RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10308
(225 letters)
>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family
proteins. This subfamily corresponds to the RRM of the
GW182 family which includes three paralogs of TNRC6
(GW182-related) proteins comprising GW182/TNGW1, TNRC6B
(containing three isoforms) and TNRC6C in mammal, a
single Drosophila ortholog (dGW182, also called Gawky)
and two Caenorhabditis elegans orthologs AIN-1 and
AIN-2, which contain multiple miRNA-binding sites and
have important functions in miRNA-mediated translational
repression, as well as mRNA degradation in Metazoa. The
GW182 family proteins directly interact with Argonaute
(Ago) proteins, and thus function as downstream
effectors in the miRNA pathway, responsible for
inhibition of translation and acceleration of mRNA
decay. Members in this family are characterized by an
abnormally high content of glycine/tryptophan (G/W)
repeats, one or more glutamine (Q)-rich motifs, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The only exception is the worm protein that does not
contain a recognizable RRM domain. The GW182 family
proteins are recruited to miRNA targets through an
interaction between their N-terminal domain and an
Argonaute protein. Then they promote translational
repression and/or degradation of miRNA targets through
their C-terminal silencing domain. .
Length = 71
Score = 122 bits (309), Expect = 1e-36
Identities = 47/70 (67%), Positives = 58/70 (82%)
Query: 56 GTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNC 115
+W++L+NLTPQIDGSTL+TLC+QHGPL FHL L H AL +YS++EEA KAQ LNNC
Sbjct: 1 SSWLVLRNLTPQIDGSTLRTLCMQHGPLLTFHLNLRHGNALIRYSSKEEAAKAQSALNNC 60
Query: 116 ILGNTTIFAE 125
+LGNTT+ AE
Sbjct: 61 VLGNTTLLAE 70
>gnl|CDD|241156 cd12712, RRM_TNRC6B, RNA recognition motif in vertebrate
trinucleotide repeat-containing gene 6B protein
(TNRC6B). This subgroup corresponds to the RRM of
TNRC6B, one of three GW182 paralogs in mammalian
genomes. It is involved in miRNA-mediated mRNA
degradation. TNRC6B is composed of an N-terminal
glycine/tryptophan (G/W)-rich region; a
ubiquitin-associated (UBA) domain and a glutamine
(Q)-rich region in the middle region; a middle G/W-rich
region, a RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal G/W-rich region, at the C-terminus.
TNRC6B directly interacts with Argonaute (Ago) proteins
through its N-terminal glycine/tryptophan (G/W)-rich
region that is called Ago protein-binding domain. TNRC6B
is enriched in P-bodies and its Q-rich domain is
responsible for P-body localization. A bipartite
C-terminal region including the middle and C-terminal
G/W-rich regions is referred as silencing domain that
triggers silencing of bound transcripts by inhibiting
protein expression and promoting mRNA decay via
deadenylation. The C-terminal half of TNRC6B comprising
an RRM domain exerts a strong translation inhibition
potential, which does not require either association
with Agos or localization to P-bodies. .
Length = 83
Score = 113 bits (283), Expect = 1e-32
Identities = 49/81 (60%), Positives = 60/81 (74%)
Query: 58 WVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCIL 117
W++L NLTPQIDGSTL+T+C+QHGPL FHL L AL +YST++EA KAQ L+ C+L
Sbjct: 3 WLVLHNLTPQIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVL 62
Query: 118 GNTTIFAEAPSDAEVQSLLAH 138
GNTTI AE +D EV LA
Sbjct: 63 GNTTILAEFATDEEVSRFLAQ 83
>gnl|CDD|241155 cd12711, RRM_TNRC6A, RNA recognition motif in vertebrate GW182
autoantigen. This subgroup corresponds to the RRM of
the GW182 autoantigen, also termed trinucleotide
repeat-containing gene 6A protein (TNRC6A), or CAG
repeat protein 26, or EMSY interactor protein, or
protein GW1, or glycine-tryptophan protein of 182 kDa, a
phosphorylated cytoplasmic autoantigen involved in
stabilizing and/or regulating translation and/or storing
several different mRNAs. GW182 is characterized by
multiple glycine/tryptophan (G/W) repeats and is a
critical component of GW bodies (GWBs, also called
mammalian processing bodies, or P bodies). The mRNAs
associated with GW182 are presumed to reside within
GWBs. GW182 has been shown to bind multiple Ago-miRNA
complexes, and thus plays a key role in miRNA-mediated
translational repression and mRNA degradation. In the
absence of Ago2, GW182 may induce translational
silencing effect. GW182 is composed of an N-terminal
G/W-rich region containing an Ago hook responsible for
Ago protein-binding; a ubiquitin-associated (UBA) domain
and a glutamine (Q)-rich region in the middle region; a
middle G/W-rich region, a RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal G/W-rich
region, at the C-terminus. A bipartite C-terminal region
including the middle and C-terminal G/W-rich regions is
referred to as silencing domain that triggers silencing
of bound transcripts by inhibiting protein expression
and promoting mRNA decay via deadenylation. .
