RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1572
(74 letters)
>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif. Binding is not
sequence specific but is highly specific for double
stranded RNA. Found in a variety of proteins including
dsRNA dependent protein kinase PKR, RNA helicases,
Drosophila staufen protein, E. coli RNase III, RNases
H1, and dsRNA dependent adenosine deaminases.
Length = 68
Score = 29.9 bits (68), Expect = 0.027
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 44 VCHGQGKTQQEAKTVAAHNAIEYL 67
G+G +++EAK AA A+ L
Sbjct: 45 TGEGEGSSKKEAKQNAAEAALRKL 68
>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif.
Length = 67
Score = 29.2 bits (66), Expect = 0.046
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 44 VCHGQGKTQQEAKTVAAHNAIEYL 67
G+G +++EAK AA A+ L
Sbjct: 43 TGEGEGSSKKEAKQRAAEAALRSL 66
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif. Sequences
gathered for seed by HMM_iterative_training Putative
motif shared by proteins that bind to dsRNA. At least
some DSRM proteins seem to bind to specific RNA
targets. Exemplified by Staufen, which is involved in
localisation of at least five different mRNAs in the
early Drosophila embryo. Also by interferon-induced
protein kinase in humans, which is part of the cellular
response to dsRNA.
Length = 66
Score = 27.3 bits (61), Expect = 0.25
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 44 VCHGQGKTQQEAKTVAAHNAIEYL 67
G G +++EAK +AA A++ L
Sbjct: 43 YGTGTGSSKKEAKQLAAEKALQKL 66
>gnl|CDD|233001 TIGR00509, bisC_fam, molybdopterin guanine dinucleotide-containing
S/N-oxide reductases. This enzyme family shares
sequence similarity and a requirement for a molydenum
cofactor as the only prosthetic group. The form of the
cofactor is a single molybdenum atom coordinated by two
molybdopterin guanine dinucleotide molecules. Members of
the family include biotin sulfoxide reductase,
dimethylsulfoxide reductase, and trimethylamine-N-oxide
reductase, although a single member may show all those
activities and related activities; it may not be
possible to resolve the primary function for members of
this family by sequence comparison alone. A number of
similar molybdoproteins in which the N-terminal region
contains a CXXXC motif and may bind an iron-sulfur
cluster are excluded from this set, including formate
dehydrogenases and nitrate reductases. Also excluded is
the A chain of a heteromeric, anaerobic DMSO reductase,
which also contains the CXXXC motif.
Length = 770
Score = 27.8 bits (62), Expect = 0.41
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 9/62 (14%)
Query: 16 TNGSNSIAFLHSTGQFQALVQLATYPVAVCHGQG---------KTQQEAKTVAAHNAIEY 66
+ G+ + H G + Q T+PV + + + KT Q A + H EY
Sbjct: 137 STGAAQVIMPHVVGDMEVYEQQTTWPVILENSKVLVLWGADPLKTSQIAWGIPDHGGYEY 196
Query: 67 LR 68
L
Sbjct: 197 LE 198
>gnl|CDD|217670 pfam03681, UPF0150, Uncharacterized protein family (UPF0150).
This family of small proteins is uncharacterized. In
CC_3185 this domain is found next to a DNA binding
helix-turn-helix domain pfam01402, which suggests that
this is some kind of ligand binding domain. The
structure of this domain suggests that these domains
oligomerise and due to structural similarities may bind
to RNA. The monomer adopts an
alpha-beta-beta-beta-alpha fold and forms a
homotetramer. Based on the properties and functions of
structural homologues of the HB8 monomer, the protein
is speculated to be involved in RNA metabolism,
including RNA binding and cleavage.
Length = 48
Score = 25.9 bits (58), Expect = 0.57
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 45 CHGQGKTQQEAKTVAAHNAIE 65
C QG+T +EA A A+E
Sbjct: 24 CITQGETLEEALENAK-EALE 43
>gnl|CDD|216101 pfam00755, Carn_acyltransf, Choline/Carnitine o-acyltransferase.
