RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043141
(135 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 = 94.6 bits (236), Expect = 3e-26
Identities = 33/59 (55%), Positives = 46/59 (77%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA 89
+ +DT++SSGPGGQ++NK ESAVR+ H+PTG++ + E+RSQHKNR AL RL+ L
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKALERLKAKLY 72
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 95.0 bits (237), Expect = 3e-24
Identities = 33/68 (48%), Positives = 48/68 (70%), Gaps = 4/68 (5%)
Query: 21 LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80
+E+ +L +DTY+SSG GGQH+NK +SAVRI H+PTG++ Q +RSQH+N+ SA
Sbjct: 230 IEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASA 285
Query: 81 LSRLRTLL 88
+ L+ L
Sbjct: 286 MKMLKAKL 293
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 94.0 bits (235), Expect = 5e-24
Identities = 28/54 (51%), Positives = 41/54 (75%)
Query: 33 EMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRT 86
+DT++SSG GGQH+N +SAVRI H+PTG++ + ++RSQHKN+ A+ LR
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRA 277
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 89.6 bits (223), Expect = 3e-22
Identities = 29/57 (50%), Positives = 42/57 (73%)
Query: 33 EMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA 89
+DT++SSG GGQH+N +SAVRI H+PTG++ + ++RSQHKN+ A+ LR L
Sbjct: 226 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLY 282
>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 = 87.1 bits (216), Expect = 2e-21
Identities = 32/54 (59%), Positives = 42/54 (77%)
Query: 35 DTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
DTY++SG GGQH+NK +SAVRI H+PTG++ Q DRSQHKN+ SA+ L+ L
Sbjct: 240 DTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKL 293
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 84.5 bits (209), Expect = 2e-20
Identities = 33/58 (56%), Positives = 43/58 (74%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
+ +DTY+SSG GGQH+N +SAVRI H+PTG++ Q ++RSQHKNR A S LR L
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARL 257
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 84.1 bits (208), Expect = 2e-20
Identities = 34/71 (47%), Positives = 50/71 (70%), Gaps = 4/71 (5%)
Query: 22 ELTDDELFR----ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNR 77
ELTDD+ + ++DTY++ G GGQH+NK ESAVRI H+PTG++ Q +RSQH N+
Sbjct: 184 ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNK 243
Query: 78 VSALSRLRTLL 88
+A+ L++ L
Sbjct: 244 ETAMKMLKSKL 254
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 81.9 bits (203), Expect = 4e-20
Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 4/65 (6%)
Query: 21 LELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80
+E+ DD+L +DTY++SG GGQH+NK +SAVR+ H+PTG++ +RSQH N+ A
Sbjct: 105 IEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALA 160
Query: 81 LSRLR 85
L+
Sbjct: 161 RKMLK 165
>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 = 83.6 bits (207), Expect = 4e-20
Identities = 29/58 (50%), Positives = 43/58 (74%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
+ +DT++SSG GGQH+N +SAVRI H+PTG++ + ++RSQHKN+ A+ LR L
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARL 279
>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 = 72.1 bits (177), Expect = 1e-16
Identities = 32/68 (47%), Positives = 42/68 (61%), Gaps = 4/68 (5%)
Query: 22 ELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81
E T+DE+ E T +SSGPGGQH+NK ESAVR H+ +G+ + +RSQH N+ A
Sbjct: 102 EATEDEIRFE----TLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLAT 157
Query: 82 SRLRTLLA 89
L LA
Sbjct: 158 LLLAVRLA 165
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 68.9 bits (169), Expect = 2e-15
Identities = 25/60 (41%), Positives = 36/60 (60%)
Query: 30 RECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLA 89
E +T +SSGPGGQH+NK +SAVR H+ +G+ + +RSQH N+ A + L