Length = 83
Score = 112 bits (282), Expect = 2e-32
Identities = 49/81 (60%), Positives = 62/81 (76%)
Query: 58 WVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCIL 117
W++LKNLTPQIDGSTL+TLC+QHGPL FHL L H AL +YS++EE +KAQ +L+ C+L
Sbjct: 3 WLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVL 62
Query: 118 GNTTIFAEAPSDAEVQSLLAH 138
GNTTI AE S+ E+ A
Sbjct: 63 GNTTILAEFASEEEISRFFAQ 83
>gnl|CDD|241157 cd12713, RRM_TNRC6C, RNA recognition motif in vertebrate
trinucleotide repeat-containing gene 6C protein
(TNRC6C). This subgroup corresponds to the RRM of
TNRC6C, one of three GW182 paralogs in mammalian
genomes. It is enriched in P-bodies and important for
efficient miRNA-mediated repression. TNRC6C is composed
of an N-terminal glycine/tryptophan (G/W)-rich region
containing an Ago hook responsible for Ago
protein-binding; a ubiquitin-associated (UBA) domain and
a glutamine (Q)-rich region in the middle region; a
middle G/W-rich region, a RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal G/W-rich
region, at the C-terminus. A bipartite C-terminal region
including the middle and C-terminal G/W-rich regions is
referred as silencing domain that triggers silencing of
bound transcripts by inhibiting protein expression and
promoting mRNA decay via deadenylation. The C-terminal
half containing the RRM domain functions as a key
effector domain mediating protein synthesis repression
by TNRC6C. .
Length = 83
Score = 107 bits (267), Expect = 3e-30
Identities = 48/82 (58%), Positives = 62/82 (75%)
Query: 57 TWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCI 116
+W++L+NLTPQIDGSTL+TLC+QHGPL FHL L A+ +YS++EEA KAQ +L+ C+
Sbjct: 2 SWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCV 61
Query: 117 LGNTTIFAEAPSDAEVQSLLAH 138
LGNTTI AE + EV LA
Sbjct: 62 LGNTTILAEFAGEEEVNRFLAQ 83
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 46.0 bits (110), Expect = 2e-07
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 73 LKTLCVQHGPLQNFHLYLNH-SLALAKYSTREEAIKAQGNLNNCILGNTTIFAE 125
L L G ++ L A ++ST E A KA LN + G + +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 46.1 bits (110), Expect = 3e-07
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL-----ALAKYSTREEAIKAQGNLN 113
+ + NL P L+ L + G +++ + + A ++ + E+A KA LN
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 114 NCILGNTTIFAE 125
L +
Sbjct: 61 GKELDGRKLKVS 72
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 41.0 bits (97), Expect = 2e-05
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL------ALAKYSTREEAIKAQGNL 112
+ + NL P L+ L + G +++ L + A ++ + E+A KA L
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 113 NNCILGNTTI 122
N L +
Sbjct: 62 NGKELDGRPL 71
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 38.7 bits (91), Expect = 1e-04
Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 59 VLLKNLTPQIDGSTL-KTLCVQHGPLQNFHLYLNHSL----ALAKYSTREEAIKAQGNLN 113
+ ++NL P + L + +G ++ L N A ++++ E+A A LN
Sbjct: 1 LYVRNLPPSVTEEDLREFFS-PYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLN 59
Query: 114 NCILGNTTI 122
