RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13491
(69 letters)
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 54.0 bits (130), Expect = 9e-12
Identities = 19/28 (67%), Positives = 25/28 (89%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVNPKR 30
+ ++ V+TA+A+DESLFRGRQIKV PKR
Sbjct: 49 SDKESVRTALALDESLFRGRQIKVMPKR 76
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 46.4 bits (110), Expect = 9e-09
Identities = 20/29 (68%), Positives = 23/29 (79%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVNPKRT 31
A RD V+ A+A+DES FRGR IKV PKRT
Sbjct: 49 ATRDSVEAAVALDESSFRGRVIKVLPKRT 77
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L)
and similar proteins. PABPs are highly conserved
proteins that bind to the poly(A) tail present at the
3' ends of most eukaryotic mRNAs. They have been
implicated in the regulation of poly(A) tail length
during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping.
ePABP-2 is predominantly located in the cytoplasm and
PABP-2 is located in the nucleus. In contrast to the
type I PABPs containing four copies of RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), the type II PABPs
contains a single highly-conserved RRM. This subfamily
also includes Saccharomyces cerevisiae RBP29 (SGN1,
YIR001C) gene encoding cytoplasmic mRNA-binding protein
Rbp29 that binds preferentially to poly(A). Although
not essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 39.6 bits (93), Expect = 3e-06
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 6 DEVQTAMAMDESLFRGRQIKV 26
V+ A+ ++ES FRGRQIKV
Sbjct: 52 SSVENALLLNESEFRGRQIKV 72
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 26.7 bits (60), Expect = 0.38
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 5 RDEVQTAMAMDESLFRGRQIKV 26
+D V A+ ++ +GR+I+V
Sbjct: 51 KDSVALALKLNGIKLKGRKIRV 72
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 27.2 bits (61), Expect = 0.62
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 15 DESLFRGRQIKVNPKRTN-RPGIST 38
D SLF + I V PK TN GIS
Sbjct: 518 DYSLFADKAIVVKPKSTNFGLGISI 542
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 26.6 bits (60), Expect = 0.72
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 42 GGPRGRGRGRVSRGA 56
GG RG GR R RGA
Sbjct: 102 GGGRGGGRQRARRGA 116
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 24.9 bits (55), Expect = 2.0
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVN 27
A++ V A+ ++ ++F GR +KVN
Sbjct: 52 AEQTSVINALKLNGAMFGGRPLKVN 76
>gnl|CDD|177546 PHA03151, PHA03151, hypothetical protein; Provisional.
Length = 259
Score = 25.1 bits (54), Expect = 3.2
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 16 ESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSR 54
E+ R R K+ + IST++ PR R R S
Sbjct: 186 EAFIRQRAQMAGKKKKGKRSISTSDDEPPRKSRRKRHSH 224
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3
subunit 7 (eIF-3). This family is made up of eukaryotic
translation initiation factor 3 subunit 7 (eIF-3
zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is
a multi-subunit complex that is required for binding of
mRNA to 40 S ribosomal subunits, stabilisation of
ternary complex binding to 40 S subunits, and
dissociation of 40 and 60 S subunits. These functions
and the complex nature of eIF3 suggest multiple
interactions with many components of the translational
machinery. The gene coding for the protein has been
implicated in cancer in mammals.
Length = 517
Score = 24.2 bits (53), Expect = 6.2
Identities = 11/42 (26%), Positives = 16/42 (38%)
Query: 27 NPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGYRPVRRA 68
P+ RGG R + R + RG +R +R A
Sbjct: 111 GPQGKRGMTSRRAKRGGQRKQKRFQTGRGGRRGARHRRLREA 152
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 24.2 bits (53), Expect = 6.9
Identities = 9/27 (33%), Positives = 9/27 (33%)
Query: 28 PKRTNRPGISTTNRGGPRGRGRGRVSR 54
P R RP R R R R R
Sbjct: 395 PLRLTRPRTGNGPRRSGAPRNRRRRKR 421
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 24.2 bits (52), Expect = 7.0
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 21 GRQIKVNPKR---TNRPGISTTNRGGPRGRGRG 50
Q + K ++ G S RG RGRGRG
Sbjct: 497 NDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRG 529
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 23.8 bits (51), Expect = 8.4
Identities = 15/49 (30%), Positives = 17/49 (34%)
Query: 14 MDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGY 62
MD GR I+VNP GG G G G GG+
Sbjct: 96 MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGGF 144
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 23.6 bits (52), Expect = 9.4
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 49 RGRVSRGAA 57
RGRV RGAA
Sbjct: 570 RGRVGRGAA 578
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 0.135 0.394
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,555,825
Number of extensions: 260737
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 31
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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)