RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3067
(141 letters)
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family. This subfamily corresponds to the RRM2
of hnRNP H protein family which 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). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA
only in the presence of cap-binding proteins.
Furthermore, hnRNP H and hnRNP H2 are almost identical;
both have been found to bind nuclear-matrix proteins.
hnRNP H activates exon inclusion by binding G-rich
intronic elements downstream of the 5' splice site in
the transcripts of c-src, human immunodeficiency virus
type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences
exons when bound to exonic elements in the transcripts
of beta-tropomyosin, HIV-1, and alpha-tropomyosin.
hnRNP H2 has been implicated in pre-mRNA 3' end
formation. hnRNP H3 may be involved in the splicing
arrest induced by heat shock. Most family members
contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. In addition, the family members have an extensive
glycine-rich region near the C-terminus, which may
allow them to homo- or heterodimerize. .
Length = 77
Score = 96.3 bits (240), Expect = 2e-27
Identities = 41/59 (69%), Positives = 47/59 (79%), Gaps = 1/59 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K++IAQFF GLEI+ NGITL D GR TGEAYVQF +E+AE AL KHKE+IGHRYI
Sbjct: 14 KEEIAQFFSGLEIVPNGITLPMDY-RGRSTGEAYVQFASQESAERALGKHKEKIGHRYI 71
>gnl|CDD|241176 cd12732, RRM2_hnRNPH3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H') and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and play an important role in efficiently
silencing the exon. Members in this family can regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. In addition, like other hnRNP H protein family
members, hnRNP H3 has an extensive glycine-rich region
near the C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 96
Score = 87.3 bits (216), Expect = 2e-23
Identities = 47/90 (52%), Positives = 54/90 (60%), Gaps = 18/90 (20%)
Query: 24 MDWKLQHTGIVEGK-----------------KDDIAQFFDGLEIISNGITLVEDPFNGRP 66
MDW L+H G + K++I QFF GLEI+ NGITL D + GR
Sbjct: 1 MDWVLKHNGPTDYDGSSGGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMD-YQGRS 59
Query: 67 TGEAYVQFVDKETAELALQKHKERIGHRYI 96
TGEA+VQF KE AE AL KHKERIGHRYI
Sbjct: 60 TGEAFVQFASKEIAENALGKHKERIGHRYI 89
>gnl|CDD|241175 cd12731, RRM2_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM2 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts. The presence of
Fox 2 can allows hnRNP H and hnRNP F to better compete
with the SR protein ASF/SF2 for binding to FGFR2 exon
IIIc. Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently
silencing the exon. In addition, the family members
have an extensive glycine-rich region near the
C-terminus, which may allow them to homo- or
heterodimerize. .
Length = 83
Score = 80.4 bits (198), Expect = 5e-21
Identities = 40/59 (67%), Positives = 46/59 (77%), Gaps = 1/59 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K++I QFF GLEI+ NGITL D GR TGEA+VQF +E AE AL+KHKERIGHRYI
Sbjct: 15 KEEIVQFFSGLEIVPNGITLPVDF-QGRSTGEAFVQFASQEIAEKALKKHKERIGHRYI 72
>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 = 75.7 bits (187), Expect = 3e-19
Identities = 31/59 (52%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++DI FF GL+I +GI +V D +GRPTGEAYV+F E A AL+KH ++G RYI
Sbjct: 13 EEDIRDFFSGLDIPPDGIHIVYDD-DGRPTGEAYVEFASPEDARRALRKHNNKMGGRYI 70
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, 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. GRSF-1
contains three potential RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 74.0 bits (182), Expect = 1e-18
Identities = 32/58 (55%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DDI FF GL+I+ +G+ +V + GR TGEAYVQF E A AL KH+E IG+RYI
Sbjct: 16 DDIIDFFRGLDIVDDGVVIVLN-RRGRKTGEAYVQFATPEMANKALLKHREEIGNRYI 72
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in
epithelial splicing regulatory protein ESRP1, ESRP2,
Drosophila RNA-binding protein Fusilli and similar
proteins. This subfamily corresponds to the RRM2 of
ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of the fibroblast growth factor
receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and
CTNND1 (also termed p120-Catenin) transcripts. They are
highly conserved paralogs and specifically bind to
GU-rich binding site. ESRP1 and ESRP2 contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The family also includes Drosophila fusilli (fus) gene
encoding RNA-binding protein Fusilli.Loss of fusilli
activity causes lethality during embryogenesis in
flies. Drosophila Fusilli can regulate endogenous FGFR2
splicing and functions as a splicing factor. It shows
high sequence homology to ESRPs and contains three RRMs
as well. It also has an N-terminal domain with unknown
function and a C-terminal domain particularly rich in
alanine, glutamine, and serine. .
Length = 80
Score = 72.0 bits (177), Expect = 1e-17
Identities = 30/63 (47%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 37 KKDDIAQFFDGLEIIS---NGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGH 93
DI FF GL + +GI V P +GRPTG+A+V F +E A+ AL KHKE +G
Sbjct: 14 TAADILAFFGGLCPVVGGPDGILFVTGP-DGRPTGDAFVLFETEEDAQRALGKHKENLGS 72
Query: 94 RYI 96
RYI
Sbjct: 73 RYI 75
>gnl|CDD|240951 cd12507, RRM1_ESRPs_Fusilli, RNA recognition motif 1 in
epithelial splicing regulatory protein ESRP1, ESRP2,
Drosophila RNA-binding protein Fusilli and similar
proteins. This subfamily corresponds to the RRM1 of
ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B). These are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of the fibroblast growth factor
receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and
CTNND1 (also termed p120-Catenin) transcripts. They are
highly conserved paralogs and specifically bind to
GU-rich binding site. ESRP1 and ESRP2 contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The family also includes Drosophila fusilli (fus) gene
encoding RNA-binding protein Fusilli. Loss of fusilli
activity causes lethality during embryogenesis in
flies. Drosophila Fusilli can regulate endogenous
fibroblast growth factor receptor 2 (FGFR2) splicing
and functions as a splicing factor. It shows high
sequence homology to ESRPs and contains three RRMs as
well. It also has an N-terminal domain with unknown
function and a C-terminal domain particularly rich in
alanine, glutamine, and serine. .
Length = 75
Score = 67.5 bits (165), Expect = 5e-16
Identities = 30/57 (52%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DIAQFF GL I G+ L GR GEA ++FVD+E +LALQ+HK +G RYI
Sbjct: 15 DIAQFFRGLNIAKGGVALCLSA-QGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYI 70
>gnl|CDD|241182 cd12738, RRM1_Fusilli, RNA recognition motif 1 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM1 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 80
Score = 59.5 bits (144), Expect = 7e-13
Identities = 29/57 (50%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DIA+FF GL I G+ L +P GR GEA V+F E +LAL++HK IG RYI
Sbjct: 15 DIAKFFRGLNIAKGGVALCLNP-QGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYI 70
>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, G-rich sequence factor 1 (GRSF-1) and
similar proteins. This subfamily corresponds to the
RRM1 of hnRNP H proteins and GRSF-1. 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. These proteins have similar RNA
binding affinities and specifically recognize the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA
only in the presence of cap-binding proteins. hnRNP H
and hnRNP H2 are almost identical; both have been found
to bind nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements
downstream of the 5' splice site in the transcripts of
c-src, human immunodeficiency virus type 1 (HIV-1),
Bcl-X, GRIN1, and myelin. It silences exons when bound
to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
hnRNP H3 may be involved in splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and play an important role in efficiently
silencing the exon. Members in this family can regulate
the alternative splicing of fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. Members in this family have an extensive
glycine-rich region near the C-terminus, which may
allow them to homo- or heterodimerize. They also
include a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. They may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 contains
three potential RRMs responsible for the RNA binding,
and two auxiliary domains (an acidic alpha-helical
domain and an N-terminal alanine-rich region) that may
play a role in protein-protein interactions and provide
binding specificity. .
