RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy93
(503 letters)
>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 = 139 bits (352), Expect = 3e-40
Identities = 53/80 (66%), Positives = 66/80 (82%)
Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
A++VKNL+ V+NELLE AF FG++ERA+VIVD+RG S EGIVEF+RKP A A++RC
Sbjct: 1 ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRC 60
Query: 249 AEGCFFLTQSLRPVIVEPLE 268
+EGCF LT S RPV+VEPLE
Sbjct: 61 SEGCFLLTASPRPVVVEPLE 80
>gnl|CDD|240580 cd12945, NOPS_NONA_like, NOPS domain, including C-terminal
coiled-coil region, in p54nrb/PSF/PSP1 homologs from
invertebrate species. The family 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 NOPS (NONA and PSP1) domain.
This model corresponds to the NOPS domain, with a long
helical C-terminal extension , found in Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA), Chironomus
tentans hrp65 gene encoding protein Hrp65 and similar
proteins. 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. The NOPS
domain specifically binds to the second RNA recognition
motif (RRM2) domain of the partner DBHS protein via a
substantial interaction surface. Its highly conserved
C-terminal residues are critical for functional DBHS
dimerization while the highly conserved C-terminal
helical extension, forming a right-handed antiparallel
heterodimeric coiled-coil, is essential for localization
of these proteins to subnuclear bodies.
Length = 100
Score = 119 bits (300), Expect = 1e-32
Identities = 54/103 (52%), Positives = 71/103 (68%), Gaps = 4/103 (3%)
Query: 259 LRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL 318
LRP +VEP+E D+ DGL E+++NKK PEF K+R +GPRFA NSFE EYG+RWKQLHEL
Sbjct: 1 LRPCVVEPMEEIDDEDGLPEKSLNKKNPEFNKERSIGPRFAEPNSFEHEYGTRWKQLHEL 60
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEEL 361
Y+ + E L++EL E E Q E+ E + E L+ E+L
Sbjct: 61 YKQKEEALKRELKMEEEKLEAQ-MEYARYEHETELLR---EQL 99
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 107 bits (269), Expect = 1e-28
Identities = 50/80 (62%), Positives = 61/80 (76%)
Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
A+ VKNL+ V+NELLE AF FG +ERA+VIVD+RG +G VEFA KPAA +AL RC
Sbjct: 1 ALTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALERC 60
Query: 249 AEGCFFLTQSLRPVIVEPLE 268
A+G F LT + RPVIVEP+E
Sbjct: 61 ADGAFLLTTTPRPVIVEPME 80
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 106 bits (265), Expect = 5e-28
Identities = 51/80 (63%), Positives = 61/80 (76%)
Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
A+ V+NL+ V+NELLE AF FG +ERA+VIVD+RG S +GIVEFA KPAA +A RC
Sbjct: 1 ALSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFERC 60
Query: 249 AEGCFFLTQSLRPVIVEPLE 268
EG F LT + RPVIVEPLE
Sbjct: 61 TEGVFLLTTTPRPVIVEPLE 80
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 103 bits (257), Expect = 8e-27
Identities = 47/80 (58%), Positives = 60/80 (75%)
Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
A+ VKNL V+NELLE AF +FG +ERA+VIVD+RG +GIVEFA KP+A +AL RC
Sbjct: 1 ALTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDRC 60
Query: 249 AEGCFFLTQSLRPVIVEPLE 268
++G F LT RPV VEP++
Sbjct: 61 SDGAFLLTAFPRPVTVEPMD 80
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 100 bits (252), Expect = 3e-26
Identities = 42/70 (60%), Positives = 55/70 (78%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
CRL++GN+ DITE + ELF YGE E+F+NKEK FGFIR+D + NA+KAKA+LDG +
Sbjct: 2 CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIM 61
Query: 174 LKGRSLKIRF 183
KGR L++RF
Sbjct: 62 RKGRQLRVRF 71
>gnl|CDD|240579 cd12931, eNOPS_SF, NOPS domain, including C-terminal helical
extension region, in the p54nrb/PSF/PSP1 family. All
members in this family contain a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRM1 and RRM2),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1) domain
with a long helical C-terminal extension. The NOPS
domain specifically binds to RRM2 domain of the partner
DBHS protein via a substantial interaction surface. Its
highly conserved C-terminal residues are critical for
functional DBHS dimerization while the highly conserved
C-terminal helical extension, forming a right-handed
antiparallel heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies. PSF
has an additional large N-terminal domain that
differentiates it from other family members. The
p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein 1 (PSP1), which are
ubiquitously expressed and are well conserved in
vertebrates. p54nrb, also termed NONO or NMT55, 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, also termed POMp100, 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, also termed PSPC1, 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. For
instance, 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.
Length = 90
Score = 98.5 bits (246), Expect = 4e-25
Identities = 45/94 (47%), Positives = 61/94 (64%), Gaps = 6/94 (6%)
Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
RPV+VEPLE DE DGL ER + KK + K+R+VGPRFA SFE+E+G RWK L+EL
Sbjct: 2 RPVVVEPLEQRDEEDGLPERNV-KKNAGYQKEREVGPRFAPPGSFEYEFGQRWKALYEL- 59
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
E ++E ++E+ R+K E EM+ + E
Sbjct: 60 ----EKQQREQLEKELKEAREKLEAEMEAARYEH 89
>gnl|CDD|149257 pfam08075, NOPS, NOPS (NUC059) domain. This domain is found at the
C-terminus of NONA and PSP1 proteins adjacent to 1 or 2
pfam00076 domains.
Length = 52
Score = 84.0 bits (208), Expect = 2e-20
Identities = 32/53 (60%), Positives = 42/53 (79%), Gaps = 1/53 (1%)
Query: 261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWK 313
PVIVEP+E D+ DGL E+ + KK+P+++K+R+ GPRFA SFE EYGSRWK
Sbjct: 1 PVIVEPMEQNDDEDGLPEK-LVKKSPDYHKEREQGPRFAQPGSFEHEYGSRWK 52
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 79.6 bits (196), Expect = 1e-18
Identities = 38/70 (54%), Positives = 54/70 (77%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
CRL++GN+ DITE D +LF+ YGE E+FIN+++ FGFIR++ + A+ AKA+LDG +
Sbjct: 2 CRLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTI 61
Query: 174 LKGRSLKIRF 183
LK R L+IRF
Sbjct: 62 LKNRPLRIRF 71
>gnl|CDD|240584 cd12949, NOPS_PSPC1, NOPS domain, including C-terminal coiled-coil
region, in paraspeckle protein component 1 (PSPC1) and
similar proteins. The family 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 NOPS (NONA and PSP1) domain.
This model corresponds to the NOPS domain, with a long
helical C-terminal extension, of paraspeckle component 1
(PSPC1, also termed PSP1), a novel nucleolar factor that
accumulates within a new nucleoplasmic compartment,
termed paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Although its cellular function
remains unknown currently, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NONO), which localizes to paraspeckles in an
RNA-dependent manner. The NOPS domain specifically binds
to the second RNA recognition motif (RRM2) domain of the
partner DBHS protein via a substantial interaction
surface. Its highly conserved C-terminal residues are
critical for functional DBHS dimerization while the
highly conserved C-terminal helical extension, forming a
right-handed antiparallel heterodimeric coiled-coil, is
essential for localization of these proteins to
subnuclear bodies.
Length = 94
Score = 76.6 bits (188), Expect = 3e-17
Identities = 41/93 (44%), Positives = 59/93 (63%), Gaps = 6/93 (6%)
Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
RPVIVEP+E D+ DGL E+ + +KT +++K+R+ PRFA +FEFEY SRWK L E+
Sbjct: 2 RPVIVEPMEQFDDEDGLPEKLM-QKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEM- 59
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
E ++E R I ++K E EM+ + E
Sbjct: 60 ----EKQQREQVDRNIREAKEKLEAEMEAARHE 88
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 74.6 bits (183), Expect = 8e-17
Identities = 35/70 (50%), Positives = 52/70 (74%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
CRL++GN+ DITE++ +LF YGE E+FINK K FGFI+++ + A+ AKA+LD
Sbjct: 2 CRLFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTP 61
Query: 174 LKGRSLKIRF 183
++GR L++RF
Sbjct: 62 MRGRQLRVRF 71
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 73.4 bits (180), Expect = 2e-16
Identities = 33/69 (47%), Positives = 53/69 (76%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
RL++GN+ DITE ++ +LF+ YG+ E+FI+K+K FGFIR++ + A+ AKA+LD L
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPL 62
Query: 175 KGRSLKIRF 183
+G+ L++RF
Sbjct: 63 RGKQLRVRF 71
>gnl|CDD|240581 cd12946, NOPS_p54nrb_PSF_PSPC1, NOPS domain, including C-terminal
coiled-coil region, in p54nrb/PSF/PSPC1 family proteins.
The family 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 NOPS (NONA and
PSP1) domain. This model corresponds to the NOPS domain,
with a long helical C-terminal extension, found in the
p54nrb/PSF/PSPC1 proteins. The NOPS domain specifically
binds to the second RNA recognition motif (RRM2) domain
of the partner DBHS protein via a substantial
interaction surface. Its highly conserved C-terminal
residues are critical for functional DBHS dimerization
while the highly conserved C-terminal helical extension,
forming a right-handed antiparallel heterodimeric
coiled-coil, is essential for localization of these
proteins to subnuclear bodies. Members in the family
include 54 kDa nuclear RNA- and DNA-binding protein
(p54nrb), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF) and paraspeckle
protein component 1 (PSPC1 or PSP1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb, also termed NONO or NMT55, 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, also termed POMp100,
is 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. PSPC1 is a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. The cellular function of PSPC1 remains
unknown currently. PSF has an additional large
N-terminal domain that differentiates it from other
family members.