+L T+
Sbjct: 60 GLVLDGRTL 68
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 37.6 bits (88), Expect = 4e-04
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYSTREEAIKAQGNLN 113
+ + NL P LK L + GP+++ + + + A ++ E+A KA LN
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 114 NCILGNTTI 122
LG +
Sbjct: 61 GKELGGREL 69
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 37.3 bits (86), Expect = 6e-04
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 61 LKNLTPQIDGSTLKTLCVQHG-PLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGN 119
L N+ + L+TL G ++ F + +H +AL + ST EEAI+A +L+N LG
Sbjct: 8 LSNIPQSVTEEDLRTLFANTGGTVKAFKFFQDHKMALLQMSTVEEAIQALIDLHNYNLGE 67
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB 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. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 36.5 bits (85), Expect = 0.001
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 61 LKNLTPQIDGSTLKTLCVQH-GPLQNFHLYLNHS-LALAKYSTREEAIKAQGNLNNCILG 118
L N+ P + LK L Q G ++ F + +AL + + EEAI+A L+N L
Sbjct: 4 LSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQLS 63
Query: 119 NTT 121
++
Sbjct: 64 ESS 66
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 6/71 (8%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNCI 116
NL + + L G ++ L + S +K Y+++ A+KA+ L+
Sbjct: 6 NLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQ 65
Query: 117 LGNTTIFAEAP 127
+G + +
Sbjct: 66 IGGRKLQVDWA 76
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 36.0 bits (84), Expect = 0.002
Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 12/79 (15%)
Query: 59 VLLKNL-TP-QIDGSTL--------KTLCVQHGPLQNFHLYLNHSL--ALAKYSTREEAI 106
V+LKN+ P + C + GP+++ + N K+ T E A
Sbjct: 4 VILKNMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQ 63
Query: 107 KAQGNLNNCILGNTTIFAE 125
K LN I AE
Sbjct: 64 KCIQALNGRWFDGRQITAE 82
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 33.7 bits (78), Expect = 0.010
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 57 TWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKA 108
T +L+KNL L+ L + G L L + ++AL ++ +A KA
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKA 52
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 31.9 bits (73), Expect = 0.042
Identities = 13/60 (21%), Positives = 21/60 (35%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTTI 122
NL I K L ++G + L + TR A KA+ L+ + +
Sbjct: 8 NLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMRKGRQL 67
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and similar
proteins. This subfamily corresponds to the RRM of
Acinus, a caspase-3-activated nuclear factor that
induces apoptotic chromatin condensation after cleavage
by caspase-3 without inducing DNA fragmentation. It is
essential for apoptotic chromatin condensation and may
also participate in nuclear structural changes occurring
in normal cells. Acinus contains a P-loop motif and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), which
indicates Acinus might have ATPase and DNA/RNA-binding
activity. .
