RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11409
(320 letters)
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family 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 family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 92
Score = 174 bits (442), Expect = 4e-55
Identities = 72/83 (86%), Positives = 76/83 (91%)
Query: 63 PHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDED 122
P D +EITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ+ESSVQ LIDACI ++D
Sbjct: 10 PDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACIEEDD 69
Query: 123 KCYLCVSSPTIKDKPVQIRPWKL 145
K YLCVSSPTIKDKPVQIRPW L
Sbjct: 70 KLYLCVSSPTIKDKPVQIRPWNL 92
>gnl|CDD|241170 cd12726, RRM2_CPEB2_like, RNA recognition motif 2 found in
cytoplasmic polyadenylation element-binding protein
CPEB-2, CPEB-3, CPEB-4 and similar protiens. This
subgroup corresponds to the RRM2 of the paralog proteins
CPEB-2, CPEB-3 and CPEB-4, all well conserved in both,
vertebrates and invertebrates. Due to the high sequence
similarity, members in this family 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 family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 81
Score = 167 bits (424), Expect = 1e-52
Identities = 74/81 (91%), Positives = 80/81 (98%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
KT+FVGGVPRPL+A+ELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAF++Q SYIAAI
Sbjct: 1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAI 60
Query: 222 SARFVQLQHGEIDKRVEVKPY 242
SARFVQLQHG+IDKRVEVKPY
Sbjct: 61 SARFVQLQHGDIDKRVEVKPY 81
>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 = 131 bits (332), Expect = 8e-39
Identities = 46/81 (56%), Positives = 58/81 (71%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
+TVFVGG+P PL A ELA I++RLYGGVCY IDTD YP G RV F ++ SYI A+
Sbjct: 1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAV 60
Query: 222 SARFVQLQHGEIDKRVEVKPY 242
S FV+L +I+KRV ++PY
Sbjct: 61 SEVFVELPFNDINKRVRIRPY 81
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the 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 have 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 bind 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 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.
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 = 112
Score = 109 bits (274), Expect = 6e-30
Identities = 38/100 (38%), Positives = 45/100 (45%), Gaps = 20/100 (20%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKS--------------------YFPPKGYAFLLFQ 105
+I SFRRFG L VDWP K PKGY FLLF+
Sbjct: 13 TEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKGQHPKGYVFLLFE 72
Query: 106 DESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKL 145
E SV+ L+ AC +E + SS + K VQIRPW L
Sbjct: 73 KERSVRSLLLACSEEEGGLFRITSSSSTDSKRVQIRPWVL 112
>gnl|CDD|241169 cd12725, RRM2_CPEB1, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), 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. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 86
Score = 98.2 bits (245), Expect = 6e-26
Identities = 45/87 (51%), Positives = 61/87 (70%), Gaps = 1/87 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
DP KTVFVG + L A LA IM+ L+GGV YAGIDTD + KYP G+GRV F +Q SY+
Sbjct: 1 DPSKTVFVGALHGMLNAEALAHIMNDLFGGVVYAGIDTD-KYKYPIGSGRVTFNNQRSYM 59
Query: 219 AAISARFVQLQHGEIDKRVEVKPYVLD 245
A+ A FV+++ + K+V++ PY+ D
Sbjct: 60 KAVKAAFVEIKTPKFTKKVQIDPYLED 86
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), 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. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 75.9 bits (187), Expect = 2e-17
Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 3/83 (3%)
Query: 69 EITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVD---EDKCY 125
+ +F+ FG + V+WP K PPKGY +L+F+ E SV+ L+ AC D + Y