Length = 77
Score = 55.8 bits (135), Expect = 2e-11
Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFN--GRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+D+ FF I G + ++ GRP+GEA+++ +E E AL+KH E +GHR
Sbjct: 12 TAEDVLNFFSDCRI-KGGENGIHFTYSREGRPSGEAFIELESEEDVEKALEKHNEHMGHR 70
Query: 95 YI 96
YI
Sbjct: 71 YI 72
>gnl|CDD|241181 cd12737, RRM1_ESRP2, RNA recognition motif 1 in epithelial
splicing regulatory protein 2 (ESRP2) and similar
proteins. This subgroup corresponds to the RRM1 of
ESRP2, also termed RNA-binding motif protein 35B
(RBM35B), which has been identified as an epithelial
cell type-specific regulator of fibroblast growth
factor receptor 2 (FGFR2) splicing. It is required for
expression of epithelial FGFR2-IIIb and the regulation
of CD44, CTNND1 (also termed p120-Catenin) and ENAH
(also termed hMena) splicing. It enhances
epithelial-specific exons of CD44 and ENAH, silences
mesenchymal exons of CTNND1, or both within FGFR2.
ESRP2 contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 80
Score = 55.8 bits (134), Expect = 2e-11
Identities = 29/62 (46%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 35 EGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+ DIA+FF GL I G+ L + GR GEA V+FV+ E +LALQ+HK +G R
Sbjct: 10 QSSDQDIARFFKGLNIAKGGVALCLNA-QGRRNGEALVRFVNSEQRDLALQRHKHHMGSR 68
Query: 95 YI 96
YI
Sbjct: 69 YI 70
>gnl|CDD|241180 cd12736, RRM1_ESRP1, RNA recognition motif 1 in epithelial
splicing regulatory protein 1 (ESRP1) and similar
proteins. This subgroup corresponds to the RRM1 of
ESRP1, also termed RNA-binding motif protein 35A
(RBM35A), which has been identified as an epithelial
cell type-specific regulator of fibroblast growth
factor receptor 2 (FGFR2) splicing. It is required for
expression of epithelial FGFR2-IIIb and the regulation
of CD44, CTNND1 (p120-Catenin) and ENAH (hMena)
splicing. It enhances epithelial-specific exons of CD44
and ENAH, silences mesenchymal exons of CTNND1, or both
within FGFR2. Additional research indicated that ESRP1
functions as a tumor suppressor in colon cancer cells.
It may be involved in posttranscriptional regulation of
various genes by exerting a differential effect on
protein translation via 5' untranslated regions (UTRs)
of mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 54.3 bits (130), Expect = 9e-11
Identities = 29/62 (46%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 35 EGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+ DIA+FF GL I G L + GR GEA V+FV +E +LALQ+HK +G+R
Sbjct: 15 QSSDQDIARFFKGLNIAKGGAALCLNA-QGRRNGEALVRFVSEEHRDLALQRHKHHMGNR 73
Query: 95 YI 96
YI
Sbjct: 74 YI 75
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. 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. These proteins have similar RNA binding
affinities and specifically recognize the sequence
GGGA. They can either stimulate or repress splicing
upon binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements
downstream of the 5' splice site in the transcripts of
c-src, human immunodeficiency virus type 1 (HIV-1),
Bcl-X, GRIN1, and myelin. It silences exons when bound
to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
hnRNP H3 may be involved in the splicing arrest induced
by heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and they play an important role in
efficiently silencing the exon. For instance, members
in this family can regulate the alternative splicing of
the fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced
silencing activity within hnRNP H3. In addition, the
family members have an extensive glycine-rich region
near the C-terminus, which may allow them to homo- or
heterodimerize. The family also includes a cytoplasmic
poly(A)+ mRNA binding protein, GRSF-1, 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. GRSF-1 also contains three potential RRMs
responsible for the RNA binding, and two auxiliary
domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 48.5 bits (116), Expect = 1e-08
Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++DI +FF L ++ + + + +GR TGEA V+F E A A+ K +E +GHRYI
Sbjct: 13 TENDIFEFFSPLNPVN--VRIEYNA-DGRATGEADVEFATHEDAVAAMSKDREHMGHRYI 69
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B shows high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 47.5 bits (113), Expect = 2e-08
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
+ D+ +FF GL++ + ++ NGR G A V+F + A+ AL++H+E +G RYI
Sbjct: 13 EHDVKEFFHGLDV--EDVIFLKRH-NGRNNGNAIVKFATFQDAKEALKRHRELMGSRYIE 69
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 46.2 bits (110), Expect = 8e-08
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
K ++ FF G+ I GI ++ D G+ GEAYV+FV +E A A + H++++ R I
Sbjct: 13 KGEVLAFFAGIAIAEQGIHILYDK-TGKTLGEAYVEFVSEEDAMRAERLHRKKLKGREIL 71
Query: 98 FT 99
Sbjct: 72 LR 73
>gnl|CDD|241173 cd12729, RRM1_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM1 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts. The presence of
Fox 2 can allows hnRNP H and hnRNP F to better compete
with the SR protein ASF/SF2 for binding to FGFR2 exon
IIIc. Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical. Both of them
have been found to bind nuclear-matrix proteins. hnRNP
H activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently
silencing the exon. In addition, the family members
have an extensive glycine-rich region near the
C-terminus, which may allow them to homo- or
heterodimerize. .
Length = 79
Score = 46.4 bits (110), Expect = 1e-07
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 11/82 (13%)
Query: 17 FKVRRQEMDWKLQHTGIVEGKKDDIAQFFDGLEIISN--GITLVEDPFNGRPTGEAYVQF 74
F V+ + + W D++ +FF +I + GI + GRP+GEA+V+
Sbjct: 2 FVVKVRGLPWSCSV--------DEVQRFFSDCKIANGASGIHFIYTR-EGRPSGEAFVEL 52
Query: 75 VDKETAELALQKHKERIGHRYI 96
+E +LAL+K +E +GHRY+
Sbjct: 53 ESEEDVKLALKKDRETMGHRYV 74
>gnl|CDD|241185 cd12741, RRM2_Fusilli, RNA recognition motif 2 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM2 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 100
Score = 46.4 bits (110), Expect = 1e-07
Identities = 25/57 (43%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DG E G+ V+ P +GR TG+A+V F +E A AL KH+E IG RYI
Sbjct: 44 PPCHVLDGNE----GVLFVKKP-DGRATGDAFVLFATEEDAPKALGKHRESIGSRYI 95
>gnl|CDD|241184 cd12740, RRM2_ESRP2, RNA recognition motif 2 in epithelial
splicing regulatory protein 2 (ESRP2) and similar
proteins. This subgroup corresponds to the RRM2 of
ESRP2, also termed RNA-binding motif protein 35B
(RBM35B), which has been identified as an epithelial
cell type-specific regulator of fibroblast growth
factor receptor 2 (FGFR2) splicing. It is required for
expression of epithelial FGFR2-IIIb and the regulation
of CD44, CTNND1 (also termed p120-Catenin) and ENAH
(also termed hMena) splicing. It enhances
epithelial-specific exons of CD44 and ENAH, silences
mesenchymal exons of CTNND1, or both within FGFR2.
ESRP2 contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 107
Score = 46.5 bits (110), Expect = 2e-07
Identities = 22/45 (48%), Positives = 32/45 (71%), Gaps = 1/45 (2%)
Query: 52 SNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ G+ V+ P +GRPTG+A+V F +E A+ AL+KHK +G RYI
Sbjct: 47 TEGLLFVKYP-DGRPTGDAFVLFACEEYAQNALKKHKGILGKRYI 90
>gnl|CDD|240953 cd12509, RRM3_ESRPs_Fusilli, RNA recognition motif 3 in
epithelial splicing regulatory protein ESRP1, ESRP2,
Drosophila RNA-binding protein Fusilli and similar
proteins. This subfamily corresponds to the RRM3 of
ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of the fibroblast growth factor
receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and
CTNND1 (also termed p120-Catenin) transcripts. They are
highly conserved paralogs and specifically bind to
GU-rich binding site. ESRP1 and ESRP2 contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The family also includes Drosophila fusilli (fus) gene
encoding RNA-binding protein Fusilli. Loss of fusilli
activity causes lethality during embryogenesis in
flies. Drosophila Fusilli can regulate endogenous FGFR2
splicing and functions as a splicing factor. Fusilli
shows high sequence homology to ESRPs and contains
three RRMs as well. It also has an N-terminal domain
with unknown function and a C-terminal domain
particularly rich in alanine, glutamine, and serine. .
