RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3727
(232 letters)
>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 = 133 bits (338), Expect = 9e-41
Identities = 52/75 (69%), Positives = 62/75 (82%), Gaps = 1/75 (1%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMSKD 137
HTVHMRGLP+RA E D+ +FF P+ PV+V I Y +GR +GEADV+FATHEDA+ AMSKD
Sbjct: 1 HTVHMRGLPYRATENDIFEFFSPLNPVNVRIEYNADGRATGEADVEFATHEDAVAAMSKD 60
Query: 138 RTNMQHRYIELFLNS 152
R +M HRYIELFLNS
Sbjct: 61 REHMGHRYIELFLNS 75
>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 = 115 bits (289), Expect = 2e-33
Identities = 45/75 (60%), Positives = 59/75 (78%), Gaps = 1/75 (1%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQAMSKD 137
H VHMRGLPF+A+ +D+ +FF P+ P + I Y +GR +GEADV F +H+DA+ AM+KD
Sbjct: 1 HFVHMRGLPFQASGQDIVNFFAPLKPTRILIEYSSDGRATGEADVHFESHDDAVAAMAKD 60
Query: 138 RTNMQHRYIELFLNS 152
R +MQHRYIELFLNS
Sbjct: 61 RAHMQHRYIELFLNS 75
>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 = 111 bits (279), Expect = 5e-32
Identities = 52/76 (68%), Positives = 62/76 (81%), Gaps = 3/76 (3%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVP--VHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
H VHMRGLPFRA E D+A+FF P+ P VH+DI +GR +GEADV+F THEDA+ AMSK
Sbjct: 1 HFVHMRGLPFRATESDIANFFSPLTPIRVHIDIG-ADGRATGEADVEFVTHEDAVAAMSK 59
Query: 137 DRTNMQHRYIELFLNS 152
D+ +MQHRYIELFLNS
Sbjct: 60 DKNHMQHRYIELFLNS 75
>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 = 107 bits (269), Expect = 1e-30
Identities = 50/76 (65%), Positives = 61/76 (80%), Gaps = 1/76 (1%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQAMSKD 137
H VHMRGLP+RA E D+ +FF P+ PV V I +GR +GEADV+FATHEDA+ AMSKD
Sbjct: 1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKD 60
Query: 138 RTNMQHRYIELFLNSS 153
+ NMQHRY+ELFLNS+
Sbjct: 61 KANMQHRYVELFLNST 76
>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 = 92.6 bits (231), Expect = 1e-24
Identities = 34/73 (46%), Positives = 45/73 (61%), Gaps = 3/73 (4%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIH---YENGRPSGEADVDFATHEDAMQAMSK 136
V +RGLPF A E D+ DFF + IH ++GRP+GEA V+FA+ EDA +A+ K
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60
Query: 137 DRTNMQHRYIELF 149
M RYIE+F
Sbjct: 61 HNNKMGGRYIEVF 73
>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 = 73.5 bits (181), Expect = 3e-17
Identities = 31/76 (40%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVD------IHYENGRPSGEADVDFATHEDAMQA 133
+ MRGLP+ A D+ FF + PV + +GRP+G+A V F T EDA +A
Sbjct: 3 IIRMRGLPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRA 62
Query: 134 MSKDRTNMQHRYIELF 149
+ K + N+ RYIELF
Sbjct: 63 LGKHKENLGSRYIELF 78
>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 = 71.6 bits (176), Expect = 1e-16
Identities = 30/72 (41%), Positives = 44/72 (61%), Gaps = 1/72 (1%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDI-HYENGRPSGEADVDFATHEDAMQAMSKD 137
TV MRG PF E+ + +FF P+ PV + I ++GR +G A VD + ED +A+ ++
Sbjct: 1 FTVKMRGAPFNVKEKHIREFFSPLKPVAIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRN 60
Query: 138 RTNMQHRYIELF 149
+ M RYIELF
Sbjct: 61 KDYMGGRYIELF 72
>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 = 68.9 bits (169), Expect = 1e-15
Identities = 30/77 (38%), Positives = 47/77 (61%), Gaps = 3/77 (3%)
Query: 79 HTVHMRGLPFRANERDVADFFR--PVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMS 135
V +RGLPF ++ ++A FF +VP + + + GR +GEA V FA+ E A +A+
Sbjct: 1 GVVRLRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALG 60
Query: 136 KDRTNMQHRYIELFLNS 152
K + + HRYIE+F +S
Sbjct: 61 KHKEKIGHRYIEIFRSS 77
>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 = 68.6 bits (168), Expect = 2e-15
Identities = 33/72 (45%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMSKD 137
V +RGLP+ E D+ DFFR +V V I GR +GEA V FAT E A +A+ K
Sbjct: 4 VRLRGLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKH 63
Query: 138 RTNMQHRYIELF 149
R + +RYIE+F
Sbjct: 64 REEIGNRYIEVF 75
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 63.3 bits (155), Expect = 1e-13
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVH-VDIHYENGRPSGEADVDFATHEDAMQAMSK-DR 138
+++R LP E D+ +FF P V V + RP G A V+FA+ EDA A+ K +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 139 TNMQHRYIE 147
+ R +
Sbjct: 61 LVLDGRTLR 69
>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 = 62.0 bits (151), Expect = 6e-13
Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 5/74 (6%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMS 135
V +RGLP+ A DV +FF + IH+ GRPSGEA ++ + ED +A+
Sbjct: 2 VRIRGLPWSATAEDVLNFFSDCRIKGGENGIHFTYSREGRPSGEAFIELESEEDVEKALE 61
Query: 136 KDRTNMQHRYIELF 149
K +M HRYIE+F
Sbjct: 62 KHNEHMGHRYIEVF 75
>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 = 58.4 bits (141), Expect = 1e-11
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 81 VHMRGLPFRANERDVADFFRP------VVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
V +RGLP+ + +V FF +H I+ GRPSGEA V+ + ED A+
Sbjct: 4 VKVRGLPWSCSVDEVQRFFSDCKIANGASGIHF-IYTREGRPSGEAFVELESEEDVKLAL 62
Query: 135 SKDRTNMQHRYIELF 149
KDR M HRY+E+F
Sbjct: 63 KKDRETMGHRYVEVF 77
>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 = 57.1 bits (138), Expect = 3e-11
Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 83 MRGLPFRANERDVADFFRPVVPVHVD----IHYENGRPSGEADVDFATHEDAMQAMSKDR 138
+RGLPF E +V DFF + VD + G +G + V FAT EDA++ + +DR
Sbjct: 4 LRGLPFSVTEDNVRDFFSGLK---VDGVIFLKNRRGLNNGNSMVKFATKEDAIEGLKRDR 60
Query: 139 TNMQHRYIEL 148
M RYIE+
Sbjct: 61 QYMGSRYIEI 70
>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 = 56.5 bits (136), Expect = 9e-11
Identities = 36/94 (38%), Positives = 55/94 (58%), Gaps = 11/94 (11%)
Query: 69 WVNESSGP------SRHTVHMRGLPFRANERDVADFFR--PVVP--VHVDIHYENGRPSG 118
WV + +GP S TV +RGLPF ++ ++ FF +VP + + + Y+ GR +G
Sbjct: 3 WVLKHNGPTDYDGSSGGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQ-GRSTG 61
Query: 119 EADVDFATHEDAMQAMSKDRTNMQHRYIELFLNS 152
EA V FA+ E A A+ K + + HRYIE+F +S
Sbjct: 62 EAFVQFASKEIAENALGKHKERIGHRYIEIFKSS 95
>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 = 54.8 bits (132), Expect = 2e-10
Identities = 32/72 (44%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKDR 138
V + GLP+ A+E DV +FF V V + NGR +G A V FAT +DA +A+ + R
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGLDVEDVIF-LKRHNGRNNGNAIVKFATFQDAKEALKRHR 60
Query: 139 TNMQHRYIELFL 150
M RYIEL L
Sbjct: 61 ELMGSRYIELML 72
>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 = 54.8 bits (132), Expect = 3e-10
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 8/79 (10%)
Query: 78 RHTVHMRGLPFRANERDVADFF----RPVVP--VHVDIHYENGRPSGEADVDFATHEDA- 130
++ + +RGLP+ A D+ +F R + P VH+ ++ + GRPSG+A + + E A
Sbjct: 1 KNCIRLRGLPYEATVEDILNFLGELARSIAPQGVHMVLNAQ-GRPSGDAFIQMLSAEFAT 59
Query: 131 MQAMSKDRTNMQHRYIELF 149
A + +M RYIE+F
Sbjct: 60 RAANELHKHHMGERYIEVF 78
>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 = 55.8 bits (134), Expect = 3e-10
Identities = 32/80 (40%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVH------VDIHYENGRPSGEADVDFATHEDAMQAM 134