Length = 93
Score = 74.0 bits (181), Expect = 2e-16
Identities = 38/93 (40%), Positives = 56/93 (60%), Gaps = 6/93 (6%)
Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
RPVIVEP+E D+ DGL E+ +K +++K+R+ PRFA +FE+EY RWK L E+
Sbjct: 2 RPVIVEPMEQLDDEDGLPEKLA-QKNQQYHKEREQPPRFAQPGTFEYEYAQRWKALDEM- 59
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
E ++E R I ++K E EM+ + E
Sbjct: 60 ----EKQQREQVDRNIKEAKEKLESEMEAARHE 88
>gnl|CDD|240583 cd12948, NOPS_PSF, NOPS domain, including C-terminal coiled-coil
region, in polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF) and similar
proteins. This model contains the NOPS (NONA and PSP1)
domain PSF (also termed proline- and glutamine-rich
splicing factor, or 100 kDa DNA-pairing protein
(POMp100), or 100 kDa subunit of DNA-binding p52/p100
complex), with a long helical C-terminal extension. PSF
is a multifunctional protein that mediates diverse
activities in the cell. It is ubiquitously expressed and
highly conserved in vertebrates. PSF binds not only RNA
but also single-stranded DNA (ssDNA) as well as
double-stranded DNA (dsDNA) and facilitates the
renaturation of complementary ssDNAs. Additionally, it
promotes the formation of D-loops in superhelical duplex
DNA, and is involved in cell proliferation. PSF can also
interact with multiple factors. It is an RNA-binding
component of spliceosomes and binds to insulin-like
growth factor response element (IGFRE). Moreover, PSF
functions as a transcriptional repressor interacting
with Sin3A and mediating silencing through the
recruitment of histone deacetylases (HDACs) to the DNA
binding domain (DBD) of nuclear hormone receptors. As an
RNA-binding component of spliceosomes, PSF binds to the
insulin-like growth factor response element (IGFRE), and
acts as an independent negative regulator of the
transcriptional activity of the porcine P-450
cholesterol side-chain cleavage enzyme gene (P450scc)
IGFRE. PSF is an essential pre-mRNA splicing factor and
is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. In
addition, PSF forms a heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NONO). The PSF/p54nrb complex
displays a variety of functions, such as DNA
recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. The NOPS domain specifically binds to the
second RNA recognition motif (RRM2) domain of the
partner DBHS protein via a substantial interaction
surface. Its highly conserved C-terminal residues are
critical for functional DBHS dimerization while the
highly conserved C-terminal helical extension, forming a
right-handed antiparallel heterodimeric coiled-coil, is
essential for localization of these proteins to
subnuclear bodies.
Length = 97
Score = 69.4 bits (169), Expect = 1e-14
Identities = 41/101 (40%), Positives = 61/101 (60%), Gaps = 10/101 (9%)
Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
RPVIVEPLE D+ DGL E+ + +K P + K+R+ PRFA +FE+EY RWK L E+
Sbjct: 2 RPVIVEPLEQLDDEDGLPEK-LAQKNPMYQKERETPPRFAQPGTFEYEYSQRWKSLDEME 60
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMK----ERQAEELKR 356
+ + E + K + + ++K E EM+ E QA L++
Sbjct: 61 KQQREQVEKNMKE-----AKEKLESEMEDAYHEHQANLLRQ 96
>gnl|CDD|240582 cd12947, NOPS_p54nrb, NOPS domain, including C-terminal coiled-coil
region, in 54 kDa nuclear RNA- and DNA-binding protein
(p54nrb) and similar proteins. The family 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 NOPS (NONA and PSP1) domain.
This model corresponds to the NOPS domain, with a long
helical C-terminal extension, found in p54nrb, also
termed non-POU domain-containing octamer-binding protein
(NONO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. It 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. p54nrb is ubiquitously expressed and highly
conserved in vertebrates. It binds both single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). The NOPS
domain specifically binds to the second RNA recognition
motif (RRM2) domain of the partner DBHS protein via a
substantial interaction surface. Its highly conserved
C-terminal residues are critical for functional DBHS
dimerization while the highly conserved C-terminal
helical extension, forming a right-handed antiparallel
heterodimeric coiled-coil, is essential for paraspeckle
localization to subnuclear bodies.
Length = 94
Score = 69.0 bits (168), Expect = 1e-14
Identities = 37/93 (39%), Positives = 55/93 (59%), Gaps = 6/93 (6%)
Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
RPV VEP++ D+ +GL E+ + K +++K+R+ PRFA SFE+EY RWK L E+
Sbjct: 2 RPVTVEPMDQLDDEEGLPEKLVIK-NQQYHKEREQPPRFAQPGSFEYEYAMRWKALIEM- 59
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
E ++E R I R+K E EM+ + E
Sbjct: 60 ----EKQQQEQVDRNIKEAREKLEMEMEAARHE 88
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 66.5 bits (163), Expect = 5e-14
Identities = 19/67 (28%), Positives = 38/67 (56%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
+Y+GN+ +TE ++ F P+G +E+ + K+K + F+R D A A ++G
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 174 LKGRSLK 180
+ G+++K
Sbjct: 61 INGQTVK 67
Score = 29.1 bits (66), Expect = 0.86
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
V NL +T E L+ F FG IE + + ++G V F AAA A
Sbjct: 5 VGNLPHGLTEEELQRTFSPFGAIEE-VRVFKDKGY----AFVRFDTHEAAATA 52
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 65.7 bits (161), Expect = 1e-13
Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAK 168
L++GN+ D TE ++ ELF +G+ + + + ++K F F+ + + +A+KA
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 169 LDGHVLKGRSLKI 181
L+G L GR LK+
Sbjct: 61 LNGKELDGRPLKV 73
Score = 46.4 bits (111), Expect = 6e-07
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
+ V NL T E L F FG +E ++ D E G SK VEF + A +AL
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59
>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 = 61.9 bits (151), Expect = 3e-12
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLD 170
L++GN+ D TE D+ ELF +GE + + I ++ K F F+ + +A+KA L+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 171 GHVLKGRSLKIR 182
G L GR LK+
Sbjct: 61 GKELDGRKLKVS 72
Score = 51.2 bits (123), Expect = 1e-08
Identities = 21/59 (35%), Positives = 27/59 (45%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
+ V NL T E L F FG+IE ++ D+ G SK VEF A +AL
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKLD 170
L++GN+ D TE D+ +LF +G + + I + K F F+ + + +A+KA L+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 171 GHVLKGRSLK 180
G L GR L+
Sbjct: 61 GKELGGRELR 70
Score = 56.4 bits (137), Expect = 2e-10
Identities = 22/59 (37%), Positives = 28/59 (47%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
+ V NL T E L+ F FG IE ++ DE G SK VEF + A +AL
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEAL 59
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 56.8 bits (138), Expect = 1e-10
Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 130 IIELFKPYGETQELFINKEK-MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
+ +LF P+G +++ + K+K F F+ + A+KA L+G + GR L++ ++
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 56.4 bits (137), Expect = 2e-10
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHNADKAKAKLDG 171
LY+ N+ +TE D+ E F PYG+ + + + + K F F+ +A+ A KL+G
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 172 HVLKGRSLK 180
VL GR+L+
Sbjct: 61 LVLDGRTLR 69
Score = 37.1 bits (87), Expect = 0.001
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
+ V+NL VT E L F +G +E + +V + + VEFA A AL++
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEG-VRLVRNKDRPRGFAFVEFASPEDAEAALKKL 58
>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 = 55.7 bits (135), Expect = 4e-10
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQ--ELFINKE----KMFGFIRMDYKHNADKAKAK 168
LY+GN+ ++TE D+ +LF +GE + ++E + FGF+ M+ A+ A K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 169 LDGHVLKGRSLKIRFA 184
L+G GR+L + A
Sbjct: 61 LNGTDFGGRTLTVNEA 76
Score = 31.0 bits (71), Expect = 0.20
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
+ V NL VT E L+ FG FG++ A VI D E G S+ G VE A A+
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 59.4 bits (144), Expect = 2e-09
Identities = 42/174 (24%), Positives = 71/174 (40%), Gaps = 36/174 (20%)
Query: 106 KDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKH 160
KF N LY+ N+ + E+ + ELF +GE + + + F F+ +
Sbjct: 174 PLKKFTN---LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHE 230
Query: 161 NADKAKAKLDGHVLKG-------------------RSLKIRFAPIN---------AAIKV 192
+A KA +++G + L+ +F + + V
Sbjct: 231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYV 290
Query: 193 KNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
KNL VT+E L F G+I A V++DE+G S+ G V F+ A +A+
Sbjct: 291 KNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344
Score = 51.0 bits (122), Expect = 1e-06
Identities = 40/144 (27%), Positives = 71/144 (49%), Gaps = 14/144 (9%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
LY+G++ D+TE + +LFKP+G + + ++ + +G++ +A++A +
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 170 DGHVLKGRSLKIRF---API-----NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIV 221
+ L G+ ++I + P I VKNL V N+ L F FG+I V
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122
Query: 222 DERGNSKCEGIVEFARKPAAAQAL 245
DE G S+ G V F ++ +A A+
Sbjct: 123 DENGKSRGYGFVHFEKEESAKAAI 146
Score = 48.6 bits (116), Expect = 5e-06
Identities = 30/109 (27%), Positives = 50/109 (45%), Gaps = 11/109 (10%)
Query: 147 KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI-----RFAPINAAIK------VKNL 195
K + +GF+ + + +A A K++G +L + + + + A +K VKNL
Sbjct: 127 KSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNL 186
Query: 196 TSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
V + L F FG+I A V+ D G S+ V F + AA+A
Sbjct: 187 DPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235
Score = 36.7 bits (85), Expect = 0.028
Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 7/86 (8%)
Query: 104 QNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDY 158
+ K N LY+ N+ +T+ + ELF GE + + FGF+
Sbjct: 278 ERKMKAQGVN--LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSN 335
Query: 159 KHNADKAKAKLDGHVLKGRSLKIRFA 184
A++A ++ G +L G+ L + A
Sbjct: 336 PEEANRAVTEMHGRMLGGKPLYVALA 361
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 51.1 bits (123), Expect = 2e-08
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM---------FGFIRMDYKHNADKA 165
RL++GN+ +TE +++LF YG+ ++ K + F+ + K A+KA
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 166 KAKLDGHVLKGRSLKIRFA 184
L+G G+ L +R+A