Sbjct: 107 DEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLE 166
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 70.5 bits (172), Expect = 2e-15
Identities = 28/50 (56%), Positives = 35/50 (70%)
Query: 35 DTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRL 84
D Y+SSG GGQH+NK ESAVRI H+PT + RSQH+NR +A+ L
Sbjct: 181 DVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKML 230
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 61.3 bits (148), Expect = 4e-12
Identities = 27/58 (46%), Positives = 38/58 (65%)
Query: 31 ECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLL 88
+ ++DTY++SG GGQH+N +SAVRI H PT + +RSQ KNR A+ L+ L
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKL 255
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 47.5 bits (114), Expect = 8e-08
Identities = 31/95 (32%), Positives = 42/95 (44%), Gaps = 32/95 (33%)
Query: 21 LELTDDELFRECEMDTYKSSGPGGQHINKRESAV-------------------------R 55
L + ++EL E ++SGPGGQ++NK +AV R
Sbjct: 8 LVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHR 63
Query: 56 IKHVPTGVIA-QAAEDRSQHKNRVSALSRLRTLLA 89
I GVI +A E RSQ +NR AL RL L+
Sbjct: 64 I--TKDGVIVIKAQEFRSQERNREDALERLVALIR 96
>gnl|CDD|184621 PRK14324, glmM, phosphoglucosamine mutase; Provisional.
Length = 446
Score = 26.9 bits (60), Expect = 3.3
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 78 VSALSRLRTLLALNVRSSVKLDAYSPPPQLLQILP 112
VSAL +L ++S L+ + PQLL L
Sbjct: 345 VSALQVSALMLESKKKASEALNPFELYPQLLVNLK 379
>gnl|CDD|132730 cd06932, NR_LBD_PPAR, The ligand binding domain of peroxisome
proliferator-activated receptors. The ligand binding
domain (LBD) of peroxisome proliferator-activated
receptors (PPAR): Peroxisome proliferator-activated
receptors (PPARs) are members of the nuclear receptor
superfamily of ligand-activated transcription factors.
PPARs play important roles in regulating cellular
differentiation, development and lipid metabolism.
Activated PPAR forms a heterodimer with the retinoid X
receptor (RXR) that binds to the hormone response
element located upstream of the peroxisome proliferator
responsive genes and interacts with co-activators. There
are three subtypes of peroxisome proliferator activated
receptors, alpha, beta (or delta), and gamma, each with
a distinct tissue distribution. Several essential fatty
acids, oxidized lipids and prostaglandin J derivatives
can bind and activate PPAR. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, PPAR has a central well conserved
DNA binding domain (DBD), a variable N-terminal
regulatory domain, a flexible hinge a nd a C-terminal
ligand binding domain (LBD).
Length = 259
Score = 27.0 bits (60), Expect = 3.5
Identities = 28/107 (26%), Positives = 42/107 (39%), Gaps = 19/107 (17%)
Query: 15 SSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAED--RS 72
+ K N LELTD EL C + PG + R+ RI+ + QA E +
Sbjct: 154 AEKFNALELTDSELALFCAVIILSPDRPG---LINRKPVERIQE----HVLQALELQLKK 206
Query: 73 QHKNR-------VSALSRLRTLL---ALNVRSSVKLDAYSPPPQLLQ 109
H + + + LR L+ V+ K + + P LLQ
Sbjct: 207 NHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQ 253
>gnl|CDD|214880 smart00880, CHAD, The CHAD domain is an alpha-helical domain
functionally associated with some members of the
adenylate cyclase family. It has conserved histidines
that may chelate metals.
Length = 262
Score = 26.2 bits (58), Expect = 5.5
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 45 QHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLAL 90
H+ E+AVR P + H+ RV AL RLR+ L L
Sbjct: 7 DHLLANEAAVREDEDPEAL----------HQLRV-ALRRLRSALRL 41
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 0.127 0.361
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,342,397
Number of extensions: 528291
Number of successful extensions: 316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 24
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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 (24.3 bits)