Sbjct: 18 GLINTFKPFGSVSVEWPGKDGKHPRHPPKGYVYLIFESEKSVKALLQACTHDFLNGGEYY 77
Query: 126 LCVSSPTIKDKPVQIRPWKLTDA 148
+SS ++ K VQ+ PW L+D+
Sbjct: 78 FKISSRRMRSKEVQVIPWVLSDS 100
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 39.5 bits (93), Expect = 1e-04
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 163 TVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAIS 222
T+FVG +P EL + + +G V + D E KG V F S+ A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSK-FGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59
Query: 223 A 223
A
Sbjct: 60 A 60
Score = 35.6 bits (83), Expect = 0.003
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 63 PHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
P EE+ F +FG + V E+ KG+AF+ F+ E ++ ++A
Sbjct: 9 PDTTEEELRELFSKFGKVESVRLVRDKETGK---SKGFAFVEFESEEDAEKALEAL 61
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 37.7 bits (88), Expect = 6e-04
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
K +FVGG+P + +L + +G V + D E K P+G G + F S+ S +
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQ-FGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
Query: 222 SARFVQLQHGEIDKRVEVK 240
+ F + K+VEVK
Sbjct: 62 NEHFHDIN----GKKVEVK 76
Score = 28.9 bits (65), Expect = 0.79
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 20/82 (24%)
Query: 63 PHYDHEEITASFRRFGPL---VVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIV 119
P+ ++ F +FG + VV + H E K P+G+ F+ F+ E SV Q+++
Sbjct: 12 PNVTETDLRKYFSQFGTVTEVVVMYDH--EKKR---PRGFGFITFESEDSVDQVVNEHFH 66
Query: 120 DEDKCYLCVSSPTIKDKPVQIR 141
D I K V+++
Sbjct: 67 D------------INGKKVEVK 76
>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 = 37.2 bits (87), Expect = 0.001
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
+TVF+ +P EL + +G V YA I D + KG V F ++ S +
Sbjct: 1 RTVFIRNLPFDATEEELKELF-SQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59
Query: 222 SA 223
A
Sbjct: 60 EA 61
Score = 27.2 bits (61), Expect = 3.7
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 65 YDHEEITASFRRFGP----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
EE+ F +FG +V K KG AF+ F+ + S Q+ ++A
Sbjct: 12 ATEEELKELFSQFGEVKYARIV--KDKLTGH----SKGTAFVKFKTKESAQKCLEA 61
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 35.7 bits (83), Expect = 0.002
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 63 PHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
P E++ F +FG + V + KS KG+AF+ F+ ++ ++A
Sbjct: 8 PDTTEEDLRELFSKFGEIESVRIVRDKDGKS----KGFAFVEFESPEDAEKALEAL 59
Score = 32.3 bits (74), Expect = 0.037
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+FVG +P +L + + +G + I D + K KG V F S A+ A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSK-FGEIESVRIVRDKDGK-SKGFAFVEFESPEDAEKALEA 58
Query: 224 RFVQLQHGEID-KRVEVK 240
L E+D ++++V
Sbjct: 59 ----LNGKELDGRKLKVS 72
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 34.7 bits (80), Expect = 0.007
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+FVGG+P + E + +G V A + D + +G G V F S+++ SA
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQ-FGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 224 RFVQLQHGEIDKRVEVKP 241
++L K+VEVK
Sbjct: 61 GMLELG----GKQVEVKR 74
Score = 28.9 bits (65), Expect = 0.76
Identities = 9/48 (18%), Positives = 23/48 (47%), Gaps = 12/48 (25%)
Query: 96 PKGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPW 143
+G+ F+ F ES+V+++ A +++ + K V+++
Sbjct: 40 SRGFGFVTFDSESAVERVFSAGMLE------------LGGKQVEVKRA 75
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 34.2 bits (79), Expect = 0.010
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 12/57 (21%)
Query: 65 YDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
EE+ + F GP +V D + +S GY F+ + DE+ Q+ I+
Sbjct: 12 MTQEELRSLFEAIGPIESCKIVRD---RITGQSL----GYGFVDYVDENDAQKAINT 61
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 35.7 bits (81), Expect = 0.021