Sbjct: 61 LKSLNGKTALGKKLVVRWA 79
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 50.2 bits (120), Expect = 3e-08
Identities = 21/64 (32%), Positives = 34/64 (53%)
Query: 117 YLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG 176
Y+GNI T+ D+I LF+ +G E ++ F F+++D A A +L G + G
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPVHG 63
Query: 177 RSLK 180
R L+
Sbjct: 64 RPLR 67
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 49.9 bits (120), Expect = 3e-08
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
+L++GN+ T ++ LF+ YG E + K +GF+ M+ + +A+ A L+G+
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--YGFVHMEEEEDAEDAIKALNGYEF 58
Query: 175 KGRSLKI 181
G+ + +
Sbjct: 59 MGKRINV 65
>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 = 49.2 bits (118), Expect = 7e-08
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
RL++ N+ TE ++ ELF+ +GE E+ + + K F F+ + +A KA ++
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 169 LDGHVLKGRSLKI 181
LDG + +GR L +
Sbjct: 61 LDGSIFQGRLLHV 73
Score = 29.2 bits (66), Expect = 0.95
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQA 244
V+NL T E L F FG+I + +D+ SK V F P A
Sbjct: 4 VRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFM-FPEHAVK 56
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 49.2 bits (118), Expect = 9e-08
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKL 169
RL + N+ TE D+ +LF P+G E+ I K+K F F++ K +A+KA +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 170 DGHVLKGRSLKIRFA 184
+G +KGR + + +A
Sbjct: 61 NGKKIKGRPVAVDWA 75
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 48.2 bits (115), Expect = 2e-07
Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQ--ELFINKE--KMFGFIRMDYKHNADKAKAKLD 170
RL++ NI + D+ ++F +G E+ N+ K FGF+ +AD+A+ KL
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61
Query: 171 GHVLKGRSLKIRFA 184
G V++GR +++ A
Sbjct: 62 GTVVEGRKIEVNNA 75
>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 = 48.4 bits (116), Expect = 2e-07
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
L++ + TE ++ LF +G +E+ + K+ FGF+ + +AD A L
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 170 DGHVLKGRSLKI 181
+G L+GR +K+
Sbjct: 64 NGKELEGRVIKV 75
>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 = 48.0 bits (115), Expect = 2e-07
Identities = 25/72 (34%), Positives = 45/72 (62%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKL 169
LY+GN+ +ITE+D+ +F+P+GE + + + ++ K +GFI+ +A KA +L
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 170 DGHVLKGRSLKI 181
+G L GR +K+
Sbjct: 61 NGFELAGRPIKV 72
Score = 31.1 bits (71), Expect = 0.17
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQAL 245
V NL +T + L F FG+IE + D G SK G ++FA A +AL
Sbjct: 3 VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 52.3 bits (124), Expect = 2e-07
Identities = 26/94 (27%), Positives = 53/94 (56%), Gaps = 6/94 (6%)
Query: 101 SEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFI 154
P+++ N L++GN+ D+TE D+ ELFK +G + + + +++ F F+
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162
Query: 155 RMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA 188
+ + +A+KA +L+G L+GR L+++ A +
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRVQKAQPAS 196
>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 = 47.4 bits (113), Expect = 4e-07
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
RL++ N+ E+D+ +LF +GE E+ + K K F ++ +A KA +
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Query: 169 LDGHVLKGRSLKI 181
LDG V +GR + I
Sbjct: 64 LDGKVFQGRLIHI 76
Score = 35.4 bits (82), Expect = 0.006
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQAL 245
V+NL + LE F FG++ V +D++ G SK V F A +A
Sbjct: 7 VRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 46.1 bits (110), Expect = 9e-07
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYK--HNADKAKAKLDGHV 173
L++ NI ++ + ++ LF+ +G+ + L+ K GFI + Y A +AK L G
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTLY-TACKHRGFIMVSYYDIRAARRAKRALQGTE 62
Query: 174 LKGRSLKIRFA 184
L GR L I F+
Sbjct: 63 LGGRKLDIHFS 73
>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 = 46.2 bits (110), Expect = 9e-07
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL------FINKEKMFGFIRMDYKHNADKAKAK 168
RL++ N+ TE D+ +LF YG E+ K K F F+ +A KA A+
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Query: 169 LDGHVLKGRSLKI 181
LDG V +GR L +
Sbjct: 64 LDGTVFQGRLLHL 76
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 45.6 bits (108), Expect = 1e-06
Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
++++GN+ D ++ ++ LF+ YG + ++ F F+ + + AD+A +L+G L
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--FAFVHLRGEAAADRAIEELNGREL 59
Query: 175 KGRSL 179
GR L
Sbjct: 60 HGRKL 64
>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 = 45.6 bits (109), Expect = 1e-06
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAKAK 168
+L++G + TE D+ LF+ YG +E+ I ++K G F++ + A KA
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 169 LDGHV 173
L G V
Sbjct: 61 LHGKV 65
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 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 theThe CD
corresponds to the RRM. 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 an 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 mammalian, 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 the 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 = 79
Score = 45.7 bits (109), Expect = 2e-06
Identities = 22/55 (40%), Positives = 29/55 (52%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
VKNL + +E L F FG I A V+ DE+G SK G V F+ A +A+
Sbjct: 6 VKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60
Score = 30.7 bits (70), Expect = 0.25
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLD 170
LY+ N+ I + + E F P+G + + K FGF+ A KA +++
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63
Query: 171 GHVLKGRSLKIRFA 184
G ++ G+ L + A
Sbjct: 64 GRIIGGKPLYVALA 77
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 45.2 bits (108), Expect = 2e-06
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL-FINK-----EKMFGFIRMDYKHNA-DKAKA 167
RL++G + +TE+D+ E F +G ++ I K ++ F +I + K K+
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60
Query: 168 KLDGHVLKGRSLKIRFA 184
L+G KG LKI A
Sbjct: 61 TLNGTKWKGSVLKIEEA 77
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 43.8 bits (104), Expect = 5e-06
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHV 173
N+ T +D+ +F+ YGE +++I +++ F F+R K +A+ A +DG
Sbjct: 5 NLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKE 64
Query: 174 LKGRSLKI 181
L GR L++
Sbjct: 65 LDGRELRV 72
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 42.9 bits (101), Expect = 1e-05
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
+L++GN+ + TE +I LF+ YG+ E I K +GF+ MD K AD+A L + L
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--YGFVHMDDKTAADEAIRNLHHYKL 59
Query: 175 KGRSLKI 181
G ++ +
Sbjct: 60 HGVAINV 66
>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 = 43.0 bits (102), Expect = 1e-05
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-----FGFIRMDYKHNADKAKAK 168
RL + N+ D+TE D+ ELF GE +++ IN ++ + + + +A++A +
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
Query: 169 LDGHVLKGRSLKIRF 183
+G +L G+ +++
Sbjct: 61 FNGVLLDGQPMQVEL 75
Score = 36.4 bits (85), Expect = 0.002
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR--- 246
++V NL VT E LE FG G++++ + D G S+ V F ++ A +A++
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62
Query: 247 -RCAEG 251
+G
Sbjct: 63 GVLLDG 68
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including SCAF4,
SCAF8 and similar proteins. The biological role of SCAF4
remains unclear, but it shows high sequence similarity
to SCAF8 (also termed CDC5L complex-associated protein
7, or RNA-binding motif protein 16, or CTD-binding
SR-like protein RA8). SCAF8 is a nuclear matrix protein
that interacts specifically with a highly
serine-phosphorylated form of the carboxy-terminal
domain (CTD) of the largest subunit of RNA polymerase II
(pol II). The pol II CTD plays a role in coupling
transcription and pre-mRNA processing. In addition,
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 77
Score = 43.1 bits (102), Expect = 1e-05
Identities = 21/70 (30%), Positives = 41/70 (58%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
L++G++ +TE D+ LF+ YGE Q + + + ++ M+ + +A +A KL L
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVKLA 64
Query: 176 GRSLKIRFAP 185
G+ +K+ +AP
Sbjct: 65 GKKIKVAWAP 74
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 43.0 bits (102), Expect = 1e-05
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH- 172
LY+G +G +TE D+ + F +GE + + + + F+ + A+KA +L
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKL 61
Query: 173 VLKGRSLKIR 182
++ GR LK++
Sbjct: 62 IINGRRLKLK 71
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 42.7 bits (100), Expect = 1e-05
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
C +Y G I +TE + + F P+G+ E+ + EK + FIR +A A ++G
Sbjct: 1 CTVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTT 60
Query: 174 LKGRSLK 180
++G +K
Sbjct: 61 IEGHVVK 67
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 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 an
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. 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 mammalian, 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 the 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 = 42.9 bits (102), Expect = 1e-05
Identities = 22/53 (41%), Positives = 29/53 (54%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
VKNL + +E L+ FG +G I A V+ D+ G SK G V F AA +A
Sbjct: 6 VKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58
Score = 38.7 bits (91), Expect = 4e-04
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKLD 170
+Y+ N+G D+ + + ELF YG+ + K K FGF+ + A KA +L+
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63
Query: 171 GHVLKGRSL 179
G + G+ L
Sbjct: 64 GKEVNGKKL 72
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 42.4 bits (100), Expect = 2e-05
Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 200 TNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS 258
T E L F FGDIE ++ D+ G SK G V+F + AA AL C +S
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENC-------DKS 65
Query: 259 LRPVIVEP 266
+ V+ EP
Sbjct: 66 FKAVLAEP 73
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent 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 the 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. .
