RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6597
(305 letters)
>gnl|CDD|240710 cd12264, RRM_AKAP17A, RNA recognition motif found in A-kinase
anchor protein 17A (AKAP-17A) and similar proteins.
This subfamily corresponds to the RRM domain of
AKAP-17A, also termed 721P, or splicing factor,
arginine/serine-rich 17A (SFRS17A). It was originally
reported as the pseudoautosomal or X inactivation escape
gene 7 (XE7) and as B-lymphocyte antigen precursor. It
has been suggested that AKAP-17A is an alternative
splicing factor and an SR-related splicing protein that
interacts with the classical SR protein ASF/SF2 and the
SR-related factor ZNF265. Additional studies have
indicated that AKAP-17A is a dual-specific protein
kinase A anchoring protein (AKAP) that can bind both
type I and type II protein kinase A (PKA) with high
affinity and co-localizes with the catalytic subunit of
PKA in nuclear speckles as well as the splicing factor
SC35 in splicing factor compartments. It is involved in
regulation of pre-mRNA splicing possibly by docking a
pool of PKA in splicing factor compartments. AKAP-17A
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 121
Score = 98.9 bits (247), Expect = 7e-26
Identities = 36/75 (48%), Positives = 47/75 (62%), Gaps = 2/75 (2%)
Query: 150 GERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPYI 209
GERPDTI+L LP +WF+ ++PSE +LR VF +G+IR VDIP+ DPYR +M
Sbjct: 1 GERPDTIHLEGLPCRWFAEPRVSDKPSELVLRTVFSKFGEIRNVDIPMLDPYRKEMDDRG 60
Query: 210 SGMTLFSHAQSLIFK 224
S FS L F+
Sbjct: 61 SDT--FSFGSHLHFE 73
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 34.5 bits (80), Expect = 0.006
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 10/44 (22%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
T+++ NLP +E LR +F +G + V + +
Sbjct: 1 TLFVGNLPPDT----------TEEELRELFSKFGKVESVRLVRD 34
>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 = 33.8 bits (78), Expect = 0.012
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 10/47 (21%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYR 202
+++ NLP +E LR +F +G+I V I + +
Sbjct: 1 LFVGNLPPDT----------TEEDLRELFSKFGEIESVRIVRDKDGK 37
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 32.4 bits (74), Expect = 0.042
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
+E LRR F+ YG + +VD I P R Q Y
Sbjct: 15 TEEELRRAFERYGVVEDVD--IKRPPRGQGNAY 45
>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 = 32.2 bits (74), Expect = 0.044
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 10/43 (23%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+++ NLP T +E L+ +F +G I + I +
Sbjct: 1 LFVGNLP---PDT-------TEEDLKDLFSKFGPIESIRIVRD 33
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 30.3 bits (69), Expect = 0.21
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPY 201
+ LRRVF+ YG++ +V IP D Y
Sbjct: 11 TPDDLRRVFEKYGEVGDVYIP-RDRY 35
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 30.3 bits (68), Expect = 0.27
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 12/54 (22%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
T++L NL + +E LRR F +G I EVD I P R Q Y
Sbjct: 9 TLFLGNLDIT----------VTETDLRRAFDRFGVITEVD--IKRPGRGQTSTY 50
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 29.9 bits (68), Expect = 0.30
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 161 LPVKWFSTKARPNQP--SEAMLRRVFQNYGDIREVDIPIND 199
L VKW K + SE LR++F YGD+ +V +
Sbjct: 3 LKVKW---KRKKGNGDYSEDELRKIFSKYGDVSDVVVSSKK 40
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 30.0 bits (68), Expect = 0.32
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 10/35 (28%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDI 190
+Y+SNLP+ E L + + YG +
Sbjct: 3 LYISNLPLHM----------DEQDLETMLKPYGQV 27
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 29.5 bits (67), Expect = 0.46
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 10/43 (23%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+Y+ L + E +L F +GDI+++ IP++
Sbjct: 1 LYVGGLA----------EEVDEKVLHAAFIPFGDIKDIQIPLD 33
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 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 = 28.8 bits (65), Expect = 0.60