Length = 590
Score = 26.9 bits (60), Expect = 0.91
Identities = 11/51 (21%), Positives = 19/51 (37%)
Query: 13 LISTNGSNSIAFLHSTGQFQALVQLATYPVAVCHGQGKTQQEAKTVAAHNA 63
++ NGS + HS +V L + V K+ E V + +
Sbjct: 297 IVFKNGSTGLNAEHSPADGIPVVHLCEFVYKVDEQILKSTPEGLPVGSPSV 347
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 26.8 bits (60), Expect = 0.95
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 30 QFQALVQLATYPVAVCHGQGKTQQEAKTVAAHNAIEYL 67
+F V + + G+G++++EA+ AA A++ L
Sbjct: 194 EFTVEVAVGGKELGT--GKGRSKKEAEQAAAEQALKKL 229
>gnl|CDD|237664 PRK14294, PRK14294, chaperone protein DnaJ; Provisional.
Length = 366
Score = 26.7 bits (59), Expect = 1.2
Identities = 9/18 (50%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 41 PVAVCHGQGKTQQEAKTV 58
P CHGQG+ + KTV
Sbjct: 199 PCKTCHGQGRVRVS-KTV 215
>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional.
Length = 397
Score = 25.5 bits (56), Expect = 2.8
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 38 ATYPVAVCHGQGKTQQEAKTV 58
AT CHG G+ +Q +KT+
Sbjct: 178 ATETCPTCHGSGEVRQASKTM 198
>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial. This family
consists of bacterial examples of ribonuclease III. This
enzyme cleaves double-stranded rRNA. It is involved in
processing ribosomal RNA precursors. It is found even in
minimal genones such as Mycoplasma genitalium and
Buchnera aphidicola, and in some cases has been shown to
be an essential gene. These bacterial proteins contain a
double-stranded RNA binding motif (pfam00035) and a
ribonuclease III domain (pfam00636). Eukaryotic homologs
tend to be much longer proteins with additional domains,
localized to the nucleus, and not included in this
family [Transcription, RNA processing].
Length = 220
Score = 25.2 bits (56), Expect = 2.9
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 47 GQGKTQQEAKTVAAHNAIEYL 67
G+GK+++EA+ AA A+E L
Sbjct: 200 GKGKSKKEAEQNAAKAALEKL 220
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1. Rev1 is a translesion
synthesis (TLS) polymerase found in eukaryotes.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and
low processivity. They use damaged DNA as templates
and insert nucleotides opposite the lesions. Rev1 has
both structural and enzymatic roles. Structurally, it
is believed to interact with other nonclassical
polymerases and replication machinery to act as a
scaffold. Enzymatically, it catalyzes the specific
insertion of dCMP opposite abasic sites. Rev1
interacts with the Rev7 subunit of the B-family TLS
polymerase Pol zeta (Rev3/Rev7). Rev1 is known to
actively promote the introduction of mutations,
potentially making it a significant target for cancer
treatment.
Length = 404
Score = 25.4 bits (56), Expect = 3.3
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 37 LATYPVAVCHGQGKT 51
L PVAVCHG+G
Sbjct: 69 LKGKPVAVCHGKGPN 83
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 97
Score = 24.8 bits (54), Expect = 3.6
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 22 IAFLHSTGQFQALVQLATYPVAV 44
IA G FQAL+Q P AV
Sbjct: 33 IAIFEKNGGFQALIQYPDVPTAV 55
>gnl|CDD|236551 PRK09533, PRK09533, bifunctional transaldolase/phosoglucose
isomerase; Validated.
Length = 948
Score = 24.5 bits (54), Expect = 5.5
Identities = 7/7 (100%), Positives = 7/7 (100%)
Query: 24 FLHSTGQ 30
FLHSTGQ
Sbjct: 864 FLHSTGQ 870
>gnl|CDD|235779 PRK06327, PRK06327, dihydrolipoamide dehydrogenase; Validated.
Length = 475
Score = 24.1 bits (53), Expect = 9.7
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 7/46 (15%)
Query: 19 SNSIAFLHSTGQFQALVQLATYPVAVCHGQGKTQQEAKTVAAHNAI 64
N I L G F A Y + V T ++ + A + I
Sbjct: 112 KNKITVLKGRGSFVGKTD-AGYEIKV------TGEDETVITAKHVI 150
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 0.128 0.358
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,306,337
Number of extensions: 229165
Number of successful extensions: 188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 14
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
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)