Length = 78
Score = 42.7 bits (101), Expect = 2e-05
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
+++ N+ D E+ + +LF P+G + + NK K +GF+ M A A A L
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 170 DGHVLKGRSLKIRF 183
+G+ L GR L++ F
Sbjct: 64 NGYRLGGRVLQVSF 77
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 42.0 bits (99), Expect = 2e-05
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 116 LYLGNIGGDITENDIIELFKPYG-ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
LY+GN+ D+ E+D+ +LF+ + + + K + F+ + ADKA KL+G +L
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGG-YAFVDCPDQSWADKAIEKLNGKIL 59
Query: 175 KGRSLKI 181
+G+ +++
Sbjct: 60 QGKVIEV 66
>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 = 42.2 bits (100), Expect = 2e-05
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 117 YLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKLD 170
++GNI D TE +IE+F G + K K +GF + A A L+
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 171 GHVLKGRSLKIRFA 184
G+ GR+L++ FA
Sbjct: 62 GYEFNGRALRVDFA 75
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 42.0 bits (99), Expect = 3e-05
Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL------FINKEKMFGFIRMDYKHNADKAKA 167
CR+Y+G+I ++ E+ I + F P+G + + K K F F+ + A A
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60
Query: 168 KLDGHVLKGRSLKI 181
+++G +L GR++K+
Sbjct: 61 QMNGVMLGGRNIKV 74
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 46.1 bits (109), Expect = 3e-05
Identities = 37/135 (27%), Positives = 68/135 (50%), Gaps = 13/135 (9%)
Query: 125 ITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGRS 178
+T+ +I LF GE + + ++K+ +GF+ +A+KA L+G L+ ++
Sbjct: 15 MTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKT 74
Query: 179 LKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEG 231
+K+ +A P + +IK V L +T LE F FG I + ++ D G SK G
Sbjct: 75 IKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVG 134
Query: 232 IVEFARKPAAAQALR 246
+ F ++ A +A++
Sbjct: 135 FIRFDKRDEADRAIK 149
Score = 44.2 bits (104), Expect = 1e-04
Identities = 28/102 (27%), Positives = 52/102 (50%), Gaps = 11/102 (10%)
Query: 91 IQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGE--TQELFINK- 147
+Q T+ + + P + IK AN LY+ + +T++++ +F P+G+ T + +
Sbjct: 70 LQNKTIKVSYARPSSDSIKGAN---LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV 126
Query: 148 ---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRS--LKIRFA 184
K GFIR D + AD+A L+G G + + ++FA
Sbjct: 127 TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFA 168
Score = 39.5 bits (92), Expect = 0.003
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQ------ELFINKEKMFGFIRMDYKHNADKAKAKL 169
+++ N+ D E + +LF P+G Q +L N+ K +GF+ M A A L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 170 DGHVLKGRSLKIRF 183
+G+ L R L++ F
Sbjct: 332 NGYTLGNRVLQVSF 345
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 41.4 bits (98), Expect = 4e-05
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQALR 246
I V L T++ L F FG+IE A+VI D + G S+ G V F K +A +A +
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Score = 40.3 bits (95), Expect = 1e-04
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKA-- 165
++++G + T++ + + F +GE +E + K + +GF+ K +A++A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 166 --KAKLDGHVLK 175
+DG
Sbjct: 61 DPNPIIDGRKAN 72
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 41.4 bits (97), Expect = 5e-05
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAK 166
L+ G + ++ E D+ F +GE Q +N +K F++M + +A+ A+
Sbjct: 6 LFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAR 56
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 80
Score = 41.2 bits (97), Expect = 5e-05
Identities = 16/72 (22%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQEL-FI---NKEKMFGFIRMDYKHNADKAKAKLDG 171
+++G + D+T+ ++ E F +G+ E+ I N F FI+ + + A +A +
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65
Query: 172 HVLKGRSLKIRF 183
+LK +++ +++
Sbjct: 66 SMLKNKTMHVQY 77
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p 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 containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 40.9 bits (96), Expect = 6e-05
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
RLY+ D +E+ I E+F PYG +E+ + F F+ + +A +AK + G VL
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISN--FAFVEFESLESAIRAKDSVHGKVL 58
Query: 175 KGRSL 179
L
Sbjct: 59 NNNPL 63
>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 = 40.7 bits (96), Expect = 8e-05
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
L++ N+ D T+ + E F G + F+ K+K FG++ + +A +A +
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 170 DGHVLKGRSLKIRFA 184
GR + + FA
Sbjct: 62 KKTKFGGRKIHVEFA 76
Score = 38.0 bits (89), Expect = 9e-04
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGI--VEFARKPAAAQAL 245
V+NL T+E LE F G I+R +V ++G+ KC G V FA + A +AL
Sbjct: 4 VRNLPYDTTDEQLEEFFSEVGPIKRC-FVVKDKGSKKCRGFGYVTFALEEDAKRAL 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 = 40.5 bits (95), Expect = 9e-05
Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQ-ELFINKE--KMFGFIRMDYKHNADKAKA-KLD 170
+Y+GN+ DITE+D+ E FK T L +KE + GF +D+ A KLD
Sbjct: 1 TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60
Query: 171 GHVLKGRSLKI 181
G VL GR ++I
Sbjct: 61 GTVLCGRPIRI 71
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 40.3 bits (95), Expect = 1e-04
Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKL-DG 171
++++G + D+TE D+ + F +GE +++I K + F F+ + + A++ +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFA---DPEVAQSLCGED 57
Query: 172 HVLKGRSLKIRFA 184
H++KG S+ + A
Sbjct: 58 HIIKGVSVHVSNA 70
>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 = 40.2 bits (95), Expect = 1e-04
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGH 172
N+ D E+D+ ELF+P+G +++ K+K F F+ + +A++A KL+G
Sbjct: 6 NLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64
Score = 33.3 bits (77), Expect = 0.031
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRR 247
I+V NL+ + L F FG I R + D E G S+ V F + A +A+ +
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
>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 = 40.3 bits (95), Expect = 1e-04
Identities = 17/56 (30%), Positives = 30/56 (53%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR 247
V NL V+++ ++ F FG +++A V D G S V F R+ A +A+++
Sbjct: 5 VSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60
Score = 29.5 bits (67), Expect = 0.78
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFIN-----KEKMFGFIRMDYKHNADKAKAKL 169
+L + N+ ++++DI ELF +G ++ ++ + + + + +A KA +
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQY 61
Query: 170 DGHVLKGRSLKIRF 183
+G L GR +KI+
Sbjct: 62 NGVPLDGRPMKIQL 75
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 40.4 bits (94), Expect = 1e-04
Identities = 17/67 (25%), Positives = 36/67 (53%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
C +Y G + +TE + + F P+G+ E+ + +K + F+R + +A A ++G
Sbjct: 1 CTVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTT 60
Query: 174 LKGRSLK 180
++G +K
Sbjct: 61 IEGHVVK 67
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 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. RBM11 contains 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 of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 40.3 bits (94), Expect = 1e-04
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLD 170
L++GN+ + E + ELF G ++ I K+ K FGF+ + + A A L+
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63
Query: 171 GHVLKGRSLKIR 182
G L GR +K+
Sbjct: 64 GIRLYGRPIKVH 75
Score = 27.2 bits (60), Expect = 5.4
Identities = 15/54 (27%), Positives = 22/54 (40%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
V NL V E+L F G + + + D+ G K G V F + A+
Sbjct: 6 VGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAI 59
>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 = 40.4 bits (95), Expect = 1e-04
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYK------------HNA 162
R+Y+ N+ +E D+ E K + + I + + GF + A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 163 DKAKAKLDGHVLKGRSLKIR 182
+K L+G V K R L ++
Sbjct: 60 EKVVKDLNGKVFKNRKLFVK 79
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 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 = 93
Score = 40.3 bits (95), Expect = 2e-04
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 12/82 (14%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH-- 172
+Y G + +T+ D+ E FK Y QE++I + + + + A LD
Sbjct: 4 TVYCGKLPKKVTDEDLREFFKDYN-PQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEET 62
Query: 173 ------VLKGRSL---KIRFAP 185
LK + L KI P
Sbjct: 63 LDEIIESLKSKKLNGKKISLKP 84
>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 = 39.5 bits (93), Expect = 2e-04
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYG--ETQELFINKE----KMFGFIRMDYKHNADKAKAK 168
+L++G + D+TE D+ E F YG E+ E+ +KE + F F+ D DK +
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 169 LDGHVLKGRSLKIR 182
H + G ++++
Sbjct: 61 KY-HTINGHRVEVK 73
>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 = 39.8 bits (94), Expect = 2e-04
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 16/81 (19%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL-----------FINKEKMFGFIRMDYKHNAD 163
RLY+GN+ ITE ++++ F L IN EK F F+ +
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEF---RTVE 59
Query: 164 KAKA--KLDGHVLKGRSLKIR 182
+A A LDG + KG+ LKIR
Sbjct: 60 EATAALALDGIIFKGQPLKIR 80
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
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).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 39.3 bits (92), Expect = 2e-04
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDG 171
R+Y+GN+ GDI E DI +LF YG + + + + F F+ + +A+ A DG
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 172 HVLKGRSLKIRF 183
+ G L++ F
Sbjct: 61 YDFDGYRLRVEF 72
>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 = 43.3 bits (102), Expect = 2e-04
Identities = 22/73 (30%), Positives = 46/73 (63%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAK 168
+LY+GN+ +ITE ++ ++F+P+G+ +++ ++++ K FGFI+ A +A
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247
Query: 169 LDGHVLKGRSLKI 181
++G L GR +K+
Sbjct: 248 MNGFELAGRPIKV 260
Score = 28.7 bits (64), Expect = 8.3
Identities = 37/146 (25%), Positives = 56/146 (38%), Gaps = 26/146 (17%)
Query: 125 ITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRS 178
E D+ E F G+ +++ + K ++ Y + L G +L GR
Sbjct: 101 ARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEF-YDVESVIKALALTGQMLLGRP 159
Query: 179 LKIRF--APINAAIK----------------VKNLTSCVTNELLELAFGVFGDIERAIVI 220
+ ++ A N A K V NL +T + L F FGDIE +
Sbjct: 160 IIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLH 219
Query: 221 VD-ERGNSKCEGIVEFARKPAAAQAL 245
D E G SK G ++F A +AL
Sbjct: 220 RDPETGRSKGFGFIQFHDAEEAKEAL 245
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM3 in
hnRNP R, hnRNP Q, and APOBEC-1 complementation factor
(ACF). hnRNP R is a ubiquitously expressed nuclear
RNA-binding protein that specifically bind mRNAs with a
preference for poly(U) stretches and has been implicated
in mRNA processing and mRNA transport, and also acts as
a regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as a
component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA transport.
ACF is an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members contain three conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 72
Score = 39.1 bits (92), Expect = 2e-04
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
LY+ N+ TE + ELF YGE + + K K + F+ + + +A KA +++G L+
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVER--VKKIKDYAFVHFEERDDAVKAMEEMNGKELE 61
Query: 176 GRSLKIRFA 184
G +++ A
Sbjct: 62 GSPIEVSLA 70
Score = 35.7 bits (83), Expect = 0.004
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR 247
V+NL T E L F +G++ER I D V F + A +A+
Sbjct: 6 VRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEE 54
>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 = 38.8 bits (91), Expect = 3e-04
Identities = 16/71 (22%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-NKEKMFGFIRMDYKHNADKAKAKLDGHV 173
++Y+GN+G T+ ++ + F+ YG + +++ F F+ + +A+ A LDG
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60
Query: 174 LKGRSLKIRFA 184
+ G +++ +
Sbjct: 61 ICGNRVRVELS 71
>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 = 38.5 bits (90), Expect = 4e-04
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
R+Y+G + E D+ FK YG +E IN + FGF+ + +AD A +L+G L
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIRE--INLKNGFGFVEFEDPRDADDAVYELNGKEL 58
Query: 175 KGRSLKIRFA 184
G + + A
Sbjct: 59 CGERVIVEHA 68
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 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 = 77
Score = 38.8 bits (91), Expect = 4e-04
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
L +GN+ + T+ EL P+G + F+ + K +GF+ K +A KAK +L
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 170 DGHVLKGRSLKIRFAP 185
DG + GR L++ +A
Sbjct: 62 DGKQIGGRKLQVDWAD 77
Score = 33.8 bits (78), Expect = 0.021
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 198 CVTN--------ELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQA 244
CV N + EL FG +ER ++ E G SK G VE+A K +A +A
Sbjct: 3 CVGNLPLEFTDEQFREL-VSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which 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 the 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. Moreover, HuR has an anti-apoptotic
function during early cell stress response. It binds to
mRNAs and enhances the expression of several
anti-apoptotic proteins, such as p21waf1, p53, and
prothymosin alpha. HuR also has pro-apoptotic function
by promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. 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. .