Length = 90
Score = 32.2 bits (74), Expect = 0.043
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 73 LKTLCVQHGPLQNFHLYLNH--SLALAKYSTREEAIKAQGNLNN 114
LK L + G +++ S YST EEA+ + L+
Sbjct: 18 LKELLSETGTGVIEGFWMDKIKSHCYVTYSTVEEAVATREALHG 61
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 30.6 bits (70), Expect = 0.12
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 95 ALAKYSTREEAIKAQGNLNN-CILGNTT 121
A K+S+REEA KA L+ + +
Sbjct: 44 AFVKFSSREEAQKAIEALHGKVTMPGAS 71
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 32.6 bits (73), Expect = 0.13
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNL 112
+ + NL + L+ L + GP++ L + A ++ + E A KA L
Sbjct: 118 LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEEL 177
Query: 113 NN 114
N
Sbjct: 178 NG 179
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both nuclear and
cytoplasmic roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 86
Score = 30.0 bits (68), Expect = 0.21
Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 68 IDGSTLKTLCVQHGPLQNFHLYLNHSL-ALAKYSTREEAIKAQGNLNNC 115
I + T+C HG + ++ + + A+ ++ + + A +A+ LN
Sbjct: 15 ITVDVIYTICNPHGKVLRIVIFRKNGVQAMVEFDSVDSAQRAKAALNGA 63
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 29.5 bits (67), Expect = 0.26
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHL 88
V + NL ++ L L +Q GP+ N H+
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHI 30
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a
major component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 31.4 bits (71), Expect = 0.27
Identities = 20/51 (39%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 9 PPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGG-WSGTW 58
P R PP G GG G+P GW GG G + G QP GG W
Sbjct: 23 PGGNRYPPQG--GGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGG 71
Score = 29.1 bits (65), Expect = 1.3
Identities = 18/45 (40%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 14 GPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTW 58
G P G GG G+P GW +P+GGG G G GG W
Sbjct: 36 GQPHG--GGWGQPHGGGWG-QPHGGGWGQPHGGGWGQGGGTHNQW 77
Score = 29.1 bits (65), Expect = 1.7
Identities = 20/51 (39%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 7 WGPPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGT-SQPQGGWSG 56
W R P G GG PP G +P+GGG G G QP GG G
Sbjct: 10 WNTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWG 60
Score = 27.1 bits (60), Expect = 6.5
Identities = 15/40 (37%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 7 WGPPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWG 46
WG P G GG G+P GW GGG N W
Sbjct: 43 WGQPHGGGWGQPHGGGWGQPHGGGW----GQGGGTHNQWN 78
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 29.5 bits (67), Expect = 0.30
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 63 NLTPQIDGSTLKTLCVQHGP-LQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTT 121
N++ ++ +K + GP ++ L+ +H AL ++ + +A KA +LN G T
Sbjct: 7 NVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEGALVEFESPSDAGKASLSLNGSQFGGKT 66
Query: 122 I 122
I
Sbjct: 67 I 67
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 29.5 bits (67), Expect = 0.36
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 80 HGPLQNFHLYLNH------SLALAKYSTREEAIKAQGNLNNCILGNTTI-----FAEAP 127
G ++N HL L+ AL +Y T++EA A LN L TI F + P
Sbjct: 30 FGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDWAFVKGP 88
>gnl|CDD|203945 pfam08439, Peptidase_M3_N, Oligopeptidase F. This domain is found
to the N-terminus of the pfam01432 domain in bacterial
and archaeal proteins including Oligoendopeptidase F. An
example of this protein is Lactococcus lactis PepF.
Length = 70
Score = 29.1 bits (66), Expect = 0.37
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 67 QIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKY--STREEAIKAQ 109
+ L+ L + L+ + YL + S EE + A
Sbjct: 4 ALPEEKLEALLEEDPELKPYRFYLEEIRRQKPHTLSEEEEKLLAA 48
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.6 bits (64), Expect = 0.61
Identities = 15/39 (38%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 81 GPLQNFHLYLNHS-----LALAKYSTREEAIKAQGNLNN 114
G L F L + S A AKYS R A A L+N
Sbjct: 26 GTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLHN 64
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 27.5 bits (62), Expect = 1.2
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 79 QHGPLQNFHLYLNHSLALAKYSTREEAIKA 108
+ G + N + N AL ++ST EEA KA
Sbjct: 25 KFGTIVNIQVNYNPESALVQFSTSEEAKKA 54
>gnl|CDD|241072 cd12628, RRM2_IGF2BP1, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM2 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. It promotes mRNA
stabilization and functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD. It stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus (HCV)
5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing
HCV internal ribosome entry site (IRES)-mediated
translation initiation via the 3'-UTR. IGF2BP1 contains
four hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. It also contains two putative nuclear export
signals (NESs) and a putative nuclear localization
signal (NLS). .
