identities = 24/55 (43%), Positives = 35/55 (63%), Gaps = 6/55 (10%)
Query: 20 KKNYF----ELTDDEQFRECEM--DTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
+KN+F + DE+ + E+ +T +SSGPGGQH NK +SAVR H+ + SV
Sbjct: 88 RKNWFVGIGRFSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISV 142
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 57.1 bits (138), Expect = 9e-11
Identities = 28/62 (45%), Positives = 39/62 (62%), Gaps = 5/62 (8%)
Query: 8 YNDNCS-STSSSSKKNYFELTDDEQFR----ECEMDTYKSSGPGGQHRNKRESAVRLKHV 62
+N N TS +S + ELTDD+ + ++DTY++ G GGQH NK ESAVR+ H+
Sbjct: 166 FNANGKRQTSFASVEVLPELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHI 225
Query: 63 PT 64
PT
Sbjct: 226 PT 227
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 56.8 bits (138), Expect = 1e-10
Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 36 EMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
+DT++SSG GGQH N +SAVR+ H+PT
Sbjct: 226 RIDTFRSSGAGGQHVNTTDSAVRITHLPT 254
>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 = 55.6 bits (134), Expect = 4e-10
Identities = 24/54 (44%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 15 TSSSSKKNYFELTDDEQF----RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
TS +S E+ DD + +DTY++SG GGQH NK +SAVR+ H+PT
Sbjct: 213 TSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPT 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 = 54.7 bits (132), Expect = 7e-10
Identities = 18/35 (51%), Positives = 25/35 (71%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
+ +DT++SSG GGQH N +SAVR+ H+PT V
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVV 256
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 53.3 bits (128), Expect = 2e-09
Identities = 19/35 (54%), Positives = 25/35 (71%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
+ +DTY+SSG GGQH N +SAVR+ H+PT V
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVV 234
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 50.8 bits (121), Expect = 2e-08
Identities = 20/31 (64%), Positives = 24/31 (77%)
Query: 38 DTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
D Y+SSG GGQH NK ESAVR+ H+PT + V
Sbjct: 181 DVYRSSGAGGQHVNKTESAVRITHIPTNTVV 211
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 45.1 bits (106), Expect = 2e-06
Identities = 18/35 (51%), Positives = 26/35 (74%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSV 68
+ ++DTY++SG GGQH N +SAVR+ H PT + V
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVV 232
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 36.7 bits (86), Expect = 8e-04
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 41 KSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
++SGPGGQ+ NK +AV L+ ASS LP ++L
Sbjct: 21 RASGPGGQNVNKVSTAVELRFDIAASS------LPEFYKERLL 57
>gnl|CDD|223895 COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid
metabolism].
Length = 317
Score = 28.8 bits (65), Expect = 0.81
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 45 PGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQ 81
GG HR+ +A LK+ LD LP +LL
Sbjct: 268 LGGAHRDPEAAAEALKNALLKELHELDK-LPEEELLA 303
>gnl|CDD|193468 pfam12995, DUF3879, Domain of unknown function, E. rectale Gene
description (DUF3879). Based on Eubacterium rectale
gene EUBREC_1343. As seen in gene expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14
737), it appears to be upregulated in the presence of
Bacteroides thetaiotaomicron vs when isolated in
culture.
Length = 186
Score = 26.8 bits (59), Expect = 3.2
Identities = 15/42 (35%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 5 SCNYNDNCSSTSSSSKKNYFELTDDEQFRE---CEMDTYKSS 43
+CN S SS + FELT E E DT K S
Sbjct: 74 NCNSKKRIISIPESSMEEMFELTKKEFLMENGVHNGDTTKRS 115
>gnl|CDD|182809 PRK10884, PRK10884, SH3 domain-containing protein; Provisional.
Length = 206
Score = 26.2 bits (58), Expect = 5.1
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 36 EMDTYKSSGPGGQHR 50
E++TY SGPG Q+R
Sbjct: 31 ELNTYVRSGPGDQYR 45
>gnl|CDD|188230 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha
chain. This model represents a small clade of
ribonucleoside-diphosphate reductase, alpha chains which
are sufficiently divergent from the usual Class I RNR
alpha chains (NrdE or NrdA, TIGR02506) as to warrant
their own model. The genes from Thermus thermophilus,
Dichelobacter and Salinibacter are adjacent to the usual
RNR beta chain [Purines, pyrimidines, nucleosides, and
nucleotides, 2'-Deoxyribonucleotide metabolism].
Length = 548
Score = 26.4 bits (58), Expect = 5.3
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 26 LTDDEQFRECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNL 70
LTD+E+ +K+ Q R +A R KH+ A S+NL
Sbjct: 459 LTDEEK------SVFKTFYEISQMAIIRLAAARQKHIDQAQSLNL 497
>gnl|CDD|149033 pfam07742, BTG, BTG family.
Length = 119
Score = 24.9 bits (55), Expect = 9.4
Identities = 11/36 (30%), Positives = 13/36 (36%), Gaps = 9/36 (25%)
Query: 74 LPPPQLLQILPPKFTI---------RCSEVGPQIRP 100
L LL +LP + TI R E GP
Sbjct: 81 LDYEDLLSLLPKELTIWVDPGEVSYRIGENGPICVL 116
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
0.315 0.132 0.389
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,167,851
Number of extensions: 515317
Number of successful extensions: 421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 421
Number of HSP's successfully gapped: 25
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)