Length = 79
Score = 38.8 bits (91), Expect = 4e-04
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE---TQELFINK---EKMFGFIRMDYKHNADKAKAKL 169
LY+ + +T+ ++ LF PYG ++ L N + GFIR D + A++A L
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 170 DGHVLKGRSLKI--RFA 184
+G + G + I +FA
Sbjct: 63 NGTIPPGATEPITVKFA 79
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 38.4 bits (90), Expect = 5e-04
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 122 GGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI 181
G +TE + + F P+G + + KEK GF+ + +AD+A A+L+G ++G LK+
Sbjct: 11 GYGLTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKV 70
Query: 182 RFA 184
A
Sbjct: 71 SLA 73
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 38.5 bits (90), Expect = 5e-04
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM-----FGFIRMDYKHNADKAKAKLD 170
LY+ N+ + E D+ + KPYG+ I ++ GF RM+ + + +K +
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62
Query: 171 GHVLKGRS--LKIRFA 184
G LKG L ++FA
Sbjct: 63 GKYLKGEGEPLLVKFA 78
>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 = 38.5 bits (90), Expect = 5e-04
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKH--NADKA 165
+ L++GN+ +TE + ELF G + + I K+ K F F+ +KH + A
Sbjct: 1 DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFV--TFKHEVSVPYA 58
Query: 166 KAKLDGHVLKGRSLKIR 182
L+G L GR L+I+
Sbjct: 59 IQLLNGIRLFGRELRIK 75
Score = 27.7 bits (62), Expect = 3.2
Identities = 16/54 (29%), Positives = 23/54 (42%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
V NL + VT E+L F G +E + D G K V F + + A+
Sbjct: 6 VGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAI 59
>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 = 38.5 bits (90), Expect = 5e-04
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 6/52 (11%)
Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMD 157
++ +L++GN+ DITE+++ E FK +G E+ IN + FGF+ D
Sbjct: 2 DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFD 53
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 38.7 bits (90), Expect = 5e-04
Identities = 21/78 (26%), Positives = 44/78 (56%), Gaps = 8/78 (10%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-----FGFIRMDYKHNADKAKAKL 169
+L++G + TE ++ E+F PYG +++++ +++M F++ K A A L
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60
Query: 170 DG-HVLKG--RSLKIRFA 184
+G + ++G + L +RFA
Sbjct: 61 NGVYTMRGCDQPLIVRFA 78
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 38.0 bits (89), Expect = 6e-04
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 114 CRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
R+++GN+ D +++ D+ E+F YG+ + ++K +GF++ D + +A A A +G
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKG--YGFVQFDNEEDARAAVAGENGR 58
Query: 173 VLKGRSLKI 181
+ G+ L I
Sbjct: 59 EIAGQKLDI 67
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 38.4 bits (90), Expect = 7e-04
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 200 TNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQA 244
T+E LE+ F FG I+ VI D++ G+S +EF K +A
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 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 mammalian, such as ovary
and testis. It may play an important role in germ cell
development. 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 the 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 = 77
Score = 37.9 bits (89), Expect = 8e-04
Identities = 22/55 (40%), Positives = 28/55 (50%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
I +KNL + N+ L F FG+I V DE G SK G V F + AA +A
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRA 59
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 37.7 bits (88), Expect = 8e-04
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
+++G++ +I + F P+GE + + K K +GF+ K +A+ A +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 170 DGHVLKGRSLKI 181
+G L GR+++
Sbjct: 62 NGQWLGGRAIRT 73
Score = 34.7 bits (80), Expect = 0.011
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
I V +L+ + E L AF FG+I A V+ D + G SK G V F +K A A++
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ 59
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 41.4 bits (98), Expect = 9e-04
Identities = 30/102 (29%), Positives = 53/102 (51%), Gaps = 18/102 (17%)
Query: 313 KQLHELYEHETEMLRKEL---AQREIDRERQKAEWEMKER------------QAEE-LKR 356
K++ E + E E L+KE A+ E+ + R + E E+KER Q EE L R
Sbjct: 35 KRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERRLLQREETLDR 94
Query: 357 RDEELMKK--HAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
+ E L KK + E+ + L+ +E++L ++ + + EQ++
Sbjct: 95 KMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQRE 136
>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 = 37.6 bits (88), Expect = 0.001
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAK 168
+L + N+ + T+ ++ ELF P+G+ + + F + F F+ K A A
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
Query: 169 LDGHVLKGRSLKIRFA 184
L L GR L + +A
Sbjct: 61 LKSTHLYGRHLVLEYA 76
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 37.7 bits (88), Expect = 0.001
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
V NL VT +LL F G I+ +I + + VE+ +AA AL
Sbjct: 3 VGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYA--FVEYYDHRSAAAAL 54
Score = 35.0 bits (81), Expect = 0.008
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 116 LYLGNIGGDITENDIIELFK---PYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
LY+GN+ +TE+ + ELF P + + + + F+ +A A ++G
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 173 VLKGRSLKIRFA 184
++ G+ +K+ +A
Sbjct: 61 LILGQEIKVNWA 72
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 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. It 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 = 74
Score = 37.4 bits (87), Expect = 0.001
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
I V NL V + L+ F + G + RA + D+ G S+ G+V+F A QA+
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 37.8 bits (87), Expect = 0.001
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAKAKL 169
+++G++ +IT +DI F P+G +++ K K +GF+ K +A+ A ++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 170 DGHVLKGRSLKIRFA 184
G L GR ++ +A
Sbjct: 64 GGQWLGGRQIRTNWA 78
Score = 27.0 bits (59), Expect = 6.2
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRR 247
V +L+ +T + ++ AF FG I A V+ D G SK G V F K A A+++
Sbjct: 6 VGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 37.5 bits (88), Expect = 0.001
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGET-----QELFINKEKMFGFIRMDYKHNADKAKAK 168
L++ N ++DI +LF+ YGE L NK + F +++ +A A A
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60
Query: 169 LDGHVLKGRSL 179
L+G + +G L
Sbjct: 61 LNGKLGEGYKL 71
>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 = 37.2 bits (87), Expect = 0.001
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI---NKEKM------FGFIRMDYKHNADKAK 166
+Y+ N+ + E+D+ +F +GE + + I EK F F+ +A+ A
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA- 61
Query: 167 AKLDGHVLKGRSLKI 181
+L+G L GR + +
Sbjct: 62 LQLNGTELGGRKISV 76
Score = 30.7 bits (70), Expect = 0.31
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVI---VDERGNSKCEG--IVEFARKPAAAQA 244
I V+NL + + L F FG++E +I I DE+ G V F +A A
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVE-SIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 245 L 245
L
Sbjct: 62 L 62
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM1 of the majority of family members that include
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), heterogeneous
nuclear ribonucleoprotein L (hnRNP-L), heterogeneous
nuclear ribonucleoprotein L-like (hnRNP-LL),
polypyrimidine tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB 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. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA than
PTB does but is a weaker repressor of splicing in vitro.
PTBP2 also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 37.2 bits (87), Expect = 0.001
Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 10/74 (13%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH--- 172
L+L N+ D+TE+D+I L P+G+ + + + K + MD + + AK+ + +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMD---SVESAKS-MVDYYLT 57
Query: 173 ---VLKGRSLKIRF 183
+++GR + I++
Sbjct: 58 VPALIRGRRVYIQY 71
>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 = 37.6 bits (87), Expect = 0.001
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAKAKL 169
LY+ N+ +TE+++ ++F+ YG + + ++K G F+R D + A A + L
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 170 DGHVLKGRS--LKIRFA 184
+G + G + L +R+A
Sbjct: 63 NGTIPPGSTMPLSVRYA 79
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
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. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR 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 AU-rich RNA element (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. .
Length = 84
Score = 37.7 bits (87), Expect = 0.001
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
+++ N+G D E + ++F P+G + + NK K FGF+ M A A A L
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 170 DGHVLKGRSLKIRF 183
+G+ L + L++ F
Sbjct: 64 NGYRLGDKILQVSF 77
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD 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. .
Length = 86
Score = 37.8 bits (87), Expect = 0.001
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
+++ N+ D E+ + +LF P+G + + NK K FGF+ M A A A L
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 170 DGHVLKGRSLKIRF 183
+G+ L R L++ F
Sbjct: 66 NGYRLGDRVLQVSF 79
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 37.4 bits (86), Expect = 0.001
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAKAKL 169
+++G++ +IT DI F P+G+ +++ K K +GF+ K +A+ A +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 170 DGHVLKGRSLKIRFA 184
G L GR ++ +A
Sbjct: 64 GGQWLGGRQIRTNWA 78
Score = 27.4 bits (60), Expect = 4.3
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQAL 245
V +L+ +T E ++ AF FG I A V+ D G SK G V F K A A+
Sbjct: 6 VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 37.1 bits (86), Expect = 0.001
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEK--MFGFIRMDYKHNADKAKAKLDGH 172
R+Y+GN+ DI DI +LF YG +++ + + F F+ + +A+ A DG+
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60
Query: 173 VLKGRSLKIRF 183
G L++ F
Sbjct: 61 DYDGYRLRVEF 71
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB 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 AU-rich RNA element (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. .