Length = 76
Score = 27.7 bits (61), Expect = 1.2
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 61 LKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS---LALAKYSTREEAIKAQGNLNNCIL 117
++N+ PQ+ L L Q+G ++N S + Y RE+ +A LN L
Sbjct: 5 IRNIPPQLRWEVLDGLLAQYGTVENCEQVNTDSETAVVNVTYGNREQTRQAIMKLNGHQL 64
Query: 118 GNTTI 122
N +
Sbjct: 65 ENHAL 69
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 27.6 bits (62), Expect = 1.5
Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 72 TLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCIL----GNTTIF 123
L + ++G +++ + YS+ E+A A LN L N ++
Sbjct: 19 ELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNKPLY 74
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 28.6 bits (64), Expect = 2.9
Identities = 10/35 (28%), Positives = 11/35 (31%)
Query: 9 PPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGN 43
P PR P GGG PP + G
Sbjct: 695 PQAPRPGGPPGGGGGLPPPPDLPAAAGPAPCGSSL 729
>gnl|CDD|226681 COG4228, COG4228, Mu-like prophage DNA circulation protein [General
function prediction only].
Length = 451
Score = 28.3 bits (63), Expect = 3.2
Identities = 28/86 (32%), Positives = 33/86 (38%), Gaps = 13/86 (15%)
Query: 131 EVQSLLAHL-SATANNNNNNNGGTGGWARGSSALSNKDTWSSGGGGGNTSQLWGTPSNPS 189
V L A L SA N +N T K SS G TS L TPS PS
Sbjct: 189 IVSDLSAFLKSAFGLKGNASNLLTAP----------KVGASSLAGL--TSVLVTTPSLPS 236
Query: 190 SGGSLWGAPPLDSVDRATPSSLNSFL 215
G P+DS+ RA + L +
Sbjct: 237 RGLGGQNMAPVDSIGRALSADLAAMP 262
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 26.4 bits (59), Expect = 3.9
Identities = 12/62 (19%), Positives = 24/62 (38%)
Query: 57 TWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCI 116
T V + NL + L+ G ++ ++ + A ++ T E A A +N
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 117 LG 118
+
Sbjct: 61 IN 62
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 28.3 bits (63), Expect = 4.3
Identities = 13/41 (31%), Positives = 15/41 (36%)
Query: 2 SSNDLWGPPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGG 42
SS L + GGG G+ GGGGGG
Sbjct: 58 SSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGG 98
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 27.8 bits (62), Expect = 5.9
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 61 LKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYSTREEAIKAQGNLNNC 115
+KNL + L+ L + G + + + L+ +S EEA +A ++
Sbjct: 290 VKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGR 349
Query: 116 ILG 118
+LG
Sbjct: 350 MLG 352
>gnl|CDD|185156 PRK15244, PRK15244, virulence protein SpvB; Provisional.
Length = 591
Score = 27.8 bits (61), Expect = 6.1
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 4 NDLWGPPKPRGPPPGMMGGGGKPPSNGWMV 33
N++ PP PPP MMGG P + W +
Sbjct: 363 NNMMPPP----PPPPMMGGNSSRPKSKWAI 388
>gnl|CDD|178257 PLN02651, PLN02651, cysteine desulfurase.
Length = 364
Score = 27.3 bits (61), Expect = 6.3
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 181 LWGTPSNPSSGGSLWGAPPLDSVDRA 206
L NP S L+G D+V++A
Sbjct: 23 LIEHFGNPHSRTHLYGWESEDAVEKA 48
>gnl|CDD|234944 PRK01345, PRK01345, heat shock protein HtpX; Provisional.
Length = 317
Score = 27.3 bits (61), Expect = 7.7
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 1/37 (2%)
Query: 19 MMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWS 55
M G P + R + G G G + +G WS
Sbjct: 282 MGGRSAAPTAAAAAPRQSRGPWGQG-SGGGRRRGPWS 317
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 26.7 bits (59), Expect = 8.8
Identities = 18/44 (40%), Positives = 21/44 (47%)
Query: 13 RGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSG 56
G G G GG+ S G R +GGGGGG G S+P G
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGG 171
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 27.1 bits (60), Expect = 9.6
Identities = 11/33 (33%), Positives = 11/33 (33%), Gaps = 9/33 (27%)
Query: 12 PRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNT 44
P G P GM GG G G G T
Sbjct: 625 PGGMPGGMPGGAGPAG---------AGASSGPT 648
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
0.309 0.131 0.422
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,529,056
Number of extensions: 1041519
Number of successful extensions: 1115
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1058
Number of HSP's successfully gapped: 98
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 57 (25.9 bits)