RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4441
(249 letters)
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end)
protein family. This subfamily corresponds to the RRM1
domain in the Spen (split end) 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 possesses 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 known as 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 = 108 bits (273), Expect = 7e-31
Identities = 49/79 (62%), Positives = 61/79 (77%), Gaps = 1/79 (1%)
Query: 74 YKVLCVSALHPKASDELIKDTLYREYKKFGDLSIRLSHDL-DERVAYVCFRSAEDARDAK 132
YK LCVS L K SDE I+D LY E+KKFGD+S+R+ HD DERVAYV FR EDAR+AK
Sbjct: 1 YKTLCVSNLPSKLSDEDIEDVLYHEFKKFGDVSVRVLHDGEDERVAYVNFRHPEDAREAK 60
Query: 133 HSKPRIILYDKVAVVDPVY 151
H+K R++L+D+ V+PVY
Sbjct: 61 HAKGRLVLFDRPLNVEPVY 79
>gnl|CDD|240997 cd12553, RRM1_RBM15, RNA recognition motif 1 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM1 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 contains
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 = 78
Score = 82.7 bits (204), Expect = 1e-20
Identities = 39/78 (50%), Positives = 57/78 (73%)
Query: 74 YKVLCVSALHPKASDELIKDTLYREYKKFGDLSIRLSHDLDERVAYVCFRSAEDARDAKH 133
YK L +S L + SDE ++D L+ E+KKFGD+S+++S DERVA+V FR EDAR AKH
Sbjct: 1 YKTLKISELGSQLSDEAVEDGLFHEFKKFGDVSVKISRLGDERVAFVNFRRPEDARAAKH 60
Query: 134 SKPRIILYDKVAVVDPVY 151
++ R++LYD+ ++ VY
Sbjct: 61 ARGRLVLYDRPLKIEAVY 78
>gnl|CDD|240998 cd12554, RRM1_RBM15B, RNA recognition motif 1 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subfamily corresponds to the RRM1 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 = 81
Score = 71.0 bits (174), Expect = 4e-16
Identities = 41/80 (51%), Positives = 58/80 (72%), Gaps = 2/80 (2%)
Query: 74 YKVLCVSALHPKASDELIKDTLYREYKKFGDLSIRLSHDLD-ERVAYVCFRSAEDARDAK 132
YK L VS L DEL++D L+ ++K+FGD+S++LSH + RVAYV FR EDAR+A+
Sbjct: 2 YKTLLVSNLGSALPDELLEDALFHQFKRFGDISVKLSHTPELGRVAYVNFRHPEDAREAR 61
Query: 133 HSK-PRIILYDKVAVVDPVY 151
H+K R++LYD+ V+PVY
Sbjct: 62 HAKSRRLLLYDRPLKVEPVY 81
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 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 = 50.8 bits (122), Expect = 7e-09
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 77 LCVSALHPKASDELIKDTLYREYKKFGD-LSIRLSHDLDERVAYVCFRSAEDARDAKHS 134
+ V L ++SD +KD L+ E+KK G S+++ ER A V FR EDA A
Sbjct: 2 IIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKVHGTGSERYAIVFFRKPEDAEKALEV 60
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 77 LCVSALHPKASDELIKDTLYREYKKFGD-LSIRLSHDLDER---VAYVCFRSAEDARDAK 132
L V L P ++E +++ KFG+ S+R+ D D + A+V F S EDA A
Sbjct: 1 LFVGNLPPDTTEEDLRELF----SKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKAL 56
Query: 133 HSKPRIILYDKVAVVD 148
+ L + V
Sbjct: 57 EALNGKELDGRKLKVS 72
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 38.3 bits (90), Expect = 2e-04
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 76 VLCVSALHPKASDELIKDTLYREYKKFGDL-SIRLSHDLDERV----AYVCFRSAEDARD 130
L V L P ++E +++ KFG + S+RL D + A+V F S EDA
Sbjct: 1 TLFVGNLPPDTTEEELRELF----SKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEK 56
Query: 131 AKHSKPRIILYDKVAVV 147
A + L + V
Sbjct: 57 ALEALNGKELDGRPLKV 73
>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 = 38.0 bits (89), Expect = 3e-04
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 79 VSALHPKASDELIKDTLYREYKKFGD-LSIRLSHDLDER---VAYVCFRSAEDARDAKHS 134
V L P ++E +KD KFG SIR+ D R A+V F EDA A +
Sbjct: 3 VGNLPPDTTEEDLKDLF----SKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEA 58
Query: 135 KPRIILYDKV 144
L +
Sbjct: 59 LNGKELGGRE 68
>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 = 35.2 bits (82), Expect = 0.002
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 95 LYREYKKFGDL-SIRLSHDLDERVAYVCFRSAEDARDAKHSKPRIILYDKVAVVDP 149
LY+ + FG++ I+L A+V F + E A A ++ + VD
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