+ MRGLPF A DV F P PV + + Y +GRP+G+A V FA E A A+
Sbjct: 19 IRMRGLPFTATPTDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNAL 78
Query: 135 SKDRTNMQHRYIELFLNSSS 154
K + + RYIELF ++++
Sbjct: 79 KKHKGILGKRYIELFRSTAA 98
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 54.5 bits (132), Expect = 3e-10
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 80 TVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
T+ + LP E ++ + F V V + E G+ G A V+F + EDA +A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 137 -DRTNMQHRYIEL 148
+ + R +++
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 54.3 bits (130), Expect = 7e-10
Identities = 31/80 (38%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVH------VDIHYENGRPSGEADVDFATHEDAMQAM 134
V MRGLPF A +V FF PV + + Y + RP+G+A V FA E A A+
Sbjct: 19 VRMRGLPFTATAEEVLAFFGQHCPVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNAL 78
Query: 135 SKDRTNMQHRYIELFLNSSS 154
K + + RYIELF ++++
Sbjct: 79 KKHKDLLGKRYIELFRSTAA 98
>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 = 50.8 bits (121), Expect = 8e-09
Identities = 29/75 (38%), Positives = 46/75 (61%), Gaps = 3/75 (4%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMSKD 137
V +RGLPF ++ ++ FF +VP + + + GR +GEA V FA+ E A +A+ K
Sbjct: 4 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKH 63
Query: 138 RTNMQHRYIELFLNS 152
+ + HRYIE+F +S
Sbjct: 64 KERIGHRYIEIFKSS 78
>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 = 50.7 bits (121), Expect = 1e-08
Identities = 32/79 (40%), Positives = 43/79 (54%), Gaps = 10/79 (12%)
Query: 81 VHMRGLPFRANERDVADFFRP--VVPVHVD--------IHYENGRPSGEADVDFATHEDA 130
V MRGLP+ + V +FF P HV + +GR +G+A V FAT EDA
Sbjct: 20 VRMRGLPYDCTAKQVLEFFTTGDTPPCHVLDGNEGVLFVKKPDGRATGDAFVLFATEEDA 79
Query: 131 MQAMSKDRTNMQHRYIELF 149
+A+ K R ++ RYIELF
Sbjct: 80 PKALGKHRESIGSRYIELF 98
>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 = 48.5 bits (116), Expect = 5e-08
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMSKD 137
+ ++ +PF + +V FF + IH + G+ GEA V+F + EDAM+A
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLH 61
Query: 138 RTNMQHRYIEL 148
R ++ R I L
Sbjct: 62 RKKLKGREILL 72
>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 = 48.4 bits (116), Expect = 5e-08
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 9/76 (11%)
Query: 81 VHMRGLPFRANERDVADFFRPV-VP---VHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
+ ++ LP+ A D+ FF + +P VH+ G GEA + FAT EDA AMS+
Sbjct: 4 IRLQNLPWEAGSLDIRRFFSGLTIPDGGVHI-----IGGEMGEAFIAFATDEDARLAMSR 58
Query: 137 DRTNMQHRYIELFLNS 152
D ++ ++LFL+S
Sbjct: 59 DGQTIKGSKVKLFLSS 74
>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 = 47.8 bits (114), Expect = 9e-08
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQAMSKD 137
V ++ LPF A ++ DFF V+P V + Y +NG P+GEA V F TH +AM A+ ++
Sbjct: 3 VKVQNLPFTATIEEILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAV-RE 61
Query: 138 RTN--MQHRYIELF 149
+ R ++L
Sbjct: 62 LNGRPIGTRKVKLT 75
>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 = 47.3 bits (113), Expect = 1e-07
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPV-HVDIHYE-NGRPSGEADVDFATHEDAMQAMSK-D 137
+ + LP E D+ + F + V I + +G+ G A V+F + EDA +A+ +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 138 RTNMQHRYIEL 148
+ R +++
Sbjct: 61 GKELDGRKLKV 71
>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 = 46.7 bits (111), Expect = 2e-07
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 10/80 (12%)
Query: 78 RHTVHMRGLPFRANERDVADFF-------RPVVPVHVDIHYENGRPSGEADVDFATHEDA 130
R + +RGLP+ A D+ +F RP VH+ ++ + GRPSG+A + + E A
Sbjct: 1 RDCIRLRGLPYTATIEDILEFLGEFAADIRP-HGVHMVLNQQ-GRPSGDAFIQMKSAERA 58
Query: 131 MQAMSK-DRTNMQHRYIELF 149
A K + M+ RY+E+F
Sbjct: 59 FLAAQKCHKKMMKDRYVEVF 78
>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 = 46.2 bits (110), Expect = 3e-07
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 80 TVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
T+ + L + A + D+ +FF+ VV V + +GR G V+FAT E A +A+ K
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEK 59
Query: 137 DRTNMQHRYIELFLNSSSPR 156
+ R E+ ++ ++ R
Sbjct: 60 SGEELLGR--EIRVDLATER 77
>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 = 45.6 bits (108), Expect = 6e-07
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHYEN-GRPSGEADVDFATHEDAMQAMSKDRT 139
V + GLPF E D+ DFF + + + ++ GR +G A V F + D +A+ ++R
Sbjct: 4 VSLHGLPFSVLEHDIRDFFHGLRIDAIHLLKDHVGRNNGNALVKFYSPHDTFEALKRNRM 63
Query: 140 NMQHRYIEL 148
M RYIE+
Sbjct: 64 LMGQRYIEV 72
>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 = 44.4 bits (105), Expect = 1e-06
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQAMSKD 137
V RGLP++++++D+A FFR + V + GR +GEA + F E A+ +
Sbjct: 2 VRARGLPWQSSDQDIAQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRH 61
Query: 138 RTNMQHRYIELF 149
+ +M RYIE++
Sbjct: 62 KHHMGTRYIEVY 73
>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 = 44.5 bits (105), Expect = 2e-06
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 5/81 (6%)
Query: 73 SSGPSRH--TVHMRGLPFRANERDVADFFRP--VVPVHVDIHY-ENGRPSGEADVDFATH 127
S P V+++GLP+ A + V DFF+ +V + I Y NG+ +GE V+F
Sbjct: 2 SRSPHELGFCVYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 61
Query: 128 EDAMQAMSKDRTNMQHRYIEL 148
D A+ + + M +R+I++
Sbjct: 62 ADYKAALCRHKQYMGNRFIQV 82
>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 = 43.6 bits (103), Expect = 3e-06
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 81 VHMRGLPFRANERDVADFFRP------VVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
V +GLP+ DV +FF VH + +G+P G+A ++ + ED +A+
Sbjct: 4 VRAKGLPWSCTAEDVMNFFDDCRIRNGENGVHF-LLNRDGKPRGDALIELESEEDVQKAL 62
Query: 135 SKDRTNMQHRYIELF 149
+ R M RY+E+
Sbjct: 63 EQHRHYMGQRYVEVR 77
>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 = 42.7 bits (101), Expect = 5e-06
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 84 RGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMS-KDRT 139
R LPF E ++ + F + VH+ + E R G A V F E A++A S D +
Sbjct: 5 RNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGS 64
Query: 140 NMQHRYIELF 149
Q R + +
Sbjct: 65 IFQGRLLHVL 74
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 4/80 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVH---VDIHYENGRPSGEADVDFATHEDAMQAMSK 136
T+ +R L F + D+ DFF V P+ V E G G V FA EDA +A++K
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 137 DRTNMQHRYIELFLNSSSPR 156
+ H I L L+ + R
Sbjct: 61 LKNKKLHGRI-LRLDIAERR 79
>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 = 41.4 bits (97), Expect = 2e-05
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQAMSK 136
+ + LPF+A ++ DFF V+P V + Y E G P+G A V + +AM A+++
Sbjct: 3 IRLENLPFKATINEILDFFHGYRVIPDSVSMQYNEQGLPTGTAIVAMENYYEAMAAINE 61
>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 = 40.6 bits (95), Expect = 4e-05
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTN 140
+ ++GLP A D+ FF + +H G GEA + FAT EDA +AMS+
Sbjct: 4 IRLQGLPVVAGSEDIRHFFTGLRIPDGGVHIIGGE-LGEAFIIFATDEDARRAMSRSGGF 62
Query: 141 MQHRYIELFLNSSS 154
++ +ELFL+S +
Sbjct: 63 IKDSTVELFLSSKA 76