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDIP 196
P +E +R+ F++ G+IREV I
Sbjct: 9 PKDTTENKIRQFFKDCGEIREVKIV 33
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 28.7 bits (65), Expect = 0.62
Identities = 5/18 (27%), Positives = 13/18 (72%)
Query: 176 SEAMLRRVFQNYGDIREV 193
S+ LR +F +G+++++
Sbjct: 14 SDQELRSLFSQFGEVKDI 31
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a 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. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 28.8 bits (65), Expect = 0.72
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
+E LR +F+ +G+I V + DP + K Y
Sbjct: 11 TEDDLRGIFEPFGEIEFVQLQR-DPETGRSKGY 42
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 28.5 bits (64), Expect = 0.81
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 180 LRRVFQNYGDIREVDI---PINDPY 201
LR F+ +G+I ++DI N Y
Sbjct: 19 LREAFERFGEIIDIDIKKQGGNPAY 43
>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 = 28.7 bits (65), Expect = 0.82
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMK 206
P +E +R +F+ YG+I EV I I D Q K
Sbjct: 8 PKTATEEDVRALFEEYGNIEEVTI-IRDKDTGQSK 41
>gnl|CDD|237992 cd00025, BPI1, BPI/LBP/CETP N-terminal domain; Bactericidal
permeability-increasing protein (BPI) /
Lipopolysaccharide-binding protein (LBP) / Cholesteryl
ester transfer protein (CETP) N-terminal domain; binds
to and neutralizes lipopolysaccharides from the outer
membrane of Gram-negative bacteria.; Apolar pockets on
the concave surface bind a molecule of
phosphatidylcholine, primarily by interacting with their
acyl chains; this suggests that the pockets may also
bind the acyl chains of lipopolysaccharide.
Length = 223
Score = 30.4 bits (69), Expect = 0.84
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 11/111 (9%)
Query: 19 DAKILSAAYQLFLKPVARLNISVQIPELKITGKSLSNYEVIEKIKYWAQPEEFSSLKVTK 78
K L A Q LK + +QIP++ K + K + +E LK+
Sbjct: 7 SPKGLKFAKQQGLKVLQAELEKLQIPDILGAMKIKL----LGKGRVGLSNKEIQELKLPS 62
Query: 79 STLEFVR---LDGEIENRSKLLPVLARLDGRTIKLSGFAD----GLRVRAT 122
S+++ V LD I N S L + + + R I G + G+ ++A
Sbjct: 63 SSIKLVEVKGLDLSISNVSIGLSGVWKYNYRFILDGGNVELSVEGMNIQAD 113
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 28.4 bits (64), Expect = 0.89
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
T+++SNL +S E LR++F G+I +V + N
Sbjct: 1 TVFVSNLD---YSV-------PEDELRKLFSKCGEITDVRLVKNY 35
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 28.4 bits (64), Expect = 0.93
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 176 SEAMLRRVFQNYGDIREVDIP 196
+E LR +F +G+I V IP
Sbjct: 14 TEDELRSLFGPFGEIVYVKIP 34
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 30.6 bits (69), Expect = 1.1
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPYRAQMKPYISGMTLFSHAQ 219
+E LR++F+ +GDI +V + DP + K + G F A+
Sbjct: 199 TEQELRQIFEPFGDIEDVQLHR-DPETGRSKGF--GFIQFHDAE 239
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 28.0 bits (63), Expect = 1.1
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDIPINDPYRA 203
+E LR+ F +G++ +V IP P+RA
Sbjct: 9 TEDMTEEDLRQYFSQFGEVTDVYIPK--PFRA 38
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 28.5 bits (64), Expect = 1.2
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 11/55 (20%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPYI 209
++Y+ N+ RP+ LRR+F YG I +V IP+ D Y + + +
Sbjct: 2 SLYVRNVA-----DATRPDD-----LRRLFGKYGPIVDVYIPL-DFYTRRPRGFA 45
>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 = 28.0 bits (63), Expect = 1.3
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
T+Y+ NLP + +E L+R F +G I EV +
Sbjct: 2 TVYVGNLP----------HGLTEEELQRTFSPFGAIEEVRV 32
>gnl|CDD|99738 cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a PLP
dependent enzyme and catalyzes the committed step of
methionine biosynthesis. This pathway is unique to
microorganisms and plants, rendering the enzyme an
attractive target for the development of antimicrobials
and herbicides. This subgroup also includes
cystathionine gamma-lyases (CGL), O-acetylhomoserine
sulfhydrylases and O-acetylhomoserine thiol lyases.
CGL's are very similar to CGS's. Members of this group
are widely distributed among all three forms of life.