>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 = 33.4 bits (77), Expect = 0.013
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 89 ELIKDTLYREYKKFGDL-SIRL-------SHDLDERVAYVCFRSAEDARDA 131
+L +D L + KFG++ SIR+ L+ A+V F+ A A +A
Sbjct: 11 KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
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 is a novel 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 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 = 72
Score = 32.9 bits (76), Expect = 0.017
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 92 KDTLYREYKKFGDLSIRLSHDLDERVAYVCFRSAEDARDAKH 133
L RE+ +FG + R+ +D AY+ + S E A+ AK
Sbjct: 12 LAELEREFDRFGAIR-RIDYDPGRNYAYIEYESIEAAQAAKE 52
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 32.1 bits (74), Expect = 0.029
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 77 LCVSALHPKASDELIKDTLYREYKKFGDLSIRLSHDLDERVAYVCFRSAEDARDA 131
L V L P ++E +++ Y K + + + D A+V F S EDA A
Sbjct: 1 LYVRNLPPSVTEEDLREFF-SPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAA 54
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 31.2 bits (71), Expect = 0.11
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 79 VSALHPKASDELIKDTLYREYKKFGDLS-IRLSHDLDER-VAYVCFRSAEDARDA 131
V++L SD+ ++ + + K+G L +++ D +R A+V F + +DA++A
Sbjct: 7 VASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNA 61
>gnl|CDD|237456 PRK13641, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 32.1 bits (73), Expect = 0.22
Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 17/79 (21%)
Query: 75 KVLCV----SALHPKASDELIKDTLYREYKKFGDLSIRLSHDLDERVAYVCFRSAED--- 127
++LC+ + L P+ E+++ L+++Y+K G I ++H++D+ Y A+D
Sbjct: 165 EILCLDEPAAGLDPEGRKEMMQ--LFKDYQKAGHTVILVTHNMDDVAEY-----ADDVLV 217
Query: 128 ---ARDAKHSKPRIILYDK 143
+ KH+ P+ I DK
Sbjct: 218 LEHGKLIKHASPKEIFSDK 236
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 32.2 bits (72), Expect = 0.23
Identities = 28/179 (15%), Positives = 49/179 (27%), Gaps = 10/179 (5%)
Query: 2 KRSSSRDTPPLRNKRTRSSLGRYDDSSDERLSPERGHRSRARSPPSPRPRYAYEYRDEYG 61
K + + SS+ + ER + + E
Sbjct: 44 KELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSE 103
Query: 62 RTREAVSDRPPSYKVLCVSALHPKASDELIKDTLYREYKKFG-DLSIRLSHDLDE----R 116
+ + + + V L + ++ L +KKFG +RL D +
Sbjct: 104 SPKSRQKSKEENNTLF-VGNLPYDVT----EEDLRELFKKFGPVKRVRLVRDRETGKSRG 158
Query: 117 VAYVCFRSAEDARDAKHSKPRIILYDKVAVVDPVYETHASRSRPRSRSYSPPPPEYDRY 175
A+V F S E A A L + V RS + + + R
Sbjct: 159 FAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRG 217
>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 = 29.8 bits (68), Expect = 0.35
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 88 DELIKDTLYREYKKFGD-LSIRLSHDLDERVAYVCFRSAEDARDA 131
DE+ +D L E KFG I++ + E V YV F++ E A+
Sbjct: 22 DEIKEDVL-EECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKC 65
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 28.7 bits (64), Expect = 0.60
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 75 KVLCVSALHPKASDELIKDTLYREYKKFGDLSIRLSHDLDERVAYVCFRSAEDARDAKHS 134
KVL V+ L AS+ D+L ++K + I ++ + A+V F SAEDA++A +S
Sbjct: 2 KVLVVNNLSYSASE----DSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNS 57
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 28.7 bits (65), Expect = 0.71
Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 106 SIRLSHDLDER---VAYVCFRSAEDARDA 131
I + +D D R AYV F S EDAR A
Sbjct: 29 GIHIVYDDDGRPTGEAYVEFASPEDARRA 57
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 30.5 bits (69), Expect = 0.85
Identities = 31/120 (25%), Positives = 42/120 (35%), Gaps = 19/120 (15%)
Query: 2 KRSSSRDTPPLRNKRTRSSLGRYDDSSDERLSPERGHRSRARSPPSPRPRYAYEYRDEYG 61
+RSSS + R S S R RS R + R A RD Y
Sbjct: 7 RRSSSSLRR--SRRAARRSRRDGRVGSRGRSRYRSRRRSS-RRSSTRRAELADTERDRYR 63
Query: 62 RTREAVSDRPPSYKVLCVSALHPKASDELIKDTLYREYKKFGDLSIRLSHDLDERVAYVC 121
++ PS ++ V +L S LIK T + L DL++ VA C