>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 = 40.3 bits (95), Expect = 4e-05
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRPV-VPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKD 137
TV ++ LP E + FF+ V I G A ++F T ++A+ A++KD
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV--AVIEFETEDEALAALTKD 58
>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 = 40.3 bits (95), Expect = 4e-05
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 83 MRGLPFRANERDVADFFRPVVPV-HVDIHY-ENGRPSGEADVDFATHEDAMQAMSK 136
+ LP E D+ D F P+ + I E GR G A V+F EDA +A+
Sbjct: 3 VGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEA 58
>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 = 40.5 bits (95), Expect = 5e-05
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 78 RHTVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQA- 133
+H + + GLPF + ++ F+ V V + + +G+P G A V++ A QA
Sbjct: 2 KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRL-VTNRSGKPKGLAYVEYENESSASQAV 60
Query: 134 MSKDRTNMQHRYIELFLNSSSP 155
+ D T ++ + I + + S+ P
Sbjct: 61 LKMDGTEIKEKTISVAI-SNPP 81
>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 = 39.9 bits (93), Expect = 7e-05
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMSKD 137
V RGLP++++++D+A FFR + + GR +GEA V F E A+ +
Sbjct: 2 VRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRH 61
Query: 138 RTNMQHRYIELF 149
+ ++ RYIE++
Sbjct: 62 KHHIGQRYIEVY 73
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, 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. THOC4 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. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 39.5 bits (93), Expect = 7e-05
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPV-HVDIHY-ENGRPSGEADVDFATHEDAMQAMSK 136
+ + L F ++ D+ + F + +HY +GR G ADV F DA++AM +
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 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. 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 = 72
Score = 39.6 bits (93), Expect = 8e-05
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPV-HVDIHYEN-GRPSGEADVDFATHEDAMQAMSK 136
+ +R LPF +D+ D FR V D+ +N GR G V F + EDA +A+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEM 58
>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 = 39.1 bits (92), Expect = 2e-04
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 79 HTVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDA 130
TV +R LPF A E ++ + F V + G G A V F T E A
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55
>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 = 38.3 bits (90), Expect = 2e-04
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPV-HVDIHY-ENGRPSGEADVDFATHEDAMQAMSK 136
+ + L + E D+ + F V V V I+Y +GR G ADV F EDA +A+ +
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRP---VVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
+++ LP+ E D+ D F V V E GR G V+ T E+A A+ K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 137 -DRTNMQHRYI 146
+ T+ R +
Sbjct: 61 LNGTDFGGRTL 71
>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 = 38.1 bits (88), Expect = 3e-04
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMSKD 137
+ RGLP++++++D+A FF+ + + GR +GEA V F E A+ +
Sbjct: 2 IRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALQRH 61
Query: 138 RTNMQHRYIELF 149
+ +M RYIE++
Sbjct: 62 KHHMGSRYIEVY 73
>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 = 37.6 bits (87), Expect = 4e-04
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQAM 134
+ ++ +PF ++ DFF V+P V + + + G P+GEA V F + ++AM A+
Sbjct: 4 IKVQNMPFTVTVDEILDFFYGYQVIPGSVCLKFSDKGMPTGEAMVAFESRDEAMAAV 60
>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 = 37.6 bits (87), Expect = 4e-04
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 86 LPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAM-SKDRTNMQHR 144
L + A+E + + F + I NGRP G A V+F + EDA +A+ S + T ++ R
Sbjct: 9 LSYSASEDSLQEVFEKATSIR--IPQNNGRPKGYAFVEFESAEDAKEALNSCNNTEIEGR 66
Query: 145 YIEL 148
I L
Sbjct: 67 SIRL 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 = 37.7 bits (87), Expect = 5e-04
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMSKD 137
+ RGLP++++++D+A FF+ + GR +GEA V F + E A+ +
Sbjct: 7 IRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVSEEHRDLALQRH 66
Query: 138 RTNMQHRYIELF 149
+ +M +RYIE++
Sbjct: 67 KHHMGNRYIEVY 78
>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 = 37.0 bits (86), Expect = 7e-04
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 83 MRGLPFRANERDVADFFRP---VVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK-DR 138
+R LP+ E D+ F + VHV I ++G+ G A V F EDA++A + D
Sbjct: 7 VRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDG 66
Query: 139 TNMQHRYI 146
Q R I
Sbjct: 67 KVFQGRLI 74
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 39.2 bits (90), Expect = 0.001
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 71 NESSGPSRHTVHMRGLPFRANERDVADFFRPVVPV-HVDIHYEN--GRPSGEADVDFATH 127
+ S +T+ + LP+ E D+ + F+ PV V + + G+ G A V+F +
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESE 167
Query: 128 EDAMQAM 134
E A +A+
Sbjct: 168 ESAEKAI 174
>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 = 35.8 bits (83), Expect = 0.002
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 79 HTVHMRGLPFRANERDVADFFRPV-VP-VHVDIHYE-NGRPSGEADVDFATHEDAMQAMS 135
+ +H+ LPF +RD+ FF + +P + + G+ + A V F + D A++
Sbjct: 1 YYIHLENLPFSVEKRDIRAFFGDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAALA 60
Query: 136 KDRTNMQHRYIELF 149
+ + +R + +F
Sbjct: 61 HHKRVLYNREVYVF 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 = 35.0 bits (81), Expect = 0.003
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIHYENG---RPSGEADVDFATHEDAMQAMSK 136
T ++ LP+ E D+ +FFR + V + E G R G +F + +QA+S
Sbjct: 3 TAYLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL 62
Query: 137 DRTNMQHRYI 146
+ ++++R I
Sbjct: 63 NDESLKNRRI 72
>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 = 35.3 bits (81), Expect = 0.003
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 78 RHTVHMRGLPFRANERDV----ADFFRPVVPVHVDIHYEN-GRPSGEADVDFATHEDAMQ 132
+ + +RGLP+ A + DF + +V V + Y G+PSGEA + + + A
Sbjct: 1 KDCIRLRGLPYEAQVEHILEFLGDFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASA 60
Query: 133 AMSKDRTNM-----QHRYIELF 149
+ + RYIE+F
Sbjct: 61 CAQQRHNRYMVFGKKQRYIEVF 82
>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 = 34.6 bits (80), Expect = 0.005
Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 81 VHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKD 137
V++ G+P+ + E ++ +F + + + + GR G A + F T E A +A++ D
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60
Query: 138 RTNMQHRYI 146
+M R++
Sbjct: 61 GEDMGGRFL 69
>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 = 34.4 bits (80), Expect = 0.005
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 90 ANERDVADFFRPVVP---VHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
A+E D+ + FRP P V++ E G+ G A V F T EDA +A+ K
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