Length = 369
Score = 30.2 bits (69), Expect = 1.4
Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 157 YLSNLP-VKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPYISGMTLF 215
+L P V+ P+ P + ++ YG + ++ K +++ + LF
Sbjct: 253 FLEKHPKVERVYYPGLPSHPQHELAKKQMSGYGGVFSFELKGGL---EAAKKFLNALKLF 309
Query: 216 SHAQSL 221
S A SL
Sbjct: 310 SLAVSL 315
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 28.0 bits (63), Expect = 1.4
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 153 PDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDP 200
+ +++S L + +E L +F +G + EV + + DP
Sbjct: 1 GNKLFVSGLSTRT----------TEKELEALFSKFGRVEEVLL-MKDP 37
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 28.0 bits (63), Expect = 1.5
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 10/37 (27%)
Query: 160 NLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
NLP F EA L+++F +G + EV IP
Sbjct: 6 NLP---FKCT-------EADLKKLFSPFGFVWEVTIP 32
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs 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). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 27.7 bits (62), Expect = 1.7
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 10/43 (23%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+++ NLP +S K E L ++F +G++ EV + I+
Sbjct: 5 LFVRNLP---YSCK-------EDDLEKLFSKFGELSEVHVAID 37
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 27.5 bits (62), Expect = 1.7
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 10/44 (22%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
+Y+ NLP S +E LR F YG + V + N
Sbjct: 1 LYVRNLP---PSV-------TEEDLREFFSPYGKVEGVRLVRNK 34
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 27.6 bits (62), Expect = 2.0
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 10/38 (26%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE 192
I++ LP + T ++ LR+ F +G+I E
Sbjct: 2 KIFVGGLP---YHT------TDDS-LRKYFSQFGEIEE 29
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 27.5 bits (62), Expect = 2.0
Identities = 9/21 (42%), Positives = 16/21 (76%)
Query: 180 LRRVFQNYGDIREVDIPINDP 200
L+ +F NYG +++VD+PI+
Sbjct: 15 LKEIFSNYGTVKDVDLPIDRE 35
>gnl|CDD|212089 cd11520, SLC5sbd_SMCT2, Na(+)/monocarboxylate cotransporter SMCT2
and related proteins; solute-binding domain. SMCT2 is a
low-affinity transporter for short-chain fatty acids,
lactate, pyruvate, and nicotinate. Human SMCT2 (hSMCT2)
is encoded by the SLC5A12 gene. SMCT2 is expressed in
the kidney, small intestine, skeletal muscle, and
retina. In the kidney, it is expressed in the apical
membrane of the proximal convoluted tubule, along the
entire length of the tubule (in contrast to the
high-affinity monocarboxylate transporter SMCT1,
belonging to a different family, which is limited to the
S3 segment of the tubule). SMCT2 may initiate lactate
absorption in the early parts of the tubule. In the
retina, SMCT1 and SMCT2 may play a differential role in
monocarboxylate transport in a cell type-specific
manner, SMCT2 is expressed exclusively in Muller cells.
Nicotine transport by hSMCT2 is inhibited by several
non-steroidal anti-inflammatory drugs. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 529
Score = 29.8 bits (67), Expect = 2.2
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 259 SRKTSGGASKSMCVTYVVMCMAMEISA 285
S K S SK +C+ + VMC +M ++A
Sbjct: 371 SEKLSTWISKGLCILFGVMCTSMAVAA 397
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 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 = 78
Score = 27.6 bits (62), Expect = 2.2
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 10/43 (23%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
IY+ NL F E LR +F +G++ + IP
Sbjct: 3 IYVRNLD---FKL-------DEDDLRGIFSKFGEVESIRIPKK 35
>gnl|CDD|238191 cd00312, Esterase_lipase, Esterases and lipases (includes fungal
lipases, cholinesterases, etc.) These enzymes act on
carboxylic esters (EC: 3.1.1.-). The catalytic apparatus
involves three residues (catalytic triad): a serine, a
glutamate or aspartate and a histidine.These catalytic
residues are responsible for the nucleophilic attack on
the carbonyl carbon atom of the ester bond. In contrast
with other alpha/beta hydrolase fold family members,
p-nitrobenzyl esterase and acetylcholine esterase have a
Glu instead of Asp at the active site carboxylate.