Sbjct: 64 AYFAYLA-SSPSDELALVRSL----SVPLIKTT-----------PVSLPFDLNQTVADNC 107
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein (SXL).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 78
Score = 28.3 bits (63), Expect = 0.86
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 79 VSALHPKASDELIKDTLYREYKKFGD-LSIRLSHDLDER-VAYVCFRSAEDARDAKHSKP 136
++ L+ K E +K +LY + +FG L I L R A+V F+ A +A S
Sbjct: 4 INNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALRSMQ 63
Query: 137 RIILYDK 143
YDK
Sbjct: 64 GFPFYDK 70
>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 = 28.0 bits (63), Expect = 1.0
Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 9/60 (15%)
Query: 77 LCVSALHPKASDELIKDTLYREYKKFGDL-SIRLSHD----LDERVAYVCFRSAEDARDA 131
L V LH +++ ++ ++ FG++ ++L D + ++ F AEDA+ A
Sbjct: 1 LYVGNLHFNITEDDLRGI----FEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56
>gnl|CDD|188317 TIGR03415, ABC_choXWV_ATP, choline ABC transporter, ATP-binding
protein. Members of this protein family are the
ATP-binding subunit of a three-protein transporter. This
family belongs, more broadly, to the family of proline
and glycine-betaine transporters, but members have been
identified by direct characterization and by
bioinformatic means as choline transporters. Many
species have several closely-related members of this
family, probably with variable abilities to act
additionally on related quaternary amines [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 382
Score = 30.1 bits (68), Expect = 1.0
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 20/71 (28%)
Query: 80 SALHP----KASDELIKDTLYREYKKFGDLSIRLSHDLDE------RVAYVCFRSAEDAR 129
SAL P + DEL++ L + KK + +SHDLDE R+A + E R
Sbjct: 193 SALDPLIRTQLQDELLE--LQSKLKK---TIVFVSHDLDEALKIGNRIAIM-----EGGR 242
Query: 130 DAKHSKPRIIL 140
+H P I+
Sbjct: 243 IIQHGTPEEIV 253
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
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). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It 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 = 76
Score = 27.6 bits (62), Expect = 1.4
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 77 LCVSALHPKASDELIKDTLYREYKKFGDLS----IRLSHDLDERVAYVCFRSAEDARDA 131
+ V L PK E D L ++ G+++ +R R +V F+S EDA+ A
Sbjct: 3 IIVKNL-PKYVTE---DRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQA 57
>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 = 29.5 bits (66), Expect = 1.6
Identities = 21/70 (30%), Positives = 25/70 (35%), Gaps = 11/70 (15%)
Query: 3 RSSSRDTPPLRNKRTRSSLGRYDDSSDERLSPERGHRSRARSPPSPRPRYAYEYRDEYGR 62
R R+ LRN RS GR R S +R R R R YR GR
Sbjct: 1 RYRDRERGRLRNDTRRSDKGRERSRRRSR-SRDRSRRRRDRDY----------YRGRRGR 49
Query: 63 TREAVSDRPP 72
+R +R
Sbjct: 50 SRSRSPNRYY 59
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 29.7 bits (67), Expect = 1.7
Identities = 16/82 (19%), Positives = 22/82 (26%), Gaps = 7/82 (8%)
Query: 165 YSPPPPEYDRYYSRSPVLERRPGLPPPLPHPGERPYGYGP----PVLRHEFRRDIPPHHV 220
Y PP + L P P P + P P + +PP
Sbjct: 203 YPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQ--MPPPPP 260
Query: 221 VLPHHEFLPRGPPLHHIPPHHP 242
P + P P PP +
Sbjct: 261 QPPQQQQQP-PQPQAQPPPQNQ 281
Score = 29.0 bits (65), Expect = 2.5
Identities = 13/62 (20%), Positives = 17/62 (27%), Gaps = 1/62 (1%)
Query: 186 PGLPPPLPHPGERPYGYGPPVLRHEFRRDIPPHHVVLPHHEFLPRGPPLHHIPPHHPTYL 245
LP +P GPP + + P H + P P P L
Sbjct: 178 QVLPQGMPPRQAAFPQQGPPEQPPGYPQ-PPQGHPEQVQPQQFLPAPSQAPAQPPLPPQL 236
Query: 246 KQ 247
Q
Sbjct: 237 PQ 238
>gnl|CDD|218839 pfam05983, Med7, MED7 protein. This family consists of several
eukaryotic proteins which are homologues of the yeast
MED7 protein. Activation of gene transcription in
metazoans is a multi-step process that is triggered by
factors that recognise transcriptional enhancer sites in
DNA. These factors work with co-activators such as MED7
to direct transcriptional initiation by the RNA
polymerase II apparatus.