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 155 SMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQ 214
+ T+FVG +P + +L + + +G V + D E +G V F S+
Sbjct: 109 QKSKEENNTLFVGNLPYDVTEEDLRELFKK-FGPVKRVRLVRDRETGKSRGFAFVEFESE 167
Query: 215 ASYIAAISARFVQLQHGEI-DKRVEVKPYVLDDQ 247
S AI L E+ + + V+ Q
Sbjct: 168 ESAEKAIEE----LNGKELEGRPLRVQKAQPASQ 197
>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 = 33.8 bits (77), Expect = 0.025
Identities = 19/59 (32%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 163 TVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
T+FV +P LA +G V YA D KG G V F Q +Y A +
Sbjct: 3 TLFVRNLPYDATEESLAPHF-SKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
Score = 31.1 bits (70), Expect = 0.27
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 68 EEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACI 118
E + F +FG + P KS KG F+ F+D+ + +AC+
Sbjct: 16 ESLAPHFSKFGSVRYALPVI--DKSTGRAKGTGFVCFKDQYTY----NACL 60
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 33.1 bits (76), Expect = 0.030
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 63 PHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQ 111
+ HE + A F ++G +V V P + KG+AF+ F+ Q
Sbjct: 9 KNATHEWLKAVFSKYGTVVYVSLPRYKHTGD---IKGFAFIEFETPEEAQ 55
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 32.4 bits (74), Expect = 0.054
Identities = 11/56 (19%), Positives = 23/56 (41%), Gaps = 4/56 (7%)
Query: 63 PHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
+E+ F+ FG ++ V K + F++F D +VQ+++
Sbjct: 13 HDITEDELKEFFKEFGNVLEVRINSKGGGG---RLPNFGFVVFDDPEAVQKILANK 65
>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 = 31.4 bits (72), Expect = 0.075
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 62 TPHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
P E++ F +FGP+ + +S KG+AF+ F+DE ++ ++A
Sbjct: 7 PPDTTEEDLKDLFSKFGPIESIRIVRDETGRS----KGFAFVEFEDEEDAEKALEAL 59
Score = 29.5 bits (67), Expect = 0.36
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 6/74 (8%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+FVG +P +L + +G + I D E KG V F + A+ A
Sbjct: 1 LFVGNLPPDTTEEDLKDLF-SKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEA 58
Query: 224 RFVQLQHGEIDKRV 237
L E+ R
Sbjct: 59 ----LNGKELGGRE 68
>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 = 0.14
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISARFVQLQHGEIDKR 236
YG + + TDP+ PKG G V F+SQ + AA+ A L ++ R
Sbjct: 22 YGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDA----LGGTDLLGR 68
>gnl|CDD|185160 PRK15248, PRK15248, fimbrial outer membrane usher protein StbC;
Provisional.
Length = 853
Score = 33.7 bits (77), Expect = 0.16
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 13/88 (14%)
Query: 169 VPRPLKALELAMIM------DRLYGGVCYAGI--DTDPELKYPKGAGRVAFASQASYIAA 220
V RP+ ++ + + L+G + + GI TD + P+G + +A + +AA
Sbjct: 227 VQRPVASINSILSLGDSYTDSSLFGSLSFNGIKLVTDERM-RPQG--KRGYAPEVRGVAA 283
Query: 221 ISARFVQLQHGEI--DKRVEVKPYVLDD 246
SA V Q G++ + V P+ +DD
Sbjct: 284 SSAHVVVKQLGKVIYETNVPPGPFYIDD 311
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 30.3 bits (69), Expect = 0.25
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 95 PPKGYAFLLFQDESSVQ 111
PKG+A++ F D+SSV+
Sbjct: 39 QPKGFAYIEFLDKSSVE 55
>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 = 30.2 bits (69), Expect = 0.27
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLID 115
D +++ FR FGP + + A+ K +G+AF+ F ++ I+
Sbjct: 12 DEDDLRELFRPFGP--ISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 29.9 bits (68), Expect = 0.38
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 163 TVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAIS 222
++VG +P + +L + + +G V A + TD E +G G V + AAI
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQ-FGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59