Length = 81
Score = 45.5 bits (108), Expect = 2e-07
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 39 DDIAQFFDGL--EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
+DI F L I G+ +V + GRP+G+A++Q + E A A + HK +G RY
Sbjct: 16 EDILNFLGELARSIAPQGVHMVLNA-QGRPSGDAFIQMLSAEFATRAANELHKHHMGERY 74
Query: 96 I 96
I
Sbjct: 75 I 75
>gnl|CDD|241183 cd12739, RRM2_ESRP1, RNA recognition motif 2 in epithelial
splicing regulatory protein 1 (ESRP1) and similar
proteins. This subgroup corresponds to the RRM2 of
ESRP1, also termed RNA-binding motif protein 35A
(RBM35A), which has been identified as an epithelial
cell type-specific regulator of fibroblast growth
factor receptor 2 (FGFR2) splicing. It is required for
expression of epithelial FGFR2-IIIb and the regulation
of CD44, CTNND1 (also termed p120-Catenin) and ENAH
(also termed hMena) splicing. It enhances
epithelial-specific exons of CD44 and ENAH, silences
mesenchymal exons of CTNND1, or both within FGFR2.
Additional research indicated that ESRP1 functions as a
tumor suppressor in colon cancer cells. It may be
involved in posttranscriptional regulation of various
genes by exerting a differential effect on protein
translation via 5' untranslated regions (UTRs) of
mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 109
Score = 45.4 bits (107), Expect = 3e-07
Identities = 22/43 (51%), Positives = 30/43 (69%), Gaps = 1/43 (2%)
Query: 54 GITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
GI V P + RPTG+A+V F +E A+ AL+KHK+ +G RYI
Sbjct: 49 GILFVTYP-DSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYI 90
>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding
protein 12 (RBM12) and similar proteins. This
subfamily corresponds to the RRM3 of RBM12. RBM12, also
termed SH3/WW domain anchor protein in the nucleus
(SWAN), is ubiquitously expressed. It contains five
distinct RNA binding motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. The biological role of
RBM12 remains unclear. .
Length = 101
Score = 44.9 bits (106), Expect = 4e-07
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 35 EGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
E + + FF L+I+ + I + P NG+ TGE +V+F ++ + AL +HK+ +G+R
Sbjct: 20 EAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFVEFRNEADYKAALCRHKQYMGNR 78
Query: 95 YI 96
+I
Sbjct: 79 FI 80
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 78
Score = 43.6 bits (103), Expect = 9e-07
Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 3/59 (5%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+D++ FF GL++ +G+ +++ G G + V+F KE A L++ ++ +G RYI
Sbjct: 13 EDNVRDFFSGLKV--DGVIFLKNR-RGLNNGNSMVKFATKEDAIEGLKRDRQYMGSRYI 68
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 42.5 bits (101), Expect = 2e-06
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 35 EGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKER-IGH 93
++D+ +FF + G+ LV + RP G A+V+F E AE AL+K +
Sbjct: 9 SVTEEDLREFFSPYGKV-EGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKLNGLVLDG 65
Query: 94 RYI 96
R +
Sbjct: 66 RTL 68
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L)
and similar proteins. PABPs are highly conserved
proteins that bind to the poly(A) tail present at the
3' ends of most eukaryotic mRNAs. They have been
implicated in the regulation of poly(A) tail length
during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping.
ePABP-2 is predominantly located in the cytoplasm and
PABP-2 is located in the nucleus. In contrast to the
type I PABPs containing four copies of RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), the type II PABPs
contains a single highly-conserved RRM. This subfamily
also includes Saccharomyces cerevisiae RBP29 (SGN1,
YIR001C) gene encoding cytoplasmic mRNA-binding protein
Rbp29 that binds preferentially to poly(A). Although
not essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 42.3 bits (100), Expect = 2e-06
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+++ + F I N IT++ D F G+P G AY++F+DK + E AL
Sbjct: 14 EELQEHFKSCGTI-NRITILCDKFTGQPKGFAYIEFLDKSSVENALL 59
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 41.4 bits (98), Expect = 5e-06
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
++++ + F + + + LV D G+ G A+V+F +E AE AL+ + + + R
Sbjct: 12 TEEELRELFSKFGKVES-VRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRP 70
Query: 96 I 96
+
Sbjct: 71 L 71
>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM1 of GRSF-1, 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. GRSF-1
contains three potential RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 79
Score = 41.7 bits (98), Expect = 6e-06
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 11/83 (13%)
Query: 16 VFKVRRQEMDWKLQHTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFN--GRPTGEAYVQ 73
VF VR + + W +D+ FFD I NG V N G+P G+A ++
Sbjct: 1 VFIVRAKGLPWSC--------TAEDVMNFFDDCRI-RNGENGVHFLLNRDGKPRGDALIE 51
Query: 74 FVDKETAELALQKHKERIGHRYI 96
+E + AL++H+ +G RY+
Sbjct: 52 LESEEDVQKALEQHRHYMGQRYV 74
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic
translation initiation factor 4B (eIF-4B) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4B, a multi-domain RNA-binding protein that has
been primarily implicated in promoting the binding of
40S ribosomal subunits to mRNA during translation
initiation. It contains two RNA-binding domains; the
N-terminal well-conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), binds the 18S rRNA of the
40S ribosomal subunit and the C-terminal basic domain
(BD), including two arginine-rich motifs (ARMs), binds
mRNA during initiation, and is primarily responsible
for the stimulation of the helicase activity of eIF-4A.
eIF-4B also contains a DRYG domain (a region rich in
Asp, Arg, Tyr, and Gly amino acids) in the middle,
which is responsible for both, self-association of
eIF-4B and binding to the p170 subunit of eIF3.
Additional research indicates that eIF-4B can interact
with the poly(A) binding protein (PABP) in mammalian
cells, which can stimulate both, the eIF-4B-mediated
activation of the helicase activity of eIF-4A and
binding of poly(A) by PABP. eIF-4B has also been shown
to interact specifically with the internal ribosome
entry sites (IRES) of several picornaviruses which
facilitate cap-independent translation initiation. .
Length = 77
Score = 41.6 bits (98), Expect = 6e-06
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFN-GRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+DI +FF GL + S + L +P + GR G Y +F D+++ AL + E + +R I
Sbjct: 16 EDIKEFFRGLNVSS--VRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRI 72
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding
protein 19 (RBM19) and similar proteins. This
subfamily corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 41.2 bits (97), Expect = 6e-06
Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 3/60 (5%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K+ I +FF L+ ++ I +V++ +GR TG A+V +E + AL+++K+ +G RYI
Sbjct: 13 KEKHIREFFSPLKPVA--IRIVKND-HGRKTGFAFVDLKSEEDLKKALKRNKDYMGGRYI 69
>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM3 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and they play an important role in
efficiently silencing the exon. Members in this family
can regulate the alternative splicing of the fibroblast
growth factor receptor 2 (FGFR2) transcripts, and
function as silencers of FGFR2 exon IIIc through an
interaction with the exonic GGG motifs. The lack of
RRM1 could account for the reduced silencing activity
within hnRNP H3. In addition, like other hnRNP H
protein family members, hnRNP H3 has an extensive
glycine-rich region near the C-terminus, which may
allow it to homo- or heterodimerize. .