>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 = 33.7 bits (78), Expect = 0.008
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVH-VDIHYEN--GRPSGEADVDFATHEDAMQAM 134
TV + L + ERD+ +FF V V I + R G A V+F E A+
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 33.9 bits (78), Expect = 0.009
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPV-HVDIHYENGRPSGEADVDFATHEDAMQAMSK- 136
+ + + L R + +D+ DF R V + D H + E V+FAT+ D +A+ K
Sbjct: 1 YRLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQR---PNEGVVEFATYSDMKRAIEKL 57
Query: 137 DRTNMQHRYIEL 148
D T + R I+L
Sbjct: 58 DGTELNGRKIKL 69
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
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 = 76
Score = 33.4 bits (77), Expect = 0.013
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 12/64 (18%)
Query: 80 TVHMRGLPFRANERDVADFFRPV-------VPVHVDIHYENGRPSGEADVDFATHEDAMQ 132
+ +R +PF A ++++ + F P +P D G G A V+F T ++A
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-----GSHRGFAFVEFVTKQEAQN 56
Query: 133 AMSK 136
AM
Sbjct: 57 AMEA 60
>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 = 33.0 bits (76), Expect = 0.014
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMSK 136
TV + L + E ++ F + D+ G+ G A V+F E +A+
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEI-TDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59
Query: 137 DRTNMQHR 144
DR ++ R
Sbjct: 60 DRELIKGR 67
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 33.3 bits (77), Expect = 0.017
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 76 PSRHTVHMRGLPFRANERDVADFFRPVVPVHV-DIHY----ENGRPSGEADVDFATHEDA 130
P+ +T+ +RGL E D+ + V + D+ G G A V+F + EDA
Sbjct: 1 PT-NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59
Query: 131 MQAMSKDRTNMQHRYI 146
Q M N+ I
Sbjct: 60 TQWM-DALNNLDPFVI 74
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 35.7 bits (82), Expect = 0.019
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 152 SSSPRGGVGGSGSIGGFGGSGGGRLGGFGGS 182
+SS R G GG G SGGG GG GG+
Sbjct: 568 ASSRRSSSSG----GGGGFSGGGSGGGGGGA 594
Score = 32.6 bits (74), Expect = 0.16
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 135 SKDRTNMQHRYIELFLNSSSPRGGVGGSGSIGGFGGSGGG 174
S+ N+ Y + + S G GG S GG GG GGG
Sbjct: 554 SRSFNNLNRAYSAIASSRRSSSSGGGGGFSGGGSGGGGGG 593
Score = 29.5 bits (66), Expect = 1.7
Identities = 12/39 (30%), Positives = 15/39 (38%)
Query: 143 HRYIELFLNSSSPRGGVGGSGSIGGFGGSGGGRLGGFGG 181
+ Y F N + + S GG GG GG GG
Sbjct: 551 NNYSRSFNNLNRAYSAIASSRRSSSSGGGGGFSGGGSGG 589
>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 = 33.1 bits (75), Expect = 0.021
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTN 140
+ ++GLP A D+ FF + +H G GEA + FAT EDA M +
Sbjct: 5 IRLQGLPIVAGTMDIRHFFSGLTIPDGGVHIVGGE-LGEAFIVFATDEDARLGMMRTGGT 63
Query: 141 MQHRYIELFLNSSS 154
++ + L L+S +
Sbjct: 64 IKGSKVSLLLSSKT 77
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 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 = 79
Score = 32.6 bits (75), Expect = 0.025
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPV-HVDIHYENGRPS--GEADVDFATHEDAMQAMSK 136
T+ +R LP+ + + +FF V P+ + + G G V FA EDA +A+ +
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
>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 = 32.7 bits (74), Expect = 0.025
Identities = 16/45 (35%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 105 VHVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTNMQHRYIELF 149
V++ + Y G P G A + FATHE+A +A+S + +R+I+++
Sbjct: 30 VNLQVAY-KGDPEG-ALIQFATHEEAKKAISSTEAVLNNRFIKVY 72
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 32.8 bits (75), Expect = 0.030
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 81 VHMRGLPFRANERDVADFF-----RPV----VPVHVDIHYENGRPSGEADVDFATHEDAM 131
+++ LP + ++ +F RPV + + Y + + S F +HE+AM
Sbjct: 3 LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62
Query: 132 QAMS 135
+A++
Sbjct: 63 EALA 66
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is 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 = 79
Score = 32.0 bits (73), Expect = 0.038
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 83 MRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK-DR 138
+R L + E D+ F P+ VH+ I +P G A V + E A++A ++ D
Sbjct: 7 IRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDG 66
Query: 139 TNMQHRYIEL 148
T Q R + L
Sbjct: 67 TVFQGRLLHL 76
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 33.5 bits (76), Expect = 0.039
Identities = 34/92 (36%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 93 RDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK-DRTNMQHRYIELFL- 150
RD F VV V + E GR G V+F A A+S+ D + R+I +
Sbjct: 52 RDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA 111
Query: 151 --NSSSPRGGVGGSGSIGGFGGSGGGRLGGFG 180
S+PR GG G GG GG GGG GG G
Sbjct: 112 NDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGG 143
>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 = 32.0 bits (73), Expect = 0.045
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 80 TVHMRGLPFRANERDVADF---FRPV---VPVHVDIHYENG--RPSGEADVDFATHEDAM 131
V++ L + ++E D+ +F F PV +P + + RP G A +F++ E A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 132 QA 133
+
Sbjct: 61 KV 62
>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 = 31.9 bits (73), Expect = 0.045
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 86 LPFRANERDVADFFRPVV-PVHVDI--HYENGRPSGEADVDFATHEDAMQAMSKDRTNMQ 142
LP+ D+ F+ P V + + G+ G A V+F T E +A+ T ++
Sbjct: 8 LPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLK 67
Query: 143 HRYI 146
R I
Sbjct: 68 GRKI 71
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 31.8 bits (73), Expect = 0.049
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 9/72 (12%)
Query: 81 VHMRGLPFRANERDVADFFRP---VVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKD 137
+++ GL +E+ + F P + + + + YE + G A V+F EDA A+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID-- 58
Query: 138 RTNMQHRYIELF 149
NM ELF
Sbjct: 59 --NMN--ESELF 66
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 31.4 bits (72), Expect = 0.049
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVV-PVHVDIHYENGRPSGEADVDFATHEDAMQAMSK- 136
V + GLP A+ +D+ DF R + D+ + GE V+F + ED +A+ K
Sbjct: 1 FRVVVSGLPEGASWQDLKDFGRQAGDVTYADV---DRDQEGEGVVEFTSQEDMERALRKL 57
Query: 137 DRTNMQHRYIELF 149
D T + R + +
Sbjct: 58 DGTEFRGRRVRVE 70
>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 = 31.2 bits (71), Expect = 0.083
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 85 GLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTNM 141
GLP++ E+D+ D+F ++ V V + G+ G V FA +ED ++ +S+ R +
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ-RHMI 64
Query: 142 QHRYIEL 148
R+ ++
Sbjct: 65 DGRWCDV 71
>gnl|CDD|220015 pfam08784, RPA_C, Replication protein A C terminal. This domain
corresponds to the C terminal of the single stranded DNA
binding protein RPA (replication protein A). RPA is
involved in many DNA metabolic pathways including DNA
replication, DNA repair, recombination, cell cycle and
DNA damage checkpoints.