Query: 223 A 223
Sbjct: 60 K 60
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 29.5 bits (67), Expect = 0.50
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 63 PHYDHE-EITASFRRFGPLVVDWPHK---AESKSYFPPKGYAFLLFQDE 107
PH +E E+ F +FG + + + SK KGYAF+ F+
Sbjct: 8 PHGFYEPELRKYFSQFGTV-----TRLRLSRSKKTGKSKGYAFVEFESP 51
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 29.2 bits (66), Expect = 0.50
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 12/55 (21%)
Query: 68 EEITASFRRFGPLVVD------WPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E++ + G VVD + HKA KS KG+A++ F E++ + +
Sbjct: 13 EDLEGALAEAG--VVDVKSIKFFEHKANGKS----KGFAYVEFASEAAAAAVKEK 61
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 29.1 bits (66), Expect = 0.64
Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 16/65 (24%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISARFVQLQHGEIDKRVEVKPYVLD 245
YG V I DP +G G V FA +S +DK + KP+VLD
Sbjct: 22 YGEVVDCVIMKDPITGRSRGFGFVTFADPSS----------------VDKVLAAKPHVLD 65
Query: 246 DQMCD 250
+ D
Sbjct: 66 GREID 70
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 28.7 bits (64), Expect = 0.81
Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 68 EEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLID 115
+++ F +FG VVD K + + +G+ F+LF+D +SV++++D
Sbjct: 13 KDLKEYFSKFGE-VVDCTIKIDPVTG-RSRGFGFVLFKDAASVEKVLD 58
>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 = 28.0 bits (63), Expect = 1.3
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 187 GGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAIS 222
G V A + TD + + KG G V F S AI
Sbjct: 23 GNVLRADVKTDNDGR-SKGFGTVLFESPEDAQRAIE 57
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 28.1 bits (63), Expect = 1.3
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 62 TPHYDHEEITASFRRFGPLV-VDWPH-KAESKSYFPPKGYAFLLFQDESSVQQL 113
+P E+I F +FG +V ++ P K +K +G+ F+ F E V+++
Sbjct: 8 SPETTEEKIREYFGKFGNIVEIELPMDKKTNKR----RGFCFITFDSEEPVKKI 57
>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 = 28.0 bits (63), Expect = 1.4
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 66 DHEEITASFRRFGPL-VVDWPHKAESKSYFPPKGYAFLLFQDESSVQ 111
D +++ F +FG + + P K + K G+AF+ F+D SS +
Sbjct: 13 DEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAE 59
>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 = 27.7 bits (62), Expect = 1.9
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISARFVQLQHGEIDKR 236
+G V A + TD E +G G V F S AI A + E+D R
Sbjct: 23 FGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA----MDGKELDGR 69
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 27.6 bits (62), Expect = 1.9
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 12/54 (22%)
Query: 66 DHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLI 114
E++ F ++G +V D K K +G+AF+ F D V +++
Sbjct: 12 TEEDLREYFSQYGNVESVEIVTD---KETGK----KRGFAFVTFDDYDPVDKIV 58
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 29.5 bits (66), Expect = 2.4
Identities = 20/85 (23%), Positives = 28/85 (32%), Gaps = 13/85 (15%)
Query: 38 VPNLGPNDILKLSFPSPPQFPLQGTPHY-DHEEITASFRRFGPL-----VVDWPHKAESK 91
N+ S + + P Y ++I FG L + D A
Sbjct: 279 AKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKD---IATGL 335
Query: 92 SYFPPKGYAFLLFQDESSVQQLIDA 116
S KGYAF ++D S I A
Sbjct: 336 S----KGYAFCEYKDPSVTDVAIAA 356
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 27.6 bits (61), Expect = 2.5
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
++V +PR L EL I + YG + + D P+G V + + AAIS+
Sbjct: 3 LYVTNLPRQLTEDELRKIFEA-YGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 27.3 bits (61), Expect = 2.6
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLF 104
EE+ F FG + V P E+K KG+AF+ F
Sbjct: 14 EELRELFEAFGEISEVHLPLDKETKR---SKGFAFVSF 48
>gnl|CDD|216039 pfam00643, zf-B_box, B-box zinc finger.