Length = 75
Score = 40.8 bits (95), Expect = 1e-05
Identities = 27/59 (45%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ DIA FF L I I + D GR TGEA V+FV E A A+ K K + HRYI
Sbjct: 14 ESDIANFFSPLTPIRVHIDIGAD---GRATGEADVEFVTHEDAVAAMSKDKNHMQHRYI 69
>gnl|CDD|241193 cd12749, RRM4_RBM12, RNA recognition motif 4 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM4 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 88
Score = 41.0 bits (96), Expect = 1e-05
Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
K DI QF +G+ + N + ++ D NG+ G+A VQF ++ A + + H++++ R +F
Sbjct: 13 KKDILQFLEGIGVDENSVQVLVDN-NGQGLGQALVQFKSEDDARKSERLHRKKLNGRDVF 71
>gnl|CDD|240954 cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM1 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 74
Score = 38.8 bits (91), Expect = 6e-05
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
DI +FF GL I G+ ++ G GEA++ F E A LA+ +
Sbjct: 17 DIRRFFSGLTIPDGGVHII-----GGEMGEAFIAFATDEDARLAMSR 58
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM2 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 73
Score = 38.1 bits (89), Expect = 9e-05
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELAL 84
D I + F IS + L DP +GRP G YV+F +E A+ AL
Sbjct: 13 DSIYEAFGEYGEIS-SVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 38.1 bits (89), Expect = 1e-04
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 37 KKDDIAQFF-DGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRY 95
++DD+ +FF + E++ + + +D +GR G +V+F +E A+ AL+K E + R
Sbjct: 12 EQDDLEEFFKECGEVVD--VRIAQD-DDGRSKGFGHVEFATEEGAQKALEKSGEELLGRE 68
Query: 96 IF 97
I
Sbjct: 69 IR 70
>gnl|CDD|241186 cd12742, RRM3_ESRP1_ESRP2, RNA recognition motif in epithelial
splicing regulatory protein ESRP1, ESRP2 and similar
proteins. This subgroup corresponds to the RRM3 of
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B). These are epithelial-specific RNA binding
proteins that promote splicing of the epithelial
variant of the fibroblast growth factor receptor 2
(FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. They are highly
conserved paralogs and specifically bind to GU-rich
binding site. ESRP1 and ESRP2 contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 81
Score = 37.5 bits (87), Expect = 2e-04
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
+DI +F +I +G+ +V + GRP+G+A++Q E A LA QK HK+ + RY
Sbjct: 16 EDILEFLGEFAADIRPHGVHMVLNQ-QGRPSGDAFIQMKSAERAFLAAQKCHKKMMKDRY 74
Query: 96 I 96
+
Sbjct: 75 V 75
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
++D+ F I + I +V D GR G A+V+F D+E AE AL+ + + +G R +
Sbjct: 12 EEDLKDLFSKFGPIES-IRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 18/60 (30%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
+D++ + F I++ + LV++ + G+ G AYV+F ++E+ + AL+ +E I R +F
Sbjct: 13 EDELRKLFSKCGEITD-VRLVKN-YKGKSKGYAYVEFENEESVQEALKLDRELIKGRPMF 70
>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM3 of G-rich sequence factor 1
(GRSF-1), 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. GRSF-1 contains three potential RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for the RNA binding. In addition,
GRSF-1 has two auxiliary domains, an acidic
alpha-helical domain and an N-terminal alanine-rich
region, that may play a role in protein-protein
interactions and provide binding specificity. .
Length = 75
Score = 37.1 bits (86), Expect = 3e-04
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DI FF L+ L+E +GR TGEA V F + A A+ K + + HRYI
Sbjct: 15 QDIVNFFAPLKPTR---ILIEYSSDGRATGEADVHFESHDDAVAAMAKDRAHMQHRYI 69
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 36.3 bits (84), Expect = 5e-04
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELAL 84
+++ F G + N +T++ D F+G P G AY++F DKE+ AL
Sbjct: 14 EELEAHFHGCGSV-NRVTILCDKFSGHPKGFAYIEFSDKESVRTAL 58
>gnl|CDD|241191 cd12747, RRM2_RBM12, RNA recognition motif 2 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM2 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 75
Score = 36.3 bits (84), Expect = 5e-04
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DI FF GL I + I L++D GR G A V+F AL++++ +G RYI
Sbjct: 17 DIRDFFHGLRI--DAIHLLKDHV-GRNNGNALVKFYSPHDTFEALKRNRMLMGQRYI 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 = 36.1 bits (84), Expect = 5e-04
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 30 HTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
H I E DD+ F+ I + L DP GR G ++QF D E A+ AL++
Sbjct: 7 HFNITE---DDLRGIFEPFGEIEF-VQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
>gnl|CDD|241178 cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM3 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F, which represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts. The presence of
Fox 2 can allows hnRNP H and hnRNP F to better compete
with the SR protein ASF/SF2 for binding to FGFR2 exon
IIIc. Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; bothe have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently
silencing the exon. In addition, the family members
have an extensive glycine-rich region near the
C-terminus, which may allow them to homo- or
heterodimerize. .
Length = 76
Score = 36.2 bits (83), Expect = 6e-04
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++DI FF L + I + D GR TGEA V+F E A A+ K K + HRY+
Sbjct: 14 ENDIYNFFSPLNPVRVHIEIGPD---GRVTGEADVEFATHEDAVAAMSKDKANMQHRYV 69
>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 = 35.0 bits (81), Expect = 0.001
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 38 KDDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
++D+ + F EI S + +V D +G+ G A+V+F E AE AL+ + + + R
Sbjct: 12 EEDLRELFSKFGEIES--VRIVRDK-DGKSKGFAFVEFESPEDAEKALEALNGKELDGRK 68
Query: 96 I 96
+
Sbjct: 69 L 69
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM3 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 = 82
Score = 33.7 bits (78), Expect = 0.004
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
++++ + F + +V+D G G A+V+F KE+A+ L+
Sbjct: 13 TEEELKELFSQFGEVKYAR-IVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 33.3 bits (77), Expect = 0.006
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+++ + F+ + + +V D G G YV F K++ LAL+
Sbjct: 14 EELRKHFEDCGDV-EAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the
RRM of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). This
family also includes yeast eIF3-p33, a homolog of
vertebrate eIF-3G, plays an important role in the
initiation phase of protein synthesis in yeast. It
binds both, mRNA and rRNA, fragments due to an RRM near
its C-terminus. .
Length = 77
Score = 33.3 bits (77), Expect = 0.007
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRY 95
+ L +D G+ G A+V F +E AE A++K G Y
Sbjct: 29 VYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN---GFGY 66
>gnl|CDD|241195 cd12751, RRM5_RBM12, RNA recognition motif 5 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM5 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RBMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 76
Score = 33.0 bits (75), Expect = 0.010
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFN--GRPTGEAYVQFVDKETAELALQKHKER-IGHR 94
D+I FF G ++I + L F+ G PTGEA V F ++ A A+ +R IG R
Sbjct: 16 DEILDFFYGYQVIPGSVCL---KFSDKGMPTGEAMVAFESRDEAMAAVVDLNDRPIGSR 71
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 75
Score = 32.0 bits (73), Expect = 0.016
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKER-IGHRYI 96
++I FF G +I ++L+ + NG PTGEA V F A A+++ R IG R +
Sbjct: 15 EEILDFFYGYRVIPGSVSLLYND-NGAPTGEATVAFDTHREAMAAVRELNGRPIGTRKV 72
>gnl|CDD|241189 cd12745, RRM1_RBM12, RNA recognition motif 1 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgrup
corresponds to the RRM1 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 92
Score = 32.3 bits (73), Expect = 0.023
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 27 KLQHTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+LQ IV G D I FF GL I G+ +V G GEA++ F E A L + +
Sbjct: 6 RLQGLPIVAGTMD-IRHFFSGLTIPDGGVHIV-----GGELGEAFIVFATDEDARLGMMR 59
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 31.4 bits (72), Expect = 0.035
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+D+ F +++ ++ D GR G +V+ E A A++K
Sbjct: 14 EDLKDLFGQFGEVTS-ARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 31.2 bits (70), Expect = 0.047
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 41 IAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ Q F + + +V+D GRPTG+ +V+F K A AL++
Sbjct: 16 LEQAFSQFGPVERAVVIVDD--RGRPTGKGFVEFAAKPAARKALER 59
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 31.0 bits (70), Expect = 0.048
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 36 GKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+++ F G I N +T++ D F+G P G AY++F +++ E A+
Sbjct: 11 STAEELEAHFSGCGPI-NRVTILCDKFSGHPKGYAYIEFATRDSVEAAVA 59
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed
in all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64
at U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation
in a more limited set of tissues and cell types,
largely in meiotic and postmeiotic male germ cells, and
to a lesser extent in brain. The loss of CSTF2T will
cause male infertility, as it is necessary for
spermatogenesis and fertilization. Moreover, CSTF2T is
required for expression of genes involved in
morphological differentiation of spermatids, as well as
for genes having products that function during
interaction of motile spermatozoa with eggs. It
promotes germ cell-specific patterns of polyadenylation
by using its RRM to bind to different sequence elements
downstream of polyadenylation sites than does CstF64.