Length = 86
Score = 37.4 bits (86), Expect = 0.001
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
+++ N+ D E+ + ++F P+G + + NK K FGF+ M A A A L
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 170 DGHVLKGRSLKIRF 183
+G+ L R L++ F
Sbjct: 66 NGYRLGDRVLQVSF 79
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 37.4 bits (86), Expect = 0.001
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHNADKAKAKLDG 171
LY+GN+ D+TE I++LF G + + E + F+ +A A A ++G
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 61
Query: 172 HVLKGRSLKIRFAPINAAIK 191
+ G+ +K+ +A ++ K
Sbjct: 62 RKILGKEVKVNWATTPSSQK 81
>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 = 37.2 bits (87), Expect = 0.002
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI---------NKEKMFGFIRMDYKHNADKAK 166
LY+GN+ +TE + + F +G + I + + GF+ + +A++A
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 167 AKLDGHVLKGRSLKIRFA 184
+LDG + G LK+ +
Sbjct: 64 DELDGKDVMGYELKLGWG 81
Score = 26.5 bits (59), Expect = 9.3
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIV-----DERGNSKCEGIVEFARKPAAAQALR 246
V NL VT E+L FG FG + ++ I+ +ER ++ G V F + A +AL
Sbjct: 6 VGNLNPKVTEEVLCQEFGRFGPLA-SVKIMWPRTEEERRRNRNCGFVAFMNRADAERALD 64
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 40.1 bits (94), Expect = 0.002
Identities = 22/40 (55%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG GGGRGGG GG GG G GRG R G GGG
Sbjct: 4 GGFGGGRGGGRGGGGG-GGRGGGGRGGGRGGGRGRGRGGG 42
Score = 38.9 bits (91), Expect = 0.004
Identities = 20/40 (50%), Positives = 20/40 (50%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG GG GGG G GG G R GRG G GGGG
Sbjct: 11 GGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50
Score = 38.9 bits (91), Expect = 0.004
Identities = 16/40 (40%), Positives = 16/40 (40%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
G GG GG GGRGG G G G G G G
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRG 40
Score = 37.8 bits (88), Expect = 0.008
Identities = 26/48 (54%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 41 GGRGGGRGG------GVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDR 82
GGRGGGRGG G GGRGG RG GRG GGGGGG
Sbjct: 8 GGRGGGRGGGGGGGRGGGGRGGGRG-GGRGRGRGGGGGGRGGGGGGGP 54
Score = 37.8 bits (88), Expect = 0.010
Identities = 21/46 (45%), Positives = 21/46 (45%)
Query: 37 FMSLGGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDR 82
M G GG GG GG GG RG G G R GGGGG R
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGR 46
Score = 37.0 bits (86), Expect = 0.016
Identities = 20/47 (42%), Positives = 20/47 (42%)
Query: 448 GGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGP 494
GGR GG GG G G GR G RGG GGGGP
Sbjct: 8 GGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGP 54
Score = 34.3 bits (79), Expect = 0.11
Identities = 16/24 (66%), Positives = 16/24 (66%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDG 64
GGRG GRGGG GGRGG G P
Sbjct: 33 GGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 33.9 bits (78), Expect = 0.18
Identities = 19/50 (38%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 445 FDQGGRSGGGGGRRNDSASSGWSRREGGAGRWGP-SVDHGSRRGGSGGGG 493
GG GG GG R G G GR G G GG GGGG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50
Score = 31.6 bits (72), Expect = 0.80
Identities = 16/47 (34%), Positives = 16/47 (34%), Gaps = 11/47 (23%)
Query: 448 GGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGP 494
G G GGGR G G G G R GG GGG
Sbjct: 1 GMGGGFGGGRGG-----------GRGGGGGGGRGGGGRGGGRGGGRG 36
Score = 31.2 bits (71), Expect = 1.2
Identities = 16/46 (34%), Positives = 16/46 (34%), Gaps = 4/46 (8%)
Query: 449 GRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGP 494
G GG GG R G GG GR G G G GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGG----RGGGRGRGRGGG 42
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 37.0 bits (86), Expect = 0.002
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
+Y+GNI +TE + F YGE + + +EK F+ NA KA + H L
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGVKSHPLF 65
Query: 176 GRSLKIRFAP 185
+ KI +
Sbjct: 66 -KKFKISYGK 74
>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 = 36.5 bits (85), Expect = 0.002
Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 6/64 (9%)
Query: 124 DITENDIIELFKPYGE--TQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGR 177
+ T+ D+ +LF P+G + ++F++K K FGF+ D +A A ++G + G+
Sbjct: 9 EFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK 68
Query: 178 SLKI 181
LK+
Sbjct: 69 RLKV 72
Score = 28.8 bits (65), Expect = 1.2
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 202 ELLELAFGVFGDIERAIVIVDERGN-SKCEGIVEFARKPAAAQA 244
+L +L F FG++ A V VD+ SKC G V + +A A
Sbjct: 14 DLYQL-FAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA 56
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 36.8 bits (86), Expect = 0.002
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 10/82 (12%)
Query: 113 NCRLYLGNIGGDITENDIIELF----KPYGETQELFI----NKEKMFG--FIRMDYKHNA 162
+ RLY+ N+ +TE D++ +F E + +F + +M G F+ + A
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60
Query: 163 DKAKAKLDGHVLKGRSLKIRFA 184
KA ++G+VLKG+ + I+F
Sbjct: 61 TKALNLVNGYVLKGKPMVIQFG 82
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 36.4 bits (85), Expect = 0.002
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL- 174
L++G +G + ++ F +G + + + + + +I + A AK L G L
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60
Query: 175 -KGRSLKIRFA 184
GR L++ FA
Sbjct: 61 GPGRRLRVDFA 71
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, 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 A0
contains 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 = 80
Score = 36.4 bits (84), Expect = 0.003
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
+L++G + GD+ E D+ E F +G ++ + K++ FGF+ +ADKA A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA-AV 59
Query: 169 LDGHVLKGRSLKIRFA 184
+ H + G ++++ A
Sbjct: 60 VKFHPINGHRVEVKKA 75
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 36.3 bits (84), Expect = 0.003
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM--FGFIRMDYKHNADKAKAKLDGH 172
+Y G +D+ LF+ G +++ + + FI + A A L+G
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60
Query: 173 VLKGRSLKI 181
+ G +K+
Sbjct: 61 SVDGNCIKV 69
>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 = 36.4 bits (85), Expect = 0.003
Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 120 NIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKLDGHV 173
+ TE D+ E+F YG +++ + + + FGF+ + +A +AK +L+G
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65
Query: 174 LKGRSLKIRFA 184
+ GR +++ ++
Sbjct: 66 IDGRRIRVDYS 76
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 36.1 bits (84), Expect = 0.003
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKA 167
+Y+ N+ +T ND+ ++F YG+ ++ I K+K FI + +A K
Sbjct: 2 STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61
Query: 168 KLDGHVLKGRSLKIRFA 184
L+ L GR+LK A
Sbjct: 62 ALNNKELFGRTLKCSIA 78
Score = 28.1 bits (63), Expect = 2.6
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGI--VEFARKPAAAQALR 246
+ V NL +TN L F +G + + + IV ++ K +G+ + F + A + ++
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVK-VTIVKDKETRKSKGVAFILFLDREDAHKCVK 61
>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM1 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows 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. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 75
Score = 36.1 bits (83), Expect = 0.003
Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 8/74 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV-- 173
L++ N+G +I+END+++L +P+G +L + + K ++M + A + L +
Sbjct: 3 LHVRNVGHEISENDLLQLVQPFGVVTKLVMLRAKNQALLQM---QDVSSAISALQYYTTV 59
Query: 174 ---LKGRSLKIRFA 184
++GR++ I+F+
Sbjct: 60 QPSVRGRNVYIQFS 73
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 38.2 bits (89), Expect = 0.004
Identities = 25/42 (59%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 40 LGGRGGGRGGGVGG-RGGYRGNRPDGRGSDMNESRMGGGGGG 80
LGGRGG GGG GG GGY G G G ESR GGGGG
Sbjct: 108 LGGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGR 149
Score = 35.2 bits (81), Expect = 0.044
Identities = 19/47 (40%), Positives = 20/47 (42%)
Query: 447 QGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGG 493
+GG GGGGG G GG G S G R G GGGG
Sbjct: 111 RGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGG 157
Score = 30.9 bits (70), Expect = 0.88
Identities = 19/40 (47%), Positives = 19/40 (47%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG GG GGG GG GG G G S GGGG G
Sbjct: 120 GGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAG 159
Score = 29.4 bits (66), Expect = 2.9
Identities = 18/40 (45%), Positives = 18/40 (45%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG GG GG GG GG G S R GGGGG
Sbjct: 117 GGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGG 156
Score = 29.4 bits (66), Expect = 3.3
Identities = 19/40 (47%), Positives = 19/40 (47%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
G GG GGG GG GGY G G G GGG GG
Sbjct: 121 GDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGG 160
Score = 27.8 bits (62), Expect = 8.8
Identities = 22/54 (40%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 446 DQGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGPTDYQP 499
D+GG GGGGG G SR GG GR G GG+GGG P
Sbjct: 122 DEGGYGGGGGGGG--GGYGGESRSGGGGGRAS-----GGGGGGAGGGASRPSAP 168
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC 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 AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. 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. .
Length = 85
Score = 36.2 bits (83), Expect = 0.004
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGET------QELFINKEKMFGFIRMDYKHNADKAKAKL 169
+++ N+ + E+ + +LF P+G ++ NK K FGF+ M A A A L
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 170 DGHVLKGRSLKIRF 183
+G+ L R L++ F
Sbjct: 64 NGYRLGDRVLQVSF 77
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows 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. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 35.9 bits (83), Expect = 0.004
Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 113 NCR-----LYLGNIGGDITENDIIELFKPYGETQ--ELFINKEKMFGFIRMDYKHNADKA 165
C +++ N+ D+TE D+I +G ++F + K + + A +A
Sbjct: 2 YCCPPTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEA 61
Query: 166 KAKLDGHVLKGRSLKIRF 183
A L G ++++ F
Sbjct: 62 LACKHASSLNGSTIRLAF 79
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 35.7 bits (82), Expect = 0.004
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGE--TQELFINKE----KMFGFIRMDYKHNADKAKA 167
C L++ ++ + T+ D+ + F P+G + ++FI+K+ K FGF+ D +A A
Sbjct: 5 CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64
Query: 168 KLDGHVLKGRSLKIR 182
++G + + LK++
Sbjct: 65 AMNGFQIGTKRLKVQ 79
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 39.3 bits (91), Expect = 0.005
Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKA 167
CR+Y+G+I ++ E+ I F P+G + + ++ K K F F+ + A A
Sbjct: 108 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALE 167
Query: 168 KLDGHVLKGRSLKI 181