Length = 493
Score = 29.6 bits (67), Expect = 2.3
Identities = 10/45 (22%), Positives = 19/45 (42%)
Query: 143 NMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNY 187
+K G R + LS +K+++ A+ P+ V+ Y
Sbjct: 430 GNPLLKEGLREEEEKLSRTMMKYWANFAKTGNPNTEGNLVVWPAY 474
>gnl|CDD|99799 cd06202, Nitric_oxide_synthase, The ferredoxin-reductase (FNR) like
C-terminal domain of the nitric oxide synthase (NOS)
fuses with a heme-containing N-terminal oxidase domain.
The reductase portion is similar in structure to NADPH
dependent cytochrome-450 reductase (CYPOR), having an
inserted connecting sub-domain within the FAD binding
portion of FNR. NOS differs from CYPOR in a requirement
for the cofactor tetrahydrobiopterin and unlike most
CYPOR is dimeric. Nitric oxide synthase produces nitric
oxide in the conversion of L-arginine to L-citruline.
NOS has been implicated in a variety of processes
including cytotoxicity, anti-inflamation,
neurotransmission, and vascular smooth muscle
relaxation.
Length = 406
Score = 29.6 bits (67), Expect = 2.3
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 9/43 (20%)
Query: 45 ELKITGKSLSNYEVIEKIKYWAQP------EEFSSLKVTKSTL 81
L++ GK S YE K++ P EEF SL+V S L
Sbjct: 129 RLEVLGKGSSEYE---DWKWYKNPNILEVLEEFPSLQVPASLL 168
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 27.6 bits (62), Expect = 2.3
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 11/47 (23%)
Query: 153 PDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
P+ I++ +P +E LR F +G +++V I I D
Sbjct: 2 PNRIFVGGIPPD----------TTEEELRDFFSRFGSVKDVKI-ITD 37
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 27.6 bits (61), Expect = 2.3
Identities = 16/33 (48%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
SE LRR F YG I EV I P R Q Y
Sbjct: 21 SEVELRRAFDKYGIIEEV--VIKRPARGQGGAY 51
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 27.4 bits (61), Expect = 2.4
Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 10/44 (22%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
+++SN+P ++ + LR++F +G I +V+I N+
Sbjct: 3 LHVSNIPFRF----------RDPDLRQMFGQFGPILDVEIIFNE 36
>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 = 26.9 bits (60), Expect = 3.2
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDIP 196
PN +E + +F YG++ EV +
Sbjct: 10 PNDITEEEFKELFSKYGEVSEVFLN 34
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 27.1 bits (60), Expect = 4.0
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 176 SEAMLRRVFQNYGDIREVDIPIN 198
+E LR+ F YG ++EV I +
Sbjct: 15 NENDLRKFFSQYGTVKEVKIVND 37
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 26.6 bits (59), Expect = 4.1
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDI 195
P S + L+ +F+ GD++ + +
Sbjct: 10 PKDVSTSNLKEIFEKMGDVKGIFV 33
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 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). .
Length = 82
Score = 26.4 bits (59), Expect = 5.5
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
T+++ NL F T E L++ F+ G +R V I
Sbjct: 2 TLFVKNLN---FKTT-------EETLKKHFEKCGGVRSVTIA 33
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 26.1 bits (58), Expect = 6.6
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
T+Y+SNLP FS L ++F YG + +V I
Sbjct: 3 TVYVSNLP---FSLT-------NNDLHKIFSKYGKVVKVTI 33
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 27.6 bits (60), Expect = 9.1
Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 14/90 (15%)
Query: 115 DGLRVRATEAKPDFPTRHDW----DSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKA 170
+G +R +A+P R + D+ F + + E+ D +Y+ NLP+K
Sbjct: 183 EGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKT----- 237
Query: 171 RPNQPSEAMLRRVFQNYGDIREVDIPINDP 200
+E L +F++ GDI +P +
Sbjct: 238 -----AEEELADLFKSRGDIVRASLPPSKD 262
>gnl|CDD|224110 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 245
Score = 27.2 bits (61), Expect = 9.2
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 57 EVIEKIKYWAQPEEFSSLKVTKS 79
EV+ KI+ +A+ F + KS
Sbjct: 203 EVLSKIENFAKELGFQVKGLIKS 225
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 0.133 0.386
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,301,681
Number of extensions: 1445972
Number of successful extensions: 1182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1181
Number of HSP's successfully gapped: 51
Length of query: 305
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 208
Effective length of database: 6,635,264
Effective search space: 1380134912
Effective search space used: 1380134912
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: 59 (26.4 bits)