The family also includes yeast ortholog mRNA
3'-end-processing protein RNA15 and similar proteins.
RNA15 is a core subunit of cleavage factor IA (CFIA),
an essential transcriptional 3'-end processing factor
from Saccharomyces cerevisiae. RNA recognition by CFIA
is mediated by an N-terminal RRM, which is contained in
the RNA15 subunit of the complex. The RRM of RNA15 has
a strong preference for GU-rich RNAs, mediated by a
binding pocket that is entirely conserved in both yeast
and vertebrate RNA15 orthologs.
Length = 75
Score = 30.7 bits (70), Expect = 0.051
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELAL 84
+ + + F + ++S LV D G+P G + +F D ETA A+
Sbjct: 13 EQLIEIFSEVGPVVS--FRLVTDRDTGKPKGYGFCEFEDIETAASAI 57
>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 = 30.6 bits (70), Expect = 0.059
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 70 AYVQFVDKETAELALQKHKERIGHRY 95
YVQF E+A A+ ++G Y
Sbjct: 44 CYVQFTSPESAAAAVALLNGKLGEGY 69
>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 = 30.3 bits (69), Expect = 0.078
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D + ++F I + ++ D G+ G +V F DKE+AE A +
Sbjct: 15 DSLRKYFSQFGEIEEAV-VITDRQTGKSRGYGFVTFKDKESAERACK 60
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as
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 has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 30.6 bits (69), Expect = 0.079
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHK 88
++D+ FF + I + +V DP G G +V F E A+ AL K K
Sbjct: 12 TQEDLTDFFSDVAPIKHA-VVVTDPETGESRGYGFVTFAMLEDAQEALAKLK 62
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 30.1 bits (68), Expect = 0.086
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+DD+ +FF G EI S + L D G G +V F D+E+ + AL+
Sbjct: 13 EDDVREFFKGCEITS--VRLATDKETGEFKGFGHVDFADEESLDAALK 58
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM2 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional 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. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. p54nrb forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manner. It also forms a heterodimer with polypyrimidine
tract-binding protein-associated-splicing factor (PSF).
p54nrb contains two conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 30.3 bits (68), Expect = 0.10
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 51 ISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKE 89
+ + +V+D GRPTG+ V+F K +A AL + +
Sbjct: 26 VERAVVIVDD--RGRPTGKGIVEFAGKPSARKALDRCSD 62
>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 = 29.4 bits (67), Expect = 0.14
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 49 EIISN-----GITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
EI SN + L D P G AYV+F E AE A++
Sbjct: 17 EIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58
>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 = 31.0 bits (70), Expect = 0.15
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 10/89 (11%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFT 99
D+ +FF + + + + ++D + R G AYV+F D E+ AL +
Sbjct: 105 DLYEFFSKVGKVRD-VQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQM-------LL 156
Query: 100 GHRYTVQHRAPRCETSIPVSSSTHKPGRH 128
G VQ + + E + ++TH+PG
Sbjct: 157 GRPIIVQ--SSQAEKNRAAKAATHQPGDI 183
Score = 28.3 bits (63), Expect = 1.4
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 30 HTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
H I E ++ Q F+ I + + L DP GR G ++QF D E A+ AL+
Sbjct: 195 HFNITE---QELRQIFEPFGDIED-VQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor 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. 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 = 29.6 bits (66), Expect = 0.16
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERI 91
D+ +FF + + + + ++ D + R G AYV+FVD + LA+ +R+
Sbjct: 17 DLEEFFSTVGKVRD-VRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRV 67
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 29.4 bits (67), Expect = 0.16
Identities = 11/27 (40%), Positives = 12/27 (44%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQK 86
D R G AYV F + AE AL
Sbjct: 34 DLITRRSLGYAYVNFQNPADAERALDT 60
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 29.2 bits (66), Expect = 0.19
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 39 DDIAQFF-DGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+D+ F + S + L+ D G+ G A+V+F E AL+ H + R I
Sbjct: 15 EDLLAHFKNAGAPPS--VRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKI 71
>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM5 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 77
Score = 29.1 bits (65), Expect = 0.24
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKER-IGHRYIF 97
++I FF G +I + +++ + G PTG A V + A A+ + +R IG R +
Sbjct: 15 NEILDFFHGYRVIPDSVSMQYNE-QGLPTGTAIVAMENYYEAMAAINELNDRPIGPRKVK 73
Query: 98 FT 99
+
Sbjct: 74 LS 75
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They 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.
Length = 75
Score = 28.9 bits (65), Expect = 0.24
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 58 VEDPFNGRPTGEAYVQFVDKETAELALQ 85
V+D G+ G +V FV KE AE A+Q
Sbjct: 32 VKDMQTGKSKGYGFVSFVKKEDAENAIQ 59
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic
translation initiation factor 4H (eIF-4H) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4H, also termed Williams-Beuren syndrome
chromosomal region 1 protein, which, together with
elf-4B/eIF-4G, serves as the accessory protein of RNA
helicase eIF-4A. eIF-4H contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It
stimulates protein synthesis by enhancing the helicase
activity of eIF-4A in the initiation step of mRNA
translation. .
Length = 76
Score = 28.8 bits (65), Expect = 0.27
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 32 GIVEGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELAL 84
V+G D+ F L + S + LV D + G YV+F D E+ + AL
Sbjct: 12 NTVQG---DLDAIFKDLSVKS--VRLVRDKETDKFKGFCYVEFEDVESLKEAL 59
>gnl|CDD|241187 cd12743, RRM3_Fusilli, RNA recognition motif 3 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM3 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 85
Score = 29.1 bits (65), Expect = 0.29
Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 50 IISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFF 98
I+ G+ +V + G+P+GEA++Q +++A Q + +RY+ F
Sbjct: 29 IVFQGVHMVYNA-QGQPSGEAFIQMDSEQSASACAQ----QRHNRYMVF 72
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 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. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 28.7 bits (65), Expect = 0.34
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 62 FNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTV 105
F+G G A+V + +KE A+ A+++ H Y G R V
Sbjct: 37 FSGLNRGYAFVTYTNKEAAQRAVKQ-----LHNYEIRPGKRLGV 75
>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM3 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 81
Score = 28.9 bits (65), Expect = 0.34
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKE 89
K DI FF L++ + IT + D G+ T A+V F AL HK
Sbjct: 14 KRDIRAFFGDLDLPDSQITFLSDK-KGKRTRSAFVMFKSLRDYCAALAHHKR 64
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as
cyclin D1, where it represses transcription by
disrupting complex formation. TAF15 (TAFII68), also
termed TATA-binding protein-associated factor 2N
(TAF2N), or RNA-binding protein 56 (RBP56), originally
identified as a TAF in the general transcription
initiation TFIID complex, is a novel RNA/ssDNA-binding
protein with homology to the proto-oncoproteins FUS and
EWS (also termed EWSR1), belonging to the FET family as
well. TAF15 likely functions in RNA polymerase II (RNAP
II) transcription by interacting with TFIID and
subunits of RNAP II itself. TAF15 is also associated
with U1 snRNA, chromatin and RNA, in a complex distinct
from the Sm-containing U1 snRNP that functions in
splicing. Like other members in the FET family, both
FUS and TAF15 contain an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. .
Length = 86
Score = 28.8 bits (64), Expect = 0.40
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 39 DDIAQFFDGLEIISNG-------ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ +A +F + II I L D G+ GEA V F D +A+ A+
Sbjct: 17 ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID 70
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 76
Score = 28.2 bits (63), Expect = 0.43
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 35 EGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELAL-QKHKERIGH 93
E +D I Q F I + I + DP + G A+V++ E A+LAL Q + +G
Sbjct: 11 ELGEDTIRQAFSPFGPIKS-IDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGG 69
Query: 94 RYI 96
R I
Sbjct: 70 RNI 72
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3'
processing machinery that functions in UGUA-mediated
poly(A) site recognition, the regulation of alternative
poly(A) site selection, mRNA export, and mRNA splicing.
It is a complex composed of a small 25 kDa (CFIm25)
subunit and a larger 59/68/72 kDa subunit. Two separate
genes, CPSF6 and CPSF7, code for two isoforms of the
large subunit, CFIm68 and CFIm59. Structurally related
CFIm68 and CFIm59, also termed cleavage and
polyadenylation specificity factor subunit 6 (CPSF7),
or cleavage and polyadenylation specificity factor 59
kDa subunit (CPSF59), are functionally redundant. Both
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. Their
N-terminal RRM mediates the interaction with CFIm25,
and also serves to enhance RNA binding and facilitate
RNA looping. .