Length = 103
Score = 31.5 bits (72), Expect = 0.092
Identities = 19/69 (27%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 148 LFLNSSSPRGGVGGSGSIGGFGGSGGGRLGGFGGSDPSSPFERRNPNQAYVENTALSRSA 207
L L GG+G GS G G F G D S P Q V N + +S
Sbjct: 2 LRLTKGRSGSSAGGAGPSVANTGSAMGTQGAFSGGDASVANPGLTPLQDQVLN-LIKQSC 60
Query: 208 VKDRAINVQ 216
+ ++V
Sbjct: 61 PGEEGVHVD 69
>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 = 30.8 bits (70), Expect = 0.095
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 86 LPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTNMQ 142
L F A+E + + F + V + ++GRP G V+F++ E A A+ +
Sbjct: 6 LSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL----DALG 61
Query: 143 HRYI 146
+
Sbjct: 62 GTDL 65
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 32.9 bits (75), Expect = 0.12
Identities = 21/76 (27%), Positives = 25/76 (32%), Gaps = 14/76 (18%)
Query: 9 GRPAPYDRNDRFGGANRFGGGSGPGPIRGGPPRGGFRGGFNNDRWNDRPGGFAGPRPGGR 68
G P+ +R GG F GG R G R F+ +R R GG R
Sbjct: 561 GDAQPHTGGERRGGGRGF----------GGERREGGR-NFSGER---REGGRGDGRRFSG 606
Query: 69 WVNESSGPSRHTVHMR 84
E P R R
Sbjct: 607 ERREGRAPRRDDSTGR 622
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 32.8 bits (75), Expect = 0.12
Identities = 19/50 (38%), Positives = 19/50 (38%)
Query: 19 RFGGANRFGGGSGPGPIRGGPPRGGFRGGFNNDRWNDRPGGFAGPRPGGR 68
GG G G G G GG GG RGG GG G R GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50
Score = 29.7 bits (67), Expect = 1.3
Identities = 20/61 (32%), Positives = 20/61 (32%), Gaps = 8/61 (13%)
Query: 6 GGFGRPAPYDRNDRFGGANRFGGGSGPGPIRGGPPRGGFRGGFNNDRWNDRPGGFAGPRP 65
GGFG R GG GG G G RGG GG R GG G
Sbjct: 4 GGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGG--------RGGGGGGGPG 55
Query: 66 G 66
Sbjct: 56 K 56
Score = 29.3 bits (66), Expect = 1.5
Identities = 16/29 (55%), Positives = 16/29 (55%)
Query: 156 RGGVGGSGSIGGFGGSGGGRLGGFGGSDP 184
RGG G G G GG GGGR GG GG
Sbjct: 27 RGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55
Score = 27.4 bits (61), Expect = 7.2
Identities = 16/28 (57%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 156 RGGVGGSGSIG--GFGGSGGGRLGGFGG 181
RGG G G G G GG GGGR GG G
Sbjct: 10 RGGGRGGGGGGGRGGGGRGGGRGGGRGR 37
Score = 27.0 bits (60), Expect = 8.1
Identities = 15/27 (55%), Positives = 15/27 (55%)
Query: 155 PRGGVGGSGSIGGFGGSGGGRLGGFGG 181
RGG G G GG GG GGG GG G
Sbjct: 30 GRGGGRGRGRGGGGGGRGGGGGGGPGK 56
>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 = 30.8 bits (70), Expect = 0.12
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 99 FRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAM-SKDRTNMQHRYIEL 148
+ P+V V++ + + RP G A V F DA A+ DRT R IE+
Sbjct: 24 YGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEI 74
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 30.3 bits (69), Expect = 0.15
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 16/67 (23%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDIHYE----------NGRPSGEADVDFATHE 128
T+ + GLP ER++A FRP YE G VDF++ +
Sbjct: 1 RTLFVSGLPSDVKERELAHLFRPF------PGYEASRLVFKEKKGGEKQPVGFVDFSSAQ 54
Query: 129 DAMQAMS 135
A AM
Sbjct: 55 CAAAAMD 61
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 32.9 bits (75), Expect = 0.16
Identities = 28/121 (23%), Positives = 42/121 (34%), Gaps = 16/121 (13%)
Query: 63 PRPGGRWVNESSGPSRHTVHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADV 122
R V+ ++ S + + F + A P +
Sbjct: 1 GRSSSTMVSAAASTSLSSSRPQLSSFSSRSPQSAT----------------RSPRASSIK 44
Query: 123 DFATHEDAMQAMSKDRTNMQHRYIELFLNSSSPRGGVGGSGSIGGFGGSGGGRLGGFGGS 182
A+ + A S + + + + L S+ GG GG G GGFGG GGG GG GG
Sbjct: 45 CSASASASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
Query: 183 D 183
Sbjct: 105 R 105
>gnl|CDD|233241 TIGR01034, metK, S-adenosylmethionine synthetase. Tandem isozymes
of this S-adenosylmethionine synthetase in E. coli are
designated MetK and MetX [Central intermediary
metabolism, Other].
Length = 377
Score = 32.3 bits (74), Expect = 0.17
Identities = 24/114 (21%), Positives = 39/114 (34%), Gaps = 28/114 (24%)
Query: 97 DFFRPVVPVHVDIHYENGRPSGEADVDFATHED------AMQAMSKDR-------TNMQH 143
+ RP V + YE+ +P + +T D ++ +
Sbjct: 155 PWLRPDGKSQVTVQYEDNKPVRVDTIVLSTQHDPDISQKDLREAIIEEIIKPVLPAEYLD 214
Query: 144 RYIELFLNSS------SPRGGVGGSG------SIGGFGGSGGGRLGGFGGSDPS 185
+ F+N + P G G +G + GG+ GG G F G DPS
Sbjct: 215 EKTKFFINPTGRFVIGGPMGDTGLTGRKIIVDTYGGWARHGG---GAFSGKDPS 265
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 30.0 bits (68), Expect = 0.19
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 80 TVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEAD---VDFATHEDAMQA 133
T+H+ G+ +E D+ +FF V V + G A V+FA E A+ A
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRL-----CGDRQHSARFAFVEFADAESALSA 56
Query: 134 MSKD 137
++
Sbjct: 57 LNLS 60
>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 = 30.1 bits (68), Expect = 0.22
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIH--YEN-GRPSGEADVDFATHEDAMQA 133
++ R PF + +V FF P DI+ Y++ G GEA V F + E AM+A
Sbjct: 3 IYARNFPFDVTKVEVQKFFAPFNIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA 58
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 32.0 bits (73), Expect = 0.22
Identities = 21/48 (43%), Positives = 23/48 (47%), Gaps = 13/48 (27%)
Query: 160 GGSGSIGGFGGSGGGRLGGFGGSDPSSPFE------------RRNPNQ 195
G +G+ GGFGG GG GGF GS FE RRNPN
Sbjct: 69 GAAGANGGFGGGAGG-FGGFDGSGGFGGFEDIFSSFFGGGGARRNPNA 115
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 29.5 bits (67), Expect = 0.29
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIH---YENGRPSGEADVDFATHEDAMQAMSK 136
TV+++G P A D+ +FF V +I + + G V+F T EDA + + K
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKV-NNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59
>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 = 29.9 bits (67), Expect = 0.32
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 15/58 (25%)
Query: 80 TVHMRGLPFRANERDVADFFR-------------PVVPVHVDIHYENGRPSGEADVDF 124
T++++GL ++ADFF+ P+V ++ D E G+P G+A V +
Sbjct: 2 TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTD--KETGKPKGDATVSY 57
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 29.5 bits (67), Expect = 0.37
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 4/71 (5%)
Query: 80 TVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
+ + GL R E+++ F V V + E G G V F + EDA A+
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 137 -DRTNMQHRYI 146
+ ++ R I
Sbjct: 63 LNGKELEGRVI 73
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 31.2 bits (70), Expect = 0.42
Identities = 18/65 (27%), Positives = 21/65 (32%), Gaps = 1/65 (1%)
Query: 115 RPSGEADVDFATHEDAMQAMSKDRTNMQHRYIELFLNSSSPRGGVGGSGSIGGFGGSGGG 174
RP+ + + K N I S RG G G GG GG G G
Sbjct: 479 RPANGKGNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGG-GGRGRG 537
Query: 175 RLGGF 179
GF
Sbjct: 538 YNRGF 542
>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 = 29.0 bits (65), Expect = 0.54
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 82 HMRGLPFRANERDVADFFRPV------VPVHVDIHYENGRPSGEADVDFATHEDAMQAMS 135
H+ +P+ ++D+ F + V V VD NG+ G+A V F + +DA ++
Sbjct: 3 HISNIPYSITKKDILQFLEGIGVDENSVQVLVD---NNGQGLGQALVQFKSEDDARKSER 59
Query: 136 KDRTNMQHR 144
R + R
Sbjct: 60 LHRKKLNGR 68
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 28.4 bits (64), Expect = 0.57
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQA 133
V++ LP+RA ERDV FF+ + +I+ +NG V+F DA A
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIR-EINLKNGF----GFVEFEDPRDADDA 49
>gnl|CDD|114135 pfam05394, AvrB_AvrC, Avirulence protein. This family consists of
several avirulence proteins from Pseudomonas syringae
and Xanthomonas campestris.