Length = 42
Score = 26.3 bits (58), Expect = 2.7
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 245 DDQMCDECQGVRCGGKFAPFFCANVCCLQYYCEHCWATIHS 285
+++C E + K +C + C Q CE C + H
Sbjct: 2 KERLCPEHEE-----KPLELYCED--CQQLLCEECALSGHK 35
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein
orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which
is a putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 27.6 bits (62), Expect = 2.7
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 63 PHYDHEEITASFRRFGPLV---VDWPHKAESKS 92
P E + F RFGPL + WP E +
Sbjct: 11 PKVTEEVLCQEFGRFGPLASVKIMWPRTEEERR 43
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 27.1 bits (61), Expect = 2.7
Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 63 PHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
P E++ F +G + V ++ P+G+AF+ F + +
Sbjct: 8 PSVTEEDLREFFSPYGKVEGVRLV-----RNKDRPRGFAFVEFASPEDAEAALKKL 58
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 27.2 bits (61), Expect = 2.8
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 161 RKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQA 215
+FVGG+P EL R +G V I TD KG G V F +Q
Sbjct: 2 PNRIFVGGIPPDTTEEELRDFFSR-FGSVKDVKIITD-RAGVSKGYGFVTFETQE 54
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 27.2 bits (61), Expect = 3.0
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 62 TPHYDHEEITASFRRFGPLVVDWPHKA--ESKSYFPPKGYAFLLFQDESSVQQLIDA 116
P+ E++ + FG ++ KA + K+ KGY F+ F + + I+
Sbjct: 9 PPNTTDEDLEKLCQPFGKII---STKAILDKKTN-KCKGYGFVDFDSPEAALKAIEG 61
>gnl|CDD|238733 cd01456, vWA_ywmD_type, VWA ywmD type:Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Not much is known about the function of the
members of this subgroup. All members of this subgroup
however have a conserved MIDAS motif. .
Length = 206
Score = 28.5 bits (64), Expect = 3.6
Identities = 13/69 (18%), Positives = 22/69 (31%), Gaps = 9/69 (13%)
Query: 42 GPNDILKLSFPSPPQFPLQGTPHYDHEEITASF------RRFGPLVVDWPHKAESKSYFP 95
P D+ L P+ G P + A+ + PL AE+ +Y
Sbjct: 75 NPLDVRVLVPKGCLTAPVNGFPSAQRSALDAALNSLQTPTGWTPLA---AALAEAAAYVD 131
Query: 96 PKGYAFLLF 104
P ++
Sbjct: 132 PGRVNVVVL 140
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 29.2 bits (66), Expect = 3.9
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 21/63 (33%)
Query: 184 RLYGGVCYAGIDTDPELKYPKGAG-RVAFASQASYIAAISARFVQLQH-GEIDKRVEVKP 241
+L GVCYA +D G RV V+LQ D++V++KP
Sbjct: 80 KLKAGVCYAALDV------VNSRGQRVLVG-------------VRLQQVAGRDRKVDIKP 120
Query: 242 YVL 244
+ +
Sbjct: 121 FAI 123
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed 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. .
Length = 73
Score = 26.4 bits (59), Expect = 4.4
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+G V A + D K G V++ + S AAI A
Sbjct: 22 FGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 26.4 bits (59), Expect = 5.5
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 68 EEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQD 106
E+ F ++GPL W + PP G+AF+ F+D
Sbjct: 14 RELEDEFEKYGPLRSVWVARN------PP-GFAFVEFED 45
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 26.5 bits (59), Expect = 5.6
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 74 FRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSV 110
F + GPL V P K PK +AF+ F+ E SV
Sbjct: 22 FLQAGPLEGVKIPKDPNGK----PKSFAFVTFKHEVSV 55
>gnl|CDD|169215 PRK08091, PRK08091, ribulose-phosphate 3-epimerase; Validated.