+++G +L GR++K+
Sbjct: 168 QMNGQMLGGRNIKV 181
Score = 32.3 bits (73), Expect = 0.61
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAKAK 168
R+Y+ ++ D++E DI +F+ +GE + K +GFI + + +A A
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265
Query: 169 LDGHVLKGRSLKI 181
++ L G+ L++
Sbjct: 266 MNLFDLGGQYLRV 278
>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 = 35.6 bits (82), Expect = 0.005
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKE-KMFGFIRMDYKHNADKAKAKL 169
L++ N+ +T+ D+ + F + + E + +GF+ +A +A AKL
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 170 DGHVLKGRSLKIRFA 184
L GR L++ A
Sbjct: 62 KNKKLHGRILRLDIA 76
Score = 31.3 bits (71), Expect = 0.18
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRR 247
V+NL VT E L F I+ A+V+ D E G S+ G V FA A +AL +
Sbjct: 4 VRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 35.7 bits (83), Expect = 0.005
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAKAK 168
R+Y+ ++ D++E+DI +F+ +G+ + K K +GFI + +A A A
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61
Query: 169 LDGHVLKGRSLKI 181
++ L G+ L++
Sbjct: 62 MNLFDLGGQQLRV 74
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 35.4 bits (82), Expect = 0.006
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 199 VTNELLELAFGVFGDIERAIVIVDERGN-SKCEGIVEFARKPAAAQAL 245
VT + L AF FG+I+ V+ D++ SK V+FA+ +AA+A+
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61
Score = 35.0 bits (81), Expect = 0.008
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAK 166
N RL++ G +TE+D+ E F P+GE Q++++ K+K +++ +A +A
Sbjct: 3 NSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61
Query: 167 AKLDGHVLKGRSLKIR 182
+++G L G + ++
Sbjct: 62 EEMNGKCLGGDTKPLK 77
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 38.7 bits (91), Expect = 0.006
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 322 ETEMLRKELAQREID---RERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEE 378
E + LR +L Q E + R+++K E E + RQ +EL+R EE +++ E +Q +EE
Sbjct: 200 ELDELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQ-EERAEEE 258
Query: 379 DLRRRQNDNSMFLVEQQQ 396
R R + E +Q
Sbjct: 259 AERERMLEKQAEDEELEQ 276
Score = 35.3 bits (82), Expect = 0.069
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMK--KHAEE 368
+++ E E E E K Q+++ E + E ER+ EE +R EE +K ++ E
Sbjct: 104 IIERIQE--EDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQRE 161
Query: 369 MQLRLAQQEEDLRRRQ 384
R ++E + R R+
Sbjct: 162 KAEREEEREAERRERK 177
Score = 34.1 bits (79), Expect = 0.14
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+ E E + E L++E A+ E +RER + E +E + +H E++ +
Sbjct: 237 RAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQ 296
Query: 373 LAQQEEDLRRRQNDNSMFLVEQQQ 396
+ ++EE RR ++
Sbjct: 297 IEEKEE--RRAAEREEELEEGERL 318
Score = 33.7 bits (78), Expect = 0.22
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKR---RDEELMKKHAEEMQLRLAQQEEDL 380
E ++ ++E+ R R++ E +ER EE E +++K AE+ +L +QE
Sbjct: 224 EAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEEL---EQENAE 280
Query: 381 RRRQ 384
+RR
Sbjct: 281 KRRM 284
Score = 33.0 bits (76), Expect = 0.30
Identities = 10/58 (17%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
+L++++ +RE R+ + E + ++ E++ E + ++ E Q + +Q++
Sbjct: 74 AVLQEQIEEREKRRQEEY---EERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLRE 128
Score = 31.4 bits (72), Expect = 1.1
Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 320 EHETEMLRKELA-----QREIDRERQK---AEWEMKERQAEELKRRDEELMKKHAEEMQL 371
E E LR + + E+D R E+E KERQ E+ EE K+ ++ +L
Sbjct: 181 EREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEK-----EEAEKRRRQKQEL 235
Query: 372 ---RLAQQEEDLRRRQ 384
R Q EE R Q
Sbjct: 236 QRAREEQIEEKEERLQ 251
Score = 31.0 bits (71), Expect = 1.5
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 328 KELAQREIDRERQKAEW-EMKERQAEELKRRDEELMKKHAE--EMQLRLAQQEEDLRRRQ 384
+E A+RE +RE ++ E E KER+ L+ + EE + E E++ L Q+E + + RQ
Sbjct: 160 REKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQ 219
Score = 30.3 bits (69), Expect = 2.6
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR--LAQQ-EE 378
E + ++ E E + ER+ E +ER + L +E K+ E + R L +Q EE
Sbjct: 28 EKKRIKAE----EKEEERRIDEMMEEERL-KALAEEEERERKRKEERREGRAVLQEQIEE 82
Query: 379 DLRRRQNDNSMFLVEQQQ 396
+RRQ + L E++Q
Sbjct: 83 REKRRQEEYEERLQEREQ 100
Score = 30.3 bits (69), Expect = 2.7
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR---L 373
+LY+ E E ++ + E ++ R++ + E++ + E+++ ++E L ++ AEE R L
Sbjct: 207 DLYQEEYERKERQKEKEEAEK-RRRQKQELQRAREEQIEEKEERLQEERAEEEAERERML 265
Query: 374 AQQEEDLRRRQ 384
+Q ED Q
Sbjct: 266 EKQAEDEELEQ 276
Score = 29.5 bits (67), Expect = 4.6
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 9/81 (11%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQA--------EELKRRDEELMKK 364
K+ + E R + E +RER++ E + R E+ ++ + E +
Sbjct: 37 KEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQ 96
Query: 365 HAEEMQLRLAQ-QEEDLRRRQ 384
E+M + + QEED Q
Sbjct: 97 EREQMDEIIERIQEEDEAEAQ 117
Score = 29.1 bits (66), Expect = 5.1
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRD-EELMKKHAEEMQL 371
K+ + E E E R+ E +R + AE E +ER+ +E +R L ++ E +
Sbjct: 29 KKRIKAEEKEEE--RRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKR 86
Query: 372 RLAQQEEDLRRRQ 384
R + EE L+ R+
Sbjct: 87 RQEEYEERLQERE 99
Score = 28.3 bits (64), Expect = 8.9
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 9/72 (12%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
E+ R Q E ER + + E + E +++K AE+ +L E+ RR
Sbjct: 234 ELQRAREEQIEEKEER-------LQEERAEEEAERERMLEKQAEDEELEQENAEK--RRM 284
Query: 384 QNDNSMFLVEQQ 395
+ +EQQ
Sbjct: 285 KRLEHRRELEQQ 296
Score = 28.3 bits (64), Expect = 9.0
Identities = 12/61 (19%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEE---LMKKHAEEMQLRLAQQEEDLRRR 383
+E +RE E+++ ++ +Q E R+E + EE + + Q+E++ +
Sbjct: 168 EREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEK 227
Query: 384 Q 384
+
Sbjct: 228 R 228
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 35.2 bits (81), Expect = 0.006
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
++++GN+ T +++ LF+ +G E +K K + F+ M+ + A A L+G +
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVE--CDKVKDYAFVHMEREEEALAAIEALNGKEV 59
Query: 175 KGRSLKI 181
KGR + +
Sbjct: 60 KGRRINV 66
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at their
amino terminus. This family represents the rest of these
proteins.
Length = 244
Score = 38.2 bits (89), Expect = 0.006
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEEL--KRRDEELMKKHAEEMQLRLA 374
E E E + L + + Q E D R + E E E A EL K + EE + E+ L
Sbjct: 1 EEAEREQQELEERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELE 60
Query: 375 QQEEDLRRRQND 386
++ L
Sbjct: 61 EENRRLEEEAAA 72
Score = 33.2 bits (76), Expect = 0.24
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDE-ELMKKHAEEMQLRLAQQE 377
E E E R E + ER++ E E+ E AE K +E E + ++Q L + +
Sbjct: 57 DELEEENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQELREAQ 116
Query: 378 EDLRR 382
E R
Sbjct: 117 EAHER 121
Score = 30.1 bits (68), Expect = 2.4
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 2/69 (2%)
Query: 317 ELYEHETEMLRKEL--AQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLA 374
E E + +KEL + +K + E +E Q E K + E + EE
Sbjct: 15 EQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASE 74
Query: 375 QQEEDLRRR 383
++ E L
Sbjct: 75 EERERLEAE 83
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 35.4 bits (81), Expect = 0.006
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIER-------AIVIVDERG 225
V+NL + VT E+LE +F FG +ER A V +ER
Sbjct: 6 VRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEERD 46
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 35.7 bits (83), Expect = 0.007
Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN--------KEKMFGFIRMDYKH 160
++ ++ +Y+G + ++TE DI+ +F YGE + IN K K F F+ + +
Sbjct: 5 QYKDSAYIYIGGLPYELTEGDILCVFSQYGEI--VDINLVRDKKTGKSKGFAFLAYEDQR 62
Query: 161 NADKAKAKLDGHVLKGRSLKI 181
+ A L+G L GR++++
Sbjct: 63 STILAVDNLNGIKLLGRTIRV 83
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 38.1 bits (88), Expect = 0.008
Identities = 48/213 (22%), Positives = 85/213 (39%), Gaps = 39/213 (18%)
Query: 46 GRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQN 105
G GG G GN + + N G GG D T
Sbjct: 66 GNGGSSACGLGSMGNMANMAST--NSLNSLGSGGSDDNDTN------------------- 104
Query: 106 KDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHN 161
+ L + + D+T+ ++ LF+ G I ++ FG+ +D+
Sbjct: 105 -----NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSE 159
Query: 162 ADKAKA--KLDGHVLKGRSLKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGD 213
AD +A L+G ++ + LK+ +A P +IK V NL +T++ L+ FG +G
Sbjct: 160 ADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQ 219
Query: 214 IERAIVIVDE-RGNSKCEGIVEFARKPAAAQAL 245
I + ++ D+ G + V F ++ A +A+
Sbjct: 220 IVQKNILRDKLTGTPRGVAFVRFNKREEAQEAI 252
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 37.4 bits (87), Expect = 0.008
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+Q E E E E +K +RE +R+ ++ E +E++ EE +R++ E + +E +
Sbjct: 18 RQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQEEYEK 77
Query: 373 LAQQ 376
L
Sbjct: 78 LKSS 81
Score = 27.7 bits (62), Expect = 9.7
Identities = 14/62 (22%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 324 EMLRKELAQREIDRERQKA-EWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
++ K+ A+ E + R++ E E +ER+ + E +K EE++ +++E+ R
Sbjct: 2 KIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEER 61
Query: 383 RQ 384
++
Sbjct: 62 KE 63
>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 = 38.3 bits (89), Expect = 0.009
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAK 168
R+Y+GN+ + E+ I EL + +G+ + + K+ K + F D A A
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356
Query: 169 LDGHVLKGRSLKIRFAPINA 188
L+G L ++ A + A
Sbjct: 357 LNGKDTGDNKLHVQRACVGA 376
Score = 32.2 bits (73), Expect = 0.65
Identities = 30/110 (27%), Positives = 42/110 (38%), Gaps = 15/110 (13%)
Query: 85 TEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFK--------- 135
EK++A LP Q + + A RLY+G I + E +++ F
Sbjct: 149 PEKLLAEGSIITPLPVLPYQQQATRQAR--RLYVGGIPPEFVEEAVVDFFNDLMIATGYH 206
Query: 136 ---PYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR 182
+ INKEK F F+ A A A LD + LKIR
Sbjct: 207 KAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA-LDSIIYSNVFLKIR 255
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, 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-1 contains 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
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 34.9 bits (80), Expect = 0.009
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQA 244
+ NL T + E FG++ER ++ E G+SK G VE+ +K +AA+A
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARA 57
Score = 31.1 bits (70), Expect = 0.20
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
L + N+ T+ EL +P+G + F+ K +GF+ K +A +AK+ L
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61
Query: 170 DGHVLKGRSLKIRFA 184
G L R+L + +
Sbjct: 62 LGKQLGSRTLYVHWT 76
>gnl|CDD|181442 PRK08476, PRK08476, F0F1 ATP synthase subunit B'; Validated.