Length = 326
Score = 30.6 bits (69), Expect = 0.61
Identities = 25/88 (28%), Positives = 33/88 (37%), Gaps = 6/88 (6%)
Query: 133 AMSKDRTNMQHRYIELFLNSSSPRGGVGGSGSIGGFGGSGGG----RLGGFGGSDPS-SP 187
A +K T Y + F N+S GG +G I F RL G + S
Sbjct: 60 ASNKSNTPENMEYCQSFYNASRIAGGSIANGEITSFEELWEKATDWRLSRAGSGEALKSD 119
Query: 188 FER-RNPNQAYVENTALSRSAVKDRAIN 214
F R PN +V +VK+R N
Sbjct: 120 FASERMPNTRFVTPLRRPYHSVKERVRN 147
>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 = 28.4 bits (64), Expect = 0.72
Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 12/78 (15%)
Query: 79 HTVHMRGLPFRANERDVADFFRP-------VVPVHVD--IHYENGRPSGEADVDFATHED 129
+++R L F+ +E D+ F +P D N G A V F
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNN---GFAFVTFKDASS 57
Query: 130 AMQAMSKDRTNMQHRYIE 147
A A+ + T + R I
Sbjct: 58 AENALQLNGTELGGRKIS 75
>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 = 28.4 bits (64), Expect = 0.77
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 105 VHVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTNMQHRYIELFLNSSSPR 156
V VD + GR +GE V+F+ A A+ + FL ++SPR
Sbjct: 31 VIVD---DRGRSTGEGIVEFSRKPGAQAAIKRCSEG-------CFLLTASPR 72
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 28.3 bits (64), Expect = 0.82
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 86 LPFRANERDVADFFRP---VVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
LP A E DV F + V + + G+ G A V F++ E+A +A+
Sbjct: 7 LPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI 58
>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 = 28.4 bits (64), Expect = 0.88
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 102 VVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK-DRTNMQHRYIELFLN 151
V V + + + G+ +G V+FATHE A QA+ + + + LN
Sbjct: 26 VTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQQRFRLN 76
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily may share similar expression patterns
and functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation. It directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 28.1 bits (63), Expect = 0.96
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 4/70 (5%)
Query: 79 HTVHMRGLPFRANERDVA----DFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
TV + GLP ++A + V V +D P+G A V F + ++A+
Sbjct: 1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAV 60
Query: 135 SKDRTNMQHR 144
S+ +
Sbjct: 61 SEVFVELPFN 70
>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 = 28.2 bits (63), Expect = 0.98
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 14/71 (19%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVHVDIHY------ENGRPSGEADVDFATHEDAMQAM 134
V + +P+ +D+ D FR V ++ Y E G+ G V+F E +A+
Sbjct: 2 VFISNIPYDLKWQDLKDLFREKVG---EVTYVELFKDEEGKSRGCGVVEFKDKESVQKAL 58
Query: 135 SKDRTNMQHRY 145
+RY
Sbjct: 59 ET-----MNRY 64
>gnl|CDD|221093 pfam11359, gpUL132, Glycoprotein UL132. Glycoprotein UL132 is a
low-abundance structural component of Human
cytomegalovirus (HCMV). The function of this protein is
not fully understood.
Length = 235
Score = 29.6 bits (66), Expect = 1.0
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 162 SGSIGGFGGSGGGRLGGFGGSDPSSPFERRNPN--QAYVENTALSRSAVKDRAINV 215
SG FG G R G SS ++R N ++ + +R + D NV
Sbjct: 103 SGGSSPFGS--GSRRGQIPAGSSSSKYQRLNKGDYDELWQSQSAARETMDDDPDNV 156
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 28.1 bits (63), Expect = 1.1
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGE----ADVDFATHEDAMQAM 134
T+ +RGLP E D+ + D+ + +G A V+F + E+A + M
Sbjct: 4 TIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWM 62
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 28.0 bits (62), Expect = 1.2
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 76 PSRHTVHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMS 135
PS+ +H+R LP+ E ++ + +P + V+ G +A V+FA A+ +S
Sbjct: 1 PSK-VLHLRNLPWECTEEELIELCKPFGKI-VNTKCNVGANRNQAFVEFADLNQAIAMVS 58
>gnl|CDD|233089 TIGR00680, kdpA, K+-transporting ATPase, KdpA. Kdp is a high
affinity ATP-driven K+ transport system in Escherichia
coli. It is composed of three membrane-bound subunits,
KdpA, KdpB and KdpC and one small peptide, KdpF. KdpA is
the K+-transporting subunit of this complex. During
assembly of the complex, KdpA and KdpC bind to each
other. This interaction is thought to stabilize the
complex [medline:9858692]. Data indicates that KdpC
might connect the KdpA, the K+-transporting subunit, to
KdpB, the ATP-hydrolyzing (energy providing) subunit
[medline:9858692] [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 563
Score = 29.9 bits (67), Expect = 1.3
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 155 PRGGVGGSGSIGGFGGSGGGRLGGFGGSDPSSPFERRNPNQAYVENTAL 203
PRG V +I G +GGG F + + PFE +VE A+
Sbjct: 219 PRGPVASQEAIKELGTNGGG----FFNINSAHPFENPTNFANFVETVAI 263
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 28.0 bits (63), Expect = 1.3
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 85 GLPFRANERDVADFFRPVVPV-HVDIHYE--NGRPSGEADVDFATHEDAMQAMSKDRTN 140
GL ERD+ + F P+ V + Y+ GR G V F + EDA +A K+R N
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA--KERLN 62
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 27.6 bits (62), Expect = 1.4
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 101 PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMS 135
PVV VH+ G V+F + EDA A+
Sbjct: 24 PVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIK 58
>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 = 27.4 bits (61), Expect = 1.5
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIHY--ENGRPSGEADVDFATHEDAMQAMSKD 137
TV++ L + E DV +FF+ V + E G G VDFA E A+ D
Sbjct: 1 TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60
Query: 138 RTNMQHRYI 146
T + R I
Sbjct: 61 GTVLCGRPI 69
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 29.0 bits (65), Expect = 1.6
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 76 PSRHTVHMRGLPFRANERDVADFFRPVVPV-HVDI 109
P +T + L +A E+DV DFF + HV+I
Sbjct: 3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEI 37
>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 = 27.5 bits (62), Expect = 1.7
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 86 LPFRANERDVADFFRPVVPVHV-----DIHYENGRPSGEADVDFATHEDAMQAM 134
L E + + F P PV D+ R G A V+F DA +A+
Sbjct: 7 LHPDVTEAMLYEIFSPAGPVLSIRVCRDLI--TRRSLGYAYVNFQNPADAERAL 58
>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 = 27.6 bits (61), Expect = 1.8
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 99 FRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK-DRTNMQHRYIEL 148
+ P+V V+V + + RP G A V F DA A+ DR + R IE+
Sbjct: 24 YGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEI 74
>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 = 27.2 bits (61), Expect = 1.9
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 86 LPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
+P+ A E + + F PVV + + G+P G +F E A A+
Sbjct: 6 IPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57
>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 = 27.2 bits (61), Expect = 2.1
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 85 GLPFRANERDVADFFRPVVPV-HVDIHY--ENGRPSGEADVDFATHEDAMQAMSK 136
L F E D+ F P + V + E GR G + FA EDA +A+ +
Sbjct: 5 NLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
>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 = 27.2 bits (60), Expect = 2.6
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 15/59 (25%)
Query: 79 HTVHMRGLPFRANERDVADFFR-------------PVVPVHVDIHYENGRPSGEADVDF 124
+T+ ++GL VAD+F+ P++ ++ D E G+ GEA V F
Sbjct: 3 NTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTD--RETGKLKGEATVSF 59
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 26.7 bits (59), Expect = 2.7
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIHYENG-RPSGEADVDFATHEDAMQAM 134
TV++ LP ER+V D F P+ VDI + RP G A ++F DA A+
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPI-VDIDLKLPPRPPGYAFIEFEDARDAEDAI 55
>gnl|CDD|237656 PRK14280, PRK14280, chaperone protein DnaJ; Provisional.
Length = 376
Score = 28.5 bits (64), Expect = 2.7
Identities = 30/94 (31%), Positives = 39/94 (41%), Gaps = 20/94 (21%)
Query: 106 HVDIHYENGRPSGEADVDFATHEDAMQAMSKDRTNMQHRYIELFLNSSSPRGGVGGSGSI 165
H DI+ E G AD F +A + +S D + +Y + G G +
Sbjct: 33 HPDINKEEG-----ADEKFKEISEAYEVLSDD--QKRAQYDQF--------GHAGPNQGF 77
Query: 166 GGFGGSGGGRLGGFGGSDPSSPF-----ERRNPN 194
GG G GG GGFG D S F RR+PN
Sbjct: 78 GGGGFGGGDFGGGFGFEDIFSSFFGGGGRRRDPN 111
>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 = 26.7 bits (59), Expect = 3.0
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 86 LPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
+P+ A E + D F PVV + E G+P G ++ E A+ AM
Sbjct: 6 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 28.6 bits (64), Expect = 3.0
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 14 YDRNDRFGGANRFGGGSG--PGPIRG-GPPRGGFRG 46
YD N +F ++ GG G G IR GF+
Sbjct: 252 YDVNQKFAQVSKHGGALGIYTGKIRALNSEIRGFKN 287
>gnl|CDD|218350 pfam04959, ARS2, Arsenite-resistance protein 2. Arsenite is a
carcinogenic compound which can act as a co-mutagen by
inhibiting DNA repair. Arsenite-resistance protein 2 is
thought to play a role in arsenite resistance.