Length = 228
Score = 27.9 bits (62), Expect = 5.7
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 259 GKFAPFFCANVCCLQYYCEHCWATIHSKPGREFH--KPLVKEGA 300
G+F+PFF ++ + HC+ +H +F K V GA
Sbjct: 49 GQFSPFFTVGAIAIKQFPTHCFKDVHLMVRDQFEVAKACVAAGA 92
>gnl|CDD|140277 PTZ00250, PTZ00250, variable surface protein Vir23; Provisional.
Length = 350
Score = 28.0 bits (62), Expect = 6.6
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 225 FVQLQHGEIDKRVEVKPYVLDDQMCDECQG 254
F + E+DK++E P + D CD C+G
Sbjct: 31 FYEKLDNELDKKIEETPEI--DDKCDHCKG 58
>gnl|CDD|217903 pfam04112, Mak10, Mak10 subunit, NatC N(alpha)-terminal
acetyltransferase. NatC N(alpha)-terminal
acetyltransferases contains Mak10p, Mak31p and Mak3p
subunits. All three subunits are associated with each
other to form the active complex.
Length = 167
Score = 27.3 bits (61), Expect = 7.4
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 152 LDASMPLDPRKTVF-----VGGVPRPLKALELAMIMDRLYG 187
+D+ M + F RPL E+ IMDRL
Sbjct: 27 MDSGMIELTEEEPFDLEEAYDTGLRPLDLPEVLAIMDRLLS 67
>gnl|CDD|153223 cd03129, GAT1_Peptidase_E_like, Type 1 glutamine amidotransferase
(GATase1)-like domain found in peptidase E_like
proteins. Type 1 glutamine amidotransferase
(GATase1)-like domain found in peptidase E_like
proteins. This group contains proteins similar to the
aspartyl dipeptidases Salmonella typhimurium peptidase E
and Xenopus laevis peptidase E and, extracellular
cyanophycinases from Pseudomonas anguilliseptica BI
(CphE) and Synechocystis sp. PCC 6803 CphB. In bacteria
peptidase E is believed to play a role in degrading
peptides generated by intracellular protein breakdown or
imported into the cell as nutrient sources. Peptidase E
uniquely hydrolyses only Asp-X dipeptides (where X is
any amino acid), and one tripeptide Asp-Gly-Gly.
Cyanophycinases are intracellular exopeptidases which
hydrolyze the polymer cyanophycin (multi
L-arginyl-poly-L-aspartic acid) to the dipeptide
beta-Asp-Arg. Peptidase E and cyanophycinases are
thought to have a Ser-His-Glu catalytic triad which
differs from the Cys-His-Glu catalytic triad typical of
GATase1 domains by having a Ser in place of the reactive
Cys at the nucleophile elbow. Xenopus peptidase E is
developmentally regulated in response to thyroid hormone
and, it is thought to play a role in apoptosis during
tail reabsorption.
Length = 210
Score = 27.3 bits (61), Expect = 9.3
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 164 VFVGG--VPRPLKALE----LAMIMDRLYGGVCYAGI 194
+FVGG R L L L I+ R+ GV G
Sbjct: 84 IFVGGGNQLRLLSVLRETPLLDAILKRVARGVVIGGT 120
>gnl|CDD|171505 PRK12446, PRK12446, undecaprenyldiphospho-muramoylpentapeptide
beta-N-acetylglucosaminyltransferase; Reviewed.
Length = 352
Score = 27.5 bits (61), Expect = 9.8
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 93 YFPPKGYAFLLFQDESSVQQLIDA 116
F +GYA +L++++ +V LI
Sbjct: 295 SFERQGYASVLYEEDVTVNSLIKH 318
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
0.322 0.140 0.439
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,439,736
Number of extensions: 1578030
Number of successful extensions: 1349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1337
Number of HSP's successfully gapped: 61
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)