Length = 161
Score = 27.7 bits (62), Expect = 3.7
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 162 SRSYSPPPPEYDRYYSRSPVLERRPGLPPPLP 193
S Y PPPP Y + LE R PPP P
Sbjct: 3 SSLYPPPPPYYKLF--TDENLELRFLPPPPPP 32
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 26.4 bits (59), Expect = 4.2
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 117 VAYVCFRSAEDARDA 131
A+V FRS E+ + A
Sbjct: 44 FAFVTFRSEEERQKA 58
>gnl|CDD|177481 PHA02700, PHA02700, ORF017 DNA-binding phosphoprotein; Provisional.
Length = 106
Score = 26.9 bits (59), Expect = 5.5
Identities = 15/24 (62%), Positives = 15/24 (62%)
Query: 178 RSPVLERRPGLPPPLPHPGERPYG 201
RSPV ERRP LPP P P P G
Sbjct: 52 RSPVCERRPQLPPSPPCPVRTPPG 75
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 28.0 bits (62), Expect = 5.7
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 4/70 (5%)
Query: 13 RNKRTRSSLGRYDDSSDERLSPERGHRSRARSPPSPRPRYAYEYRDEYGRTREAVSDRPP 72
N+ +S +S DE+ + RSR + Y + EY R+ + V+D
Sbjct: 1 MNENQKSFDSDKSESEDEQKNGRVKVRSRKTDDMNK----GYSWEQEYKRSWDDVNDDKE 56
Query: 73 SYKVLCVSAL 82
V V+
Sbjct: 57 GSLVGVVAEF 66
>gnl|CDD|227441 COG5110, RPN1, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 881
Score = 27.6 bits (61), Expect = 6.9
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 74 YKVLCVSALHPKASDELIKDTLYREYKKFGDLS------IRLSHDLDERVAYVCFRSAED 127
Y CV L P D + +T + Y K GDL+ IRL + R+ ED
Sbjct: 227 YLEDCVPLL-PPPEDVALLETALKIYLKMGDLTRAVVGAIRLQ---KSKEIIEYVRAIED 282
>gnl|CDD|184209 PRK13650, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 279
Score = 27.4 bits (61), Expect = 7.2
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 80 SALHPKASDELIKDTLYREYKKFGDLSIRLSHDLDE 115
S L P+ ELIK T+ + I ++HDLDE
Sbjct: 169 SMLDPEGRLELIK-TIKGIRDDYQMTVISITHDLDE 203
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 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 = 25.6 bits (57), Expect = 8.4
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 84 PKASDELIKDTLYREYKKFGDLSIR---LSHDLDERVAYVCFRSAEDARDA 131
P I+D L+ +Y + LSIR L + R YV F S E A A
Sbjct: 10 PSFDQSDIRD-LFEQYGEI--LSIRFPSLRFNKTRRFCYVQFTSPESAAAA 57
>gnl|CDD|225969 COG3435, COG3435, Gentisate 1,2-dioxygenase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 351
Score = 27.4 bits (61), Expect = 8.8
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 21 LGRYDDSSDERLSPE-RGHRSRARSPPSPRPRYAYEYRDEYGRTREAVSD 69
+ R + S R P R R R P SP YA++ RTREA+
Sbjct: 188 VTRPEGDSLARYGPGMRPLRHRWGKPYSPLFNYAWD------RTREALER 231
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 27.0 bits (60), Expect = 9.2
Identities = 20/97 (20%), Positives = 21/97 (21%), Gaps = 2/97 (2%)
Query: 149 PVYETHASRSRPRSRSYSPPPPEYDRYYSRSPVLERRPGLPPPLP--HPGERPYGYGPPV 206
AS S P S S P SP P P P P P
Sbjct: 176 DADPASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPS 235
Query: 207 LRHEFRRDIPPHHVVLPHHEFLPRGPPLHHIPPHHPT 243
PP +P PP P
Sbjct: 236 PPPGPAAPPPPPVQQVPPLSTAKPTPPSASATPAPIG 272
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
0.317 0.138 0.430
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,797,204
Number of extensions: 1375336
Number of successful extensions: 1834
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1731
Number of HSP's successfully gapped: 117
Length of query: 249
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 155
Effective length of database: 6,768,326
Effective search space: 1049090530
Effective search space used: 1049090530
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.3 bits)