Length = 76
Score = 28.0 bits (63), Expect = 0.47
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
I E NG+ G AYV+F + A +K
Sbjct: 30 IKFFEHKANGKSKGFAYVEFASEAAAAAVKEK 61
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is 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 = 0.51
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ ++ D + R G AYV+F D+E+ LAL
Sbjct: 29 VRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of 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).
SRSF10 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. 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. .
Length = 84
Score = 28.4 bits (63), Expect = 0.53
Identities = 14/26 (53%), Positives = 15/26 (57%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQ 85
D + RP G AYVQF D AE AL
Sbjct: 35 DFYTRRPRGFAYVQFEDVRDAEDALH 60
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 27.9 bits (62), Expect = 0.55
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 35 EGKKDDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGH 93
+ K D+ ++F E++ T+ DP GR G +V F D + E L + + ++
Sbjct: 9 DTTKKDLKEYFSKFGEVVD--CTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEHKLDG 66
Query: 94 RYI 96
R I
Sbjct: 67 RVI 69
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 28.2 bits (63), Expect = 0.57
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 63 NGRPTGEAYVQFVDKETAELALQKHKERI--GHRYI 96
G+ TG A + F A A K RI G+R +
Sbjct: 37 GGKSTGIANITFKRAGDATKAYDKFNGRIDDGNRKM 72
>gnl|CDD|241192 cd12748, RRM4_RBM12B, RNA recognition motif 4 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM4 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 76
Score = 27.8 bits (62), Expect = 0.59
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
K ++ +FF I + I L+ D G GEA V+F +E A A ER+ +
Sbjct: 14 KVEVQKFFAPFNIDEDDIYLLYDD-KGVGLGEALVKFKSEEQAMKA-----ERLNGQRFL 67
Query: 98 FT 99
T
Sbjct: 68 GT 69
>gnl|CDD|241188 cd12744, RRM1_RBM12B, RNA recognition motif 1 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM1 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 79
Score = 27.9 bits (62), Expect = 0.64
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 27 KLQHTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELAL 84
+LQ +V G +D I FF GL I G+ ++ G GEA++ F E A A+
Sbjct: 5 RLQGLPVVAGSED-IRHFFTGLRIPDGGVHII-----GGELGEAFIIFATDEDARRAM 56
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 27.9 bits (63), Expect = 0.66
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 63 NGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQ 106
NG G+A ++ +E+ ELA+Q + G++ V+
Sbjct: 46 NGNLKGDALCCYLKEESVELAIQ-----LLDGTEIGRGYKMKVE 84
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 27.6 bits (61), Expect = 0.73
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K D+ +F +++ T+ DP GR G ++ F D + E L++ + R+ R I
Sbjct: 13 KKDLKDYFTKFGEVTD-CTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDGRLI 70
>gnl|CDD|218204 pfam04672, Methyltransf_19, S-adenosyl methyltransferase. This
family contains a SAM (S-adenosyl methyltransferase)
domain, with a central beta sheet with 3 alpha-helices
on both sides. Crystal packing analysis of the structure
PDB:3GIW suggests that a monomer is the solution state
oligomeric form. An unidentified ligand (UNL, cyan) was
found at the putative active site surrounded by the
residues His57, His170, Phe171, Tyr216 and Met22. The
UNL is likely to be a phenylalanine or
phenylalanine-like molecule. (details derived from
TOPSAN).
Length = 268
Score = 28.8 bits (65), Expect = 0.74
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEA 70
++A+FFDGLE++ G+ V RP GEA
Sbjct: 221 AEVARFFDGLELVEPGLVPVTR---WRPDGEA 249
>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 = 0.77
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETA-----ELALQKHKERI 91
K+DD+ + F +S + + D +G+ G AYV F+D E A EL + + R+
Sbjct: 15 KEDDLEKLFSKFGELSE-VHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRL 73
Query: 92 GH 93
H
Sbjct: 74 IH 75
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 27.4 bits (61), Expect = 0.92
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
G+ G V+F DKE+ + AL+ ++ + R +
Sbjct: 37 EGKSRGCGVVEFKDKESVQKALETMNRYELKGRKL 71
>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 = 27.7 bits (62), Expect = 0.95
Identities = 21/49 (42%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELAL-QKHKERIGHRYI---FFTGHRYT 104
D + RP G AYVQF D AE AL + R R I F G R T
Sbjct: 35 DFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFAQGDRKT 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 = 26.7 bits (60), Expect = 0.95
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 62 FNGRPTGEAYVQFVDKETAELALQKHKERI 91
+ G A+V+F +E AE A+Q +
Sbjct: 16 LLKKKPGFAFVEFSTEEAAEKAVQYLNGVL 45
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 27.3 bits (61), Expect = 1.00
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 50 IISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
II N +T G P G +V+F D+ TAE L K
Sbjct: 32 IIRNKLT-------GGPAGYCFVEFADEATAERCLHK 61
>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 = 27.2 bits (61), Expect = 1.1
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 38 KDDIAQFFDGL-EIISNGITLVEDPFNGRP-TGEAYVQFVDKETAELALQKHKERIGHRY 95
+DD+ F E+ S I +D GR G A+V F D +AE ALQ + +G R
Sbjct: 14 EDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQLNGTELGGRK 73
Query: 96 I 96
I
Sbjct: 74 I 74
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 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 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 RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 27.3 bits (61), Expect = 1.1
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+++ + F+ IS + L D R G A+V F+ E A A
Sbjct: 14 EELRELFEAFGEISE-VHLPLDKETKRSKGFAFVSFMFPEHAVKAYS 59
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, and in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; it binds RNA through its RRM domains. .
Length = 79
Score = 27.2 bits (60), Expect = 1.3
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ L+ DP +G+ G A++ F KE A+ A++
Sbjct: 31 LRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 26.8 bits (60), Expect = 1.4
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 30 HTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
H + E +D+ + F + + + + D +GR G A V F +E AE A+++
Sbjct: 9 HYDVTE---EDLEELFGRVGEVKK-VKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is 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 = 81
Score = 27.0 bits (60), Expect = 1.6
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
+G+P G AYV++ ++ +A A+ K
Sbjct: 39 SGKPKGLAYVEYENESSASQAVLK 62
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 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. The family 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 contains 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 = 80
Score = 26.9 bits (60), Expect = 1.7
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 64 GRPTGEAYVQFVDKETAELALQKHKE 89
GR TGE V+F K A+ A+++ E
Sbjct: 37 GRSTGEGIVEFSRKPGAQAAIKRCSE 62
>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 = 26.4 bits (58), Expect = 1.9
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 63 NGRPTGEAYVQFVDKETAELALQ 85
NGRP G A+V+F E A+ AL
Sbjct: 34 NGRPKGYAFVEFESAEDAKEALN 56
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 26.5 bits (58), Expect = 1.9
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 56 TLVEDPFNGRPTGEAYVQFVDKETAE--LALQKHK 88
T+ DP GR G +V F D + + L L++HK
Sbjct: 30 TIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHK 64
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic
RNA-binding protein 18 and similar proteins. This
subfamily corresponds to the RRM of RBM18, a putative
RNA-binding protein containing a well-conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The
biological role of RBM18 remains unclear. .
Length = 80
Score = 26.5 bits (59), Expect = 2.2
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 61 PFNGRPTGEAYVQFVDKETAELALQK 86
P G+P G +V F KE AE AL+
Sbjct: 38 PLKGQPRGYCFVTFETKEEAEKALKS 63
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 26.6 bits (59), Expect = 2.2
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 40 DIAQFFDGLEIISNG-------ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D+A+ F + II I L +D G P GEA V + D A A++
Sbjct: 14 DLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHAASAAIE 66
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 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. NAM8
also contains three RRMs. .