Length = 211
Score = 28.2 bits (63), Expect = 3.3
Identities = 15/65 (23%), Positives = 20/65 (30%), Gaps = 2/65 (3%)
Query: 1 MRPVSGGFGRPAPYDRNDRFGGANRFGGGSGPGPIRGGPPRGGFRGGFNNDRWNDRPGGF 60
+ P G+ P G GP GG RG N D + + G +
Sbjct: 143 LAPGLPGYPPQTPQALMPYGQPRPPMMGYGRGGPPFPPNQYGGGRG--NYDEFRGQGGYY 200
Query: 61 AGPRP 65
PR
Sbjct: 201 GKPRN 205
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 28.1 bits (63), Expect = 3.3
Identities = 20/44 (45%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 154 SPRGGVGGSGSIGGFGGSGGGRLGGF-GGSDPSSPFERRNPNQA 196
+ RGG GG G GGFGG GGG GG GG +P A
Sbjct: 120 ASRGG-GGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASA 162
>gnl|CDD|222637 pfam14266, DUF4356, Domain of unknown function (DUF4356). This
family of proteins is found in bacteria. Proteins in
this family are approximately 540 amino acids in length.
Length = 489
Score = 28.5 bits (64), Expect = 3.4
Identities = 7/41 (17%), Positives = 13/41 (31%), Gaps = 3/41 (7%)
Query: 108 DIHYENGRPSGEADVDFATHEDAMQAMSKDRTNMQHRYIEL 148
IH N + + Q + K + HR++
Sbjct: 57 QIHSVNQK---GSVSRLIAFLSGNQLLPKHNNPLMHRHLRK 94
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 28.1 bits (63), Expect = 3.5
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 79 HTVHMRGLPFRANERDVADFFR-PVVPVHVDIHYENGRPSGEADVDF 124
TV + + +A ERD+ +FF +V++ EN R S A V F
Sbjct: 5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENER-SQIAYVTF 50
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 26.4 bits (59), Expect = 3.6
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 80 TVHMRGLPFRANERD-VADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMS 135
T+ +R +P N + + F +V + V+ + E+ A V F+T E+A +A
Sbjct: 3 TLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAYR 56
Query: 136 KDRTNMQHRYIELF 149
+R+I++F
Sbjct: 57 SPEAVFNNRFIKVF 70
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 26.8 bits (60), Expect = 3.6
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 90 ANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
A E DV D F + +H+++ G G A +++ T ++A A+
Sbjct: 18 AQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 26.3 bits (58), Expect = 3.7
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 83 MRGLPFRANERDVADFFRP---VVPVHVDIHYENGRPSGEADVDFATHEDAMQAM 134
++ LPF A ++DV F + V V ++ G A V+F+T ++A+ AM
Sbjct: 5 VKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQS-ARGFAFVEFSTAKEALNAM 58
>gnl|CDD|143395 cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase
superfamily. The aldehyde dehydrogenase superfamily
(ALDH-SF) of NAD(P)+-dependent enzymes, in general,
oxidize a wide range of endogenous and exogenous
aliphatic and aromatic aldehydes to their corresponding
carboxylic acids and play an important role in
detoxification. Besides aldehyde detoxification, many
ALDH isozymes possess multiple additional catalytic and
non-catalytic functions such as participating in
metabolic pathways, or as binding proteins, or
osmoregulants, to mention a few. The enzyme has three
domains, a NAD(P)+ cofactor-binding domain, a catalytic
domain, and a bridging domain; and the active enzyme is
generally either homodimeric or homotetrameric. The
catalytic mechanism is proposed to involve cofactor
binding, resulting in a conformational change and
activation of an invariant catalytic cysteine
nucleophile. The cysteine and aldehyde substrate form an
oxyanion thiohemiacetal intermediate resulting in
hydride transfer to the cofactor and formation of a
thioacylenzyme intermediate. Hydrolysis of the
thioacylenzyme and release of the carboxylic acid
product occurs, and in most cases, the reduced cofactor
dissociates from the enzyme. The evolutionary
phylogenetic tree of ALDHs appears to have an initial
bifurcation between what has been characterized as the
classical aldehyde dehydrogenases, the ALDH family
(ALDH) and extended family members or aldehyde
dehydrogenase-like (ALDH-L) proteins. The ALDH proteins
are represented by enzymes which share a number of
highly conserved residues necessary for catalysis and
cofactor binding and they include such proteins as
retinal dehydrogenase, 10-formyltetrahydrofolate
dehydrogenase, non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase,
delta(1)-pyrroline-5-carboxylate dehydrogenases,
alpha-ketoglutaric semialdehyde dehydrogenase,
alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
aldehyde dehydrogenase and succinate-semialdehyde
dehydrogenase. Included in this larger group are all
human, Arabidopsis, Tortula, fungal, protozoan, and
Drosophila ALDHs identified in families ALDH1 through
ALDH22 with the exception of families ALDH18, ALDH19,
and ALDH20 which are present in the ALDH-like group. The
ALDH-like group is represented by such proteins as
gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA
reductase, and coenzyme A acylating aldehyde
dehydrogenase. All of these proteins have a conserved
cysteine that aligns with the catalytic cysteine of the
ALDH group.
Length = 367
Score = 28.3 bits (64), Expect = 3.8
Identities = 25/92 (27%), Positives = 36/92 (39%), Gaps = 19/92 (20%)
Query: 99 FRPVVPVHVDIHYE---------NGRPSGEADVDFATHEDAMQAMSKDRTNMQHRYIELF 149
F PV+PV I ++ N G F + +++ + R ++
Sbjct: 274 FGPVLPV---IRFKDEEEAIALANDTEYGLTAGVFTRDLNRALRVAE-----RLRAGTVY 325
Query: 150 LNSSSPRGGVGGSGSIGGFGGSGGGRLGGFGG 181
+N SS GVG GG SG GR GG G
Sbjct: 326 INDSSI--GVGPEAPFGGVKNSGIGREGGPYG 355
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 27.5 bits (61), Expect = 4.2
Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 157 GGVGGSGSIGGFGGSGGGRLGGFGGSDPSSPFERRNPNQA 196
G G G GG G GGG G FG S PS R +
Sbjct: 115 DGRGEGGGGGGGGDDGGG--GDFGSSGPSRGGPRPASSGG 152
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 27.7 bits (62), Expect = 4.6
Identities = 16/44 (36%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 144 RYIELFLNSSSPRGGVGGSGSIGGFGGS-----GGGRLGGFGGS 182
R++ L G GGSG GG GGG GG G S
Sbjct: 225 RWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGAS 268
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 26.5 bits (58), Expect = 4.8
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 85 GLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
GL ERD+ + F P+ V+V GR G A V F +D+ +AM
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 26.1 bits (57), Expect = 5.7
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 80 TVHMRGLPFRANERDV---ADFFRPVVPVHVDI-HYENGRPSGEADVDFATHEDAMQAMS 135
T+ +RGLP E D+ + F P V + + G G A V+F +DA M
Sbjct: 7 TIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDATSWME 66
Query: 136 KDRTNMQHRYIELFLNSSSPR 156
++ + + + ++ S+PR
Sbjct: 67 ANQKKLVIQGKTIAMHYSNPR 87
>gnl|CDD|233181 TIGR00913, 2A0310, amino acid permease (yeast). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 478
Score = 27.6 bits (62), Expect = 5.7
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 9/37 (24%)
Query: 37 GGPPRG--GFRGGFNNDRWNDRPGGFAGPRPGGRWVN 71
GGP G GFR W+D PG FAG GGR+
Sbjct: 169 GGPNHGYIGFR------YWHD-PGAFAGGTIGGRFKG 198
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 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 = 98
Score = 26.4 bits (59), Expect = 6.0
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 18/69 (26%)
Query: 84 RGLPFRANERDVADFF----------RPVVPVHVDIHYE--------NGRPSGEADVDFA 125
R LP +E+ + + F + V I + G+ G V+F
Sbjct: 6 RNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFT 65
Query: 126 THEDAMQAM 134