Length = 81
Score = 26.5 bits (59), Expect = 2.4
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKH 87
+ ++ + G+ G +V+F E AE ALQ
Sbjct: 29 VKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61
>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 = 26.1 bits (58), Expect = 2.4
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 71 YVQFVDKETAELALQK 86
+VQFV + AE A+Q+
Sbjct: 41 FVQFVHRAAAEAAIQQ 56
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 26.1 bits (57), Expect = 2.5
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 38 KDDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K D+ +F E++ TL DP GR G +V F + E+ + + + + ++ + I
Sbjct: 12 KKDLKDYFSKFGEVVD--CTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVI 69
>gnl|CDD|203412 pfam06228, ChuX_HutX, Haem utilisation ChuX/HutX. This family is
found within haem utilisation operons. It has a similar
structure to that of pfam05171. pfam05171 usually occurs
as a duplicated domain, but this domain occurs as a
single domain and forms a dimer. The organisation of the
dimer is very similar to that of the duplicated
pfam05171 domains. It binds haem via conserved
histidines.
Length = 141
Score = 26.8 bits (60), Expect = 2.9
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKE 78
I LV PF G+ + +QF D +
Sbjct: 91 IALVSRPFMGKES--HSLQFFDAQ 112
>gnl|CDD|181659 PRK09121, PRK09121,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase; Provisional.
Length = 339
Score = 27.3 bits (61), Expect = 3.0
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 26 WKLQHTGIVEGKKDDI-----AQFFDGLEIISNG 54
WKLQ ++EGK+D + Q G++I+S+G
Sbjct: 27 WKLQGEELIEGKQDALRLSLQEQEDAGIDIVSDG 60
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of 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). SRSF12 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. SRSF12 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. .
Length = 84
Score = 26.1 bits (57), Expect = 3.2
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELAL 84
D + RP G AY+QF D AE AL
Sbjct: 35 DFYTRRPRGFAYIQFEDVRDAEDAL 59
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response
element (IGFRE). Moreover, PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. PSF is an essential pre-mRNA
splicing factor and is dissociated from PTB and binds
to U1-70K and serine-arginine (SR) proteins during
apoptosis. PSF forms a heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO). The PSF/p54nrb complex
displays a variety of functions, such as DNA
recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), which are
responsible for interactions with RNA and for the
localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 80
Score = 25.8 bits (56), Expect = 3.3
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 51 ISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERI 91
+ + +V+D GR TG+ V+F K A A ++ E +
Sbjct: 26 VERAVVIVDD--RGRSTGKGIVEFASKPAARKAFERCTEGV 64
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 27.1 bits (60), Expect = 3.3
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 40 DIAQFFDGLEIISNGITLVE 59
D Q +DGL+I +N IT+ +
Sbjct: 75 DKMQVYDGLKITTNQITIQD 94
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 25.8 bits (57), Expect = 3.4
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
D+I +F EI + L+ P GR G A++ F +E A+ AL E +G R++
Sbjct: 13 DEIRSYFSYCGEIEE--LDLMTFPDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFL 69
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 26.1 bits (57), Expect = 3.4
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ---KHKERIG 92
+ L+ DP G G A+V F KE A+ A++ H+ R G
Sbjct: 31 LRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLYNNHEIRPG 71
>gnl|CDD|233608 TIGR01869, casC_Cse4, CRISPR-associated protein Cas7/Cse4/CasC,
subtype I-E/ECOLI. CRISPR is a term for Clustered,
Regularly Interspaced Short Palidromic Repeats. A number
of protein families appear only in association with
these repeats and are designated Cas (CRISPR-Associated)
proteins. This family is represented by CT1975 of
Chlorobium tepidum and is part of the Ecoli subtype of
CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas
Subtype Ecoli protein 4 [Mobile and extrachromosomal
element functions, Other].
Length = 325
Score = 27.1 bits (60), Expect = 3.5
Identities = 14/86 (16%), Positives = 25/86 (29%), Gaps = 6/86 (6%)
Query: 3 HCRTGEVSDRYIEVFKVRRQEMDWKLQHTGIVEGKKD-DIAQFFDGLEIISNGITLVEDP 61
G R + + +L G E + D A+ GL++ G +
Sbjct: 54 EALAGHGGIRSRRLA----TLLAKRLLELGYDEDIAEPDAAKIAYGLKLAK-GKKSDKLL 108
Query: 62 FNGRPTGEAYVQFVDKETAELALQKH 87
P + ++ ELA
Sbjct: 109 LLSAPETAWLARLAEELFDELAAAAE 134
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 26.0 bits (58), Expect = 3.5
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 64 GRPTGEAYVQFVDKETAELALQ 85
GR G+A+V F +E A AL
Sbjct: 44 GRMKGQAFVTFPSEEIATKALN 65
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM2 of the sex-lethal protein (SXL)
which governs sexual differentiation and X chromosome
dosage compensation in Drosophila melanogaster. It
induces female-specific alternative splicing of the
transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 26.0 bits (57), Expect = 3.5
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQ 85
L+ D G P G A+V++ +E A+ A+
Sbjct: 32 LLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
>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 = 27.1 bits (60), Expect = 3.8
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELAL-QKHKERIGHRYIFFTGHRYTVQHRAP 110
+ + D R G YV F + AE AL + +R+G + I R R P
Sbjct: 30 VRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPI-----RIMWSQRDP 81
Score = 27.1 bits (60), Expect = 4.2
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
NG+ G +V F +E+A+ A+QK
Sbjct: 125 NGKSRGYGFVHFEKEESAKAAIQK 148
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 27.0 bits (59), Expect = 3.8
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 35 EGKKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
E ++D I + FD I + I + DP G+ G A+V++ E A+LAL++
Sbjct: 118 ELREDTIRRAFDPFGPIKS-INMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 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 = 77
Score = 25.4 bits (56), Expect = 4.2
Identities = 17/62 (27%), Positives = 22/62 (35%), Gaps = 19/62 (30%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELAL-QKHKERIGHRYIFFTGHRYTVQHRAPRCETSIPV 118
DP G+ G +V+F D E L Q+H I R C+ IP
Sbjct: 34 DPKTGQSKGFGFVRFADYEDQVKVLSQRH--MIDGR----------------WCDVKIPN 75
Query: 119 SS 120
S
Sbjct: 76 SK 77
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 27.0 bits (61), Expect = 4.4
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 5/20 (25%)
Query: 118 VSSSTHKPGRHHTLDGPNGG 137
V+++THK TL GP GG
Sbjct: 222 VTTTTHK-----TLRGPRGG 236
>gnl|CDD|173777 cd01027, TOPRIM_RNase_M5_like, TOPRIM_ RNase M5_like: The
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain found in Ribonuclease M5:
(RNase M5) and other small primase-like proteins from
bacteria and archaea. RNase M5 catalyzes the
maturation of 5S rRNA in low G+C Gram-positive
bacteria. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). The
conserved glutamate may act as a general base in
nucleotide polymerization by primases. The DXD motif
may co-ordinate Mg2+, a cofactor required for full
catalytic function.
Length = 81
Score = 25.7 bits (57), Expect = 4.7
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 19/61 (31%)
Query: 33 IVEGKKD--DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKER 90
IVEGK D + + EII NG ++KET EL + ++
Sbjct: 6 IVEGKNDTESLKKLGIEAEIIET---------NG--------SIINKETIELIKKAYRGV 48
Query: 91 I 91
I
Sbjct: 49 I 49
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 25.4 bits (56), Expect = 4.7
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 54 GITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKE 89
G ++ D GR G YV F E A+ A++
Sbjct: 28 GARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDG 63
>gnl|CDD|215594 PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
Length = 581
Score = 26.8 bits (60), Expect = 4.9
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 53 NGITLVEDPF-----NGRPTGEAYVQFVD 76
N L+ DPF R TGE Y + VD
Sbjct: 225 NNEKLLNDPFYIGLRQPRLTGEEYDELVD 253
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation
factor 64 kDa subunit (CstF64), is the vertebrate
conterpart of yeast mRNA 3'-end-processing protein
RNA15. It is expressed in all somatic tissues and is
one of three cleavage stimulatory factor (CstF)
subunits required for polyadenylation. CstF64 contains
an N-terminal RNA recognition motif (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a CstF77-binding domain, a repeated MEARA
helical region and a conserved C-terminal domain
reported to bind the transcription factor PC-4. During
polyadenylation, CstF interacts with the pre-mRNA
through the RRM of CstF64 at U- or GU-rich sequences
within 10 to 30 nucleotides downstream of the cleavage
site. CSTF2T, also termed tauCstF64, is a paralog of
the X-linked cleavage stimulation factor CstF64 protein
that supports polyadenylation in most somatic cells. It
is expressed during meiosis and subsequent haploid
differentiation in a more limited set of tissues and
cell types, largely in meiotic and postmeiotic male
germ cells, and to a lesser extent in brain. The loss
of CSTF2T will cause male infertility, as it is
necessary for spermatogenesis and fertilization.
Moreover, CSTF2T is required for expression of genes
involved in morphological differentiation of
spermatids, as well as for genes having products that
function during interaction of motile spermatozoa with
eggs. It promotes germ cell-specific patterns of
polyadenylation by using its RRM to bind to different
sequence elements downstream of polyadenylation sites
than does CstF64. .
Length = 75
Score = 25.1 bits (55), Expect = 5.6
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQ 85
LV D G+P G + ++ D+ETA A++
Sbjct: 30 LVYDRETGKPKGYGFCEYKDQETALSAMR 58
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is 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 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 25.4 bits (55), Expect = 5.9
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
DDI F IS+ +V+D G+ G +V F +K AE A+Q+
Sbjct: 16 DDIKAAFAPFGRISDA-RVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 25.0 bits (55), Expect = 5.9
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTV 105
L DP+ G+ G AYV + + +A A KE++ + + + G+R V
Sbjct: 31 LKRDPYTGKSKGFAYVTYSNPASAIYA----KEKL-NGFEYPPGNRLKV 74
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing
Sarcoma Protein (EWS). This subgroup corresponds to
the RRM of EWS, also termed Ewing sarcoma breakpoint
region 1 protein, a member of the FET (previously TET)
(FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding
proteins whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the
FET family, EWS contains an N-terminal Ser, Gly, Gln
and Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U
RNA. It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor
gene. .
Length = 84
Score = 25.2 bits (55), Expect = 5.9
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 39 DDIAQFFDGLEIIS----NGITLVE---DPFNGRPTGEAYVQFVDKETAELALQ 85
+++A FF ++ G +V D G+P G+A V + D +A+ A++
Sbjct: 15 EELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPSAKAAVE 68
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 25.2 bits (55), Expect = 6.0
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 62 FNGRPTGEAYVQFVDKETAELALQ 85
F+G G A+V + KE A+LA++
Sbjct: 37 FSGENRGYAFVMYTTKEEAQLAIR 60
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate
probable RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 25.4 bits (55), Expect = 6.1
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERI 91
D+ FF + + + + ++ D + R G AYV+F + ++ LA+ +R+
Sbjct: 17 DLEDFFSAVGKVRD-VRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRL 67
>gnl|CDD|240960 cd12516, RRM1_RBM26, RNA recognition motif 1 of vertebrate
RNA-binding protein 26 (RBM26). This subgroup
corresponds to the RRM1 of RBM26, also known as
cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2,
which 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. .
Length = 76
Score = 25.0 bits (54), Expect = 6.2
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 62 FNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHR 102
+ G P G A +QF E A+ A+ + + +R+I HR
Sbjct: 36 YKGDPEG-ALIQFATHEEAKKAISSTEAVLNNRFIKVYWHR 75
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 25.0 bits (55), Expect = 6.7
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 65 RPTGEAYVQFVDKETAELALQ 85
RP G AY +F E AE ++
Sbjct: 44 RPLGIAYAEFSSPEQAEKVVK 64
>gnl|CDD|224572 COG1658, COG1658, Small primase-like proteins (Toprim domain)
[DNA replication, recombination, and repair].
Length = 127
Score = 25.8 bits (57), Expect = 6.9
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 33 IVEGKKDDIA--QFFDGLEIISNG 54
+VEGK D + + D II+NG
Sbjct: 14 VVEGKDDTASLKRLGDAGVIITNG 37
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar
protein interacting with the FHA domain of pKI-67
(NIFK) and similar proteins. This subgroup corresponds
to the RRM of NIFK and Nop15p. NIFK, also termed MKI67
FHA domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also
includes Saccharomyces cerevisiae YNL110C gene encoding
ribosome biogenesis protein 15 (Nop15p), also termed
nucleolar protein 15. Both, NIFK and Nop15p, contain an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 24.8 bits (55), Expect = 7.1
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 64 GRPTGEAYVQFVDKETAELA 83
G+ G A+V+F E A++
Sbjct: 38 GKSKGYAFVEFESPEVAKIV 57
>gnl|CDD|212145 cd11538, NTP-PPase_u1, Nucleoside Triphosphate
Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain
found in a group of uncharacterized proteins from
bacteria. This family corresponds to a group of
uncharacterized hypothetical proteins from bacteria,
showing a high sequence similarity to the dimeric
2-deoxyuridine 5'-triphosphate nucleotidohydrolase
(dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG
proteins. However, unlike typical tandem-domain MazG
proteins, members in this family consist of a single
MazG-like domain that contains a well conserved
divalent ion-binding motif EXX[E/D].
Length = 97
Score = 25.4 bits (56), Expect = 7.1
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 5 RTGEVSDRYIEVFKVRRQEMDW---KLQ 29
R VSD Y F + R + DW KLQ
Sbjct: 7 RVEAVSDIYAARFGIDRDD-DWYLLKLQ 33
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit
2 (NCBP2), or cell proliferation-inducing gene 55
protein, or NCBP-interacting protein 1 (NIP1). CBP20 is
the small subunit of the nuclear cap binding complex
(CBC), which is a conserved eukaryotic heterodimeric
protein complex binding to 5'-capped polymerase II
transcripts and plays a central role in the maturation
of pre-mRNA and uracil-rich small nuclear RNA (U
snRNA). CBP20 is most likely responsible for the
binding of capped RNA. It contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and interacts with the
second and third domains of CBP80, the large subunit of
CBC. .
Length = 78
Score = 24.8 bits (55), Expect = 7.3
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
D F P G +V++ +E AE A++ + ++ R I
Sbjct: 33 DRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRII 70
>gnl|CDD|224729 COG1816, Add, Adenosine deaminase [Nucleotide transport and
metabolism].
Length = 345
Score = 26.1 bits (58), Expect = 7.9
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 12 RYIEVFKVRRQEMDWKLQ-HTGIVEGKKDDIAQFFD--GLEIISNGITLVEDPF 62
++ +FK+ R KL H G G + I D G E I +GI +EDP
Sbjct: 186 LFVSLFKLARDN-GLKLTIHAG-EAGGPESIRDALDLLGAERIGHGIRAIEDPE 237
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 24.8 bits (54), Expect = 8.0
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELAL 84
+ +V DP G AYVQF D+ E AL
Sbjct: 29 VRIVRDPKTNVGKGFAYVQFKDENAVEKAL 58
>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 = 24.5 bits (54), Expect = 8.1
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 40 DIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
I QFF I + +VE G A ++F ++ A AL K +R+G I
Sbjct: 16 KIRQFFKDCGEIRE-VKIVESE-GGL---VAVIEFETEDEALAALTKDHKRLGGNEI 67
>gnl|CDD|181965 PRK09580, sufC, cysteine desulfurase ATPase component; Reviewed.
Length = 248
Score = 25.9 bits (57), Expect = 8.9
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 124 KPGRHHTLDGPNGGG--TLS 141
+PG H + GPNG G TLS
Sbjct: 25 RPGEVHAIMGPNGSGKSTLS 44
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 25.9 bits (58), Expect = 9.7
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 5/26 (19%)
Query: 57 LVEDPF-----NGRPTGEAYVQFVDK 77
L+ DP + R GE Y +FVD+
Sbjct: 204 LLNDPLYLGWRHPRIRGEEYDEFVDE 229
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 25.7 bits (57), Expect = 9.8
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 5/20 (25%)
Query: 118 VSSSTHKPGRHHTLDGPNGG 137
V+++THK TL GP GG
Sbjct: 225 VTTTTHK-----TLRGPRGG 239
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.424
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: 7,324,956
Number of extensions: 652917
Number of successful extensions: 809
Number of sequences better than 10.0: 1
Number of HSP's gapped: 792
Number of HSP's successfully gapped: 154
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
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: 54 (24.5 bits)