HE A++A+
Sbjct: 66 NHEHALKAL 74
>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 = 25.8 bits (57), Expect = 6.2
Identities = 15/38 (39%), Positives = 18/38 (47%)
Query: 99 FRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
F VV V E GR G VDF + EDA +A+
Sbjct: 23 FGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 27.3 bits (61), Expect = 6.2
Identities = 14/37 (37%), Positives = 14/37 (37%)
Query: 152 SSSPRGGVGGSGSIGGFGGSGGGRLGGFGGSDPSSPF 188
SSSP GG GGFG GFGG
Sbjct: 25 SSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGGLFGL 61
Score = 27.3 bits (61), Expect = 6.5
Identities = 11/42 (26%), Positives = 13/42 (30%)
Query: 6 GGFGRPAPYDRNDRFGGANRFGGGSGPGPIRGGPPRGGFRGG 47
G F P+ + R G PG G P F G
Sbjct: 11 GSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGF 52
>gnl|CDD|130376 TIGR01309, L30P_arch, 50S ribosomal protein L30P, archaeal. This
model represents the archaeal ribosomal protein similar
to longer (~ 250 residue) eukaryotic 60S ribosomal
protein L7 and to the much shorter (~ 60 residue)
bacterial 50S ribosomal protein L30. Protein naming
follows the SwissProt designation as L30P, while the
gene symbol rpmD follows TIGR usage [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 152
Score = 27.0 bits (60), Expect = 6.3
Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 34 PIRGGPPRGGFRGGFNNDRWNDRPGGFAGPRPGGRWVNE 72
R PPR GF+GG + R GG G R G +NE
Sbjct: 113 VFRLHPPRKGFKGGI---KTPYRDGGELGYR--GEKINE 146
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 27.5 bits (61), Expect = 7.2
Identities = 16/73 (21%), Positives = 19/73 (26%), Gaps = 7/73 (9%)
Query: 21 GGANRFGGGSGPGPIRGGPPRGGFRGGFNNDRWNDRPGGFAGPRPGGRWVNESSGPSRHT 80
G R GGG G G RG RG A P + P+
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGE------GGAKSASAKPAEKPSRRLGDAKPAGEQ 443
Query: 81 VHMRGLPFRANER 93
R P +
Sbjct: 444 QR-RRRPRKPAAA 455
>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 = 27.6 bits (61), Expect = 7.4
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 78 RHTVHMRGLPFRANERDVADFFRPVVPVHVDIHY----ENGRPSGEADVDFATHEDAMQA 133
TV + L +A ERD+ +FF V V D+ + R G A V+F E ++A
Sbjct: 89 DRTVFVLQLALKARERDLYEFFSKVGKVR-DVQCIKDRNSRRSKGVAYVEFYDVESVIKA 147
Query: 134 M 134
+
Sbjct: 148 L 148
>gnl|CDD|237213 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
Length = 471
Score = 27.4 bits (62), Expect = 7.7
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 14 YDRNDRFGGANRFG 27
++R DR GG R+G
Sbjct: 172 FERADRIGGLLRYG 185
>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional.
Length = 380
Score = 27.4 bits (61), Expect = 7.8
Identities = 14/23 (60%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 158 GVGGSGSIGGFGGSGGGRLGGFG 180
G GG GS GGFGG +GGFG
Sbjct: 76 GAGGFGS-GGFGGFDFSDMGGFG 97
>gnl|CDD|133130 cd06599, GH31_glycosidase_Aec37, Glycosyl hydrolase family 31
(GH31) domain of a bacterial protein family represented
by Escherichia coli protein Aec37. The gene encoding
Aec37 (aec-37) is located within a genomic island
(AGI-3) isolated from the extraintestinal avian
pathogenic Escherichia coli strain BEN2908. The function
of Aec37 and its orthologs is unknown; however, deletion
of a region of the genome that includes aec-37 affects
the assimilation of seven carbohydrates, decreases
growth rate of the strain in minimal medium containing
galacturonate or trehalose, and attenuates the virulence
of E. coli BEN2908 in chickens. All GH31 enzymes cleave
a terminal carbohydrate moiety from a substrate that
varies considerably in size, depending on the enzyme,
and may be either a starch or a glycoprotein.
Length = 317
Score = 27.3 bits (61), Expect = 8.0
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 4/29 (13%)
Query: 58 GGFAGPRPGG----RWVNESSGPSRHTVH 82
GGFAGP P RWV R +H
Sbjct: 267 GGFAGPAPEPELFVRWVQNGIFQPRFCIH 295
>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 27.1 bits (60), Expect = 8.2
Identities = 16/38 (42%), Positives = 17/38 (44%), Gaps = 14/38 (36%)
Query: 158 GVGGSGSIGGFGGSG--------------GGRLGGFGG 181
GVGG+ GGF G G GG GGFGG
Sbjct: 74 GVGGAAGGGGFSGEGMSMEDIFSMFGDIFGGHGGGFGG 111
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 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 = 107
Score = 26.1 bits (57), Expect = 8.4
Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 3/58 (5%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVH---VDIHYENGRPSGEADVDFATHEDAMQAM 134
T+ +R LP+ A E +A F V I GR G V F +
Sbjct: 3 TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 25.6 bits (57), Expect = 8.6
Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 24/75 (32%)
Query: 85 GLPFRANERDVADFFR--------------PVVPVHV--DIHYENGRPSGEADVDFATHE 128
LP E ++ DFF PV+ V + + ++ A V+F T E
Sbjct: 8 NLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNF--------AFVEFRTVE 59
Query: 129 DAMQAMSKDRTNMQH 143
+A A++ D +
Sbjct: 60 EATAALALDGIIFKG 74
>gnl|CDD|222234 pfam13575, DUF4135, Domain of unknown function (DUF4135). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria and archaea, and is
approximately 380 amino acids in length. The family is
found in association with pfam05147. This domain may be
involved in synthesis of a lantibiotic compound.
Length = 369
Score = 27.2 bits (61), Expect = 8.7
Identities = 23/90 (25%), Positives = 32/90 (35%), Gaps = 13/90 (14%)
Query: 107 VDIHYENGRPSGEADV--DFATHEDAMQAMSKDRTNMQHRYIELFLNSSSPRGGVGGSG- 163
D+H+EN SGE V D E + K L S V +G
Sbjct: 151 TDLHFENLIASGEYPVLIDL---ETLFHPVLKLDDEGATADAAEALRDS-----VLRTGL 202
Query: 164 -SIGGFGGSGGGRLGGFGGSDP-SSPFERR 191
+GG G + G GG + +PF+
Sbjct: 203 LPSWFWGGGEGIDISGLGGGEGQQTPFKVP 232
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 25.7 bits (57), Expect = 9.4
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 112 ENGRPSGEADVDFATHEDAMQA 133
NG+P G A V++AT EDA +A
Sbjct: 39 PNGQPRGFAFVEYATAEDAEEA 60
>gnl|CDD|143406 cd07087, ALDH_F3-13-14_CALDH-like, ALDH subfamily: Coniferyl
aldehyde dehydrogenase, ALDH families 3, 13, and 14, and
other related proteins. ALDH subfamily which includes
NAD(P)+-dependent, aldehyde dehydrogenase, family 3
member A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and
fatty aldehyde dehydrogenase, family 3 member A2
(ALDH3A2, EC=1.2.1.3), and also plant ALDH family
members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14
(YMR110C) and the protozoan family 13 member (ALDH13),
as well as coniferyl aldehyde dehydrogenases (CALDH,
EC=1.2.1.68), and other similar sequences, such as the
Pseudomonas putida benzaldehyde dehydrogenase I that is
involved in the metabolism of mandelate.
Length = 426
Score = 27.1 bits (61), Expect = 9.4
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 149 FLNSSSPRGGVGGSGSIGGFGGSGG 173
+ P GGVG SG +G + G G
Sbjct: 391 AAIPNLPFGGVGNSG-MGAYHGKAG 414
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 26.8 bits (59), Expect = 9.7
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 19 RFGGANRFGGGSGP--GPIRGGPPRGGFRGGFNNDRWNDRPGGFAGP 63
R GG + F SG G GGP GG+ GG + GGF P
Sbjct: 52 RIGGGS-FRAPSGYSRGYSGGGPSGGGYSGGGYSG------GGFGFP 91
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
0.318 0.141 0.455
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,562,925
Number of extensions: 1214284
Number of successful extensions: 2188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1806
Number of HSP's successfully gapped: 284
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.9 bits)