Length = 141
Score = 36.6 bits (85), Expect = 0.009
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEE 378
EHE E + K A+ E ++ RQKA + KE ++++ + EL K+ + LA Q++
Sbjct: 60 IEHEIETILKN-AREEANKIRQKAIAKAKEEAEKKIEAKKAELESKYEAFAKQ-LANQKQ 117
Query: 379 DLR 381
+L+
Sbjct: 118 ELK 120
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that 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 it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains 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. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 34.9 bits (80), Expect = 0.009
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
R+++G + E D+ FK YG ++ I+ ++ FGF+ D +AD A +LDG L
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRD--IDLKRGFGFVEFDDPRDADDAVYELDGKEL 58
Query: 175 KGRSLKIRFA 184
+ I A
Sbjct: 59 CNERVTIEHA 68
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 35.0 bits (81), Expect = 0.010
Identities = 15/53 (28%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM---FGFIRMDYKHNADKA 165
+Y+G I D T +++ + F+P+GE +E+ ++ +GF+ Y +A +A
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRA 57
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 38.3 bits (89), Expect = 0.010
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 314 QLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRL 373
+L L +EL + D E +A + E + R EE ++ +E RL
Sbjct: 319 RLEALQGSPAYQDAEELERARADAEALQAAAADARQAIREAESRLEE-ERRRLDEEAGRL 377
Query: 374 AQQEEDLR 381
E +LR
Sbjct: 378 DDAERELR 385
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 34.8 bits (80), Expect = 0.011
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
+L++G + D E + ++F YG+ E+ + + + FGF+ + +A A
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 169 LDGHVLKGRSLKI 181
++G + GR +++
Sbjct: 62 MNGKSVDGRQIRV 74
Score = 29.4 bits (66), Expect = 0.85
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 200 TNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRR 247
+ LE F +G I +V+ D E S+ G V F A A+
Sbjct: 13 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 34.8 bits (81), Expect = 0.011
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 116 LYLGNIGGDITENDII----ELFKPYGETQELFINK-EKMFG--FIRMDYKHNADKAKAK 168
LY+ N+ I ++++ LF +G ++ +K KM G F+ +A A
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRA 61
Query: 169 LDGHVLKGRSLKIRFA 184
L G + ++I++A
Sbjct: 62 LQGFPFYDKPMRIQYA 77
>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 = 34.8 bits (81), Expect = 0.012
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGET------QELFINKEKMFGFIRMDYKHNADKAKAKL 169
LY+G++ D+TE + E+F P G ++L + + ++ +A++A L
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 170 DGHVLKGRSLKI 181
+ V+KG+ ++I
Sbjct: 62 NFDVIKGKPIRI 73
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 37.0 bits (86), Expect = 0.012
Identities = 19/45 (42%), Positives = 29/45 (64%), Gaps = 3/45 (6%)
Query: 320 EHETEMLRKELAQREIDRER-QKAEWEMKERQAEELKRRDEELMK 363
E ET L +EL + I +ER ++ E E +E+ AEE K R+EE++
Sbjct: 141 EDETAALLRELEK--IKKERAEEKEREEEEKAAEEEKAREEEILT 183
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 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 = 70
Score = 34.4 bits (79), Expect = 0.013
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
R+ + N+ D+T+ ++ +L Y + + ++K K + + A +A AKL
Sbjct: 1 RIVIRNLPADVTKQEVHDLLSDY-QVKYCDVDKSKRTAQVTLLNGDQASRAIAKLHQSSY 59
Query: 175 KGRSLKIRFAP 185
K R + ++ P
Sbjct: 60 KERKISVQLQP 70
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 34.5 bits (80), Expect = 0.013
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
I VKNL VT + L F G++ V+ G S+ G V F + A QA++
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVK 59
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 34.5 bits (80), Expect = 0.013
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIER-AIVIVDERGNSKCEGIVEFARKPAAAQALR 246
+ V LT V + L+ F +G ++ + I E + VEF A +A++
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58
Score = 30.2 bits (69), Expect = 0.41
Identities = 15/73 (20%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQ--ELFINKE----KMFGFIRMDYKHNADKAKAKL 169
L++G + ++ ++ + E+F YG + +L I++E + + ++ + +A+KA +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 170 DGHVLKGRSLKIR 182
DG + G+ + +
Sbjct: 61 DGGQIDGQEVTVE 73
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 34.6 bits (79), Expect = 0.013
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
R+Y+G + E D+ FK YG+ E ++ + +GF+ D +AD A +L+G L
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILE--VDLKNGYGFVEFDDLRDADDAVYELNGKDL 58
Query: 175 KG 176
G
Sbjct: 59 CG 60
>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 = 34.5 bits (80), Expect = 0.013
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
++NL T E L+ F FG+++ A ++ D G+SK V+F K +A + L
Sbjct: 5 IRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Score = 28.3 bits (64), Expect = 2.5
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKA-----KAK 168
N+ D TE ++ ELF +GE + I K+K+ F++ K +A K A+
Sbjct: 7 NLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAE 66
Query: 169 LDGHVLKGRSLKIRFA 184
G L GR L + A
Sbjct: 67 DSGLSLDGRRLIVTLA 82
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 37.7 bits (88), Expect = 0.014
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 5/85 (5%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
++L E + L K+L + E +RE+++ + +E+ +EL+R+ E +K E
Sbjct: 207 EELLARLESKEAALEKQL-RLEFEREKEELRKKYEEKLRQELERQAEAHEQKLKNE---- 261
Query: 373 LAQQEEDLRRRQNDNSMFLVEQQQG 397
LA Q +L+R N VE+++
Sbjct: 262 LALQAIELQREFNKEIKEKVEEERN 286
Score = 37.3 bits (87), Expect = 0.018
Identities = 33/118 (27%), Positives = 55/118 (46%), Gaps = 11/118 (9%)
Query: 268 ELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLR 327
EL E + ER + +K E + + E + + KQL +E E E LR
Sbjct: 181 ELKAEEEEELERALKEKREELLSK----LEEELLARLESKEAALEKQLRLEFEREKEELR 236
Query: 328 KELAQR---EIDRERQKAEWEMKER---QAEELKRRDEELMKKH-AEEMQLRLAQQEE 378
K+ ++ E++R+ + E ++K QA EL+R + +K+ EE RLA+ E
Sbjct: 237 KKYEEKLRQELERQAEAHEQKLKNELALQAIELQREFNKEIKEKVEEERNGRLAKLAE 294
Score = 33.5 bits (77), Expect = 0.31
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+ L E E L +EL R ++ + E +++ E EEL KK+ E+++
Sbjct: 192 RALKEKREELLSKLEEELLAR-LESKEAALEKQLRLEFEREK----EELRKKYEEKLRQE 246
Query: 373 LAQQEEDL 380
L +Q E
Sbjct: 247 LERQAEAH 254
Score = 29.2 bits (66), Expect = 5.3
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 326 LRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM-----QLRLAQQEEDL 380
L K+LA+ + + E ++ E +KE++ E L + +EEL+ + + QLRL + E
Sbjct: 175 LSKKLAELKAE-EEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRLEFEREKE 233
Query: 381 RRRQN 385
R+
Sbjct: 234 ELRKK 238
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
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.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 34.1 bits (78), Expect = 0.014
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
R+Y+G + + E DI F YG+ E I+ + +GF+ + +AD A +L+G L
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLE--IDLKNGYGFVEFEDSRDADDAVYELNGKDL 58
Query: 175 KGRSLKIRFA 184
G + + A
Sbjct: 59 CGERVIVEHA 68
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 34.5 bits (80), Expect = 0.014
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 113 NCRLYLGNIGGDITENDIIEL----FKPYGETQELFINKEKMFGFIRMDYKHNADKAK-A 167
N LY+G I I E+ F +G+ +++ + K F+R Y+ +A+ AK A
Sbjct: 1 NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEA 60
Query: 168 KLDGHVLKGRSLKIRFA 184
D + G L +R+A
Sbjct: 61 MADQSLDGGEVLNVRWA 77
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 37.5 bits (88), Expect = 0.015
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 13/75 (17%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKE------RQAE-ELKRRDEELMKKHAEEMQLR 372
E E + + +E A++E + +++A E KE + E EL+ R EL ++++ R
Sbjct: 37 EEEAKRILEE-AKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNEL-----QKLEKR 90
Query: 373 LAQQEEDLRRRQNDN 387
L Q+EE+L R+
Sbjct: 91 LLQKEENLDRKLELL 105
Score = 35.9 bits (84), Expect = 0.045
Identities = 28/102 (27%), Positives = 51/102 (50%), Gaps = 18/102 (17%)
Query: 313 KQLHELYEHETEMLRKEL---AQREIDRERQKAEWEMKE------------RQAEE-LKR 356
K++ E + E E ++KE A+ EI + R + E E++E Q EE L R
Sbjct: 41 KRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDR 100
Query: 357 RDEELMKK--HAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
+ E L K+ E+ + L Q++++L +++ + + EQ Q
Sbjct: 101 KLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQ 142
Score = 29.0 bits (66), Expect = 6.5
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 18/90 (20%)
Query: 287 EFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELA----QREIDRERQKA 342
E +K R N FE E R +L +L E +L+KE +++ ++
Sbjct: 65 EIHKLR---------NEFEKELRERRNELQKL---EKRLLQKEENLDRKLELLEKREEEL 112
Query: 343 EWEMK--ERQAEELKRRDEELMKKHAEEMQ 370
E + K E++ +EL++++EEL + E++Q
Sbjct: 113 EKKEKELEQKQQELEKKEEELEELIEEQLQ 142
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains 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 effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 34.4 bits (79), Expect = 0.016
Identities = 17/75 (22%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGE--TQELFI----NKEKMFGFIRMDYKHNADKAKA 167
C L++ ++ + + +++++F P+G + ++F+ N+ K FGF+ D +A A
Sbjct: 5 CNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQ 64
Query: 168 KLDGHVLKGRSLKIR 182
++G + + LK++
Sbjct: 65 AMNGFQIGMKRLKVQ 79
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 34.2 bits (78), Expect = 0.016
Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAK 168
C +++G I D+ E++++ +F+ G E+ F K + + F+ KH A +A +
Sbjct: 2 CEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRE 61
Query: 169 LDGHVLK-GRSLKI 181
L+ + ++ GR L +
Sbjct: 62 LNNYEIRPGRLLGV 75
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding
protein 7 (RBM7). This subfamily corresponds to the RRM
of RBM7, a 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. RBM7 interacts with
splicing factors SAP145 (the spliceosomal splicing
factor 3b subunit 2) and SRp20. It 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.
RBM7 contains 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. .
Length = 75
Score = 34.1 bits (78), Expect = 0.016
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKLD 170
L++GN+ +TE I ELF G ++ I K K F F+ ++ + A L+
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63
Query: 171 GHVLKGRSLKIR 182
G L GR L I+
Sbjct: 64 GIKLYGRPLNIQ 75
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 36.4 bits (85), Expect = 0.017
Identities = 34/95 (35%), Positives = 49/95 (51%), Gaps = 18/95 (18%)
Query: 320 EHETEMLRKEL---AQREIDRERQKAEWEMKER------------QAEE-LKRRDEELMK 363
+ E E L+KE A+ EI + R +AE E+KER Q EE L R+DE L K
Sbjct: 44 KKEAEALKKEALLEAKEEIHKLRAEAERELKERRNELQRQEKRLLQKEETLDRKDESLEK 103
Query: 364 KHA--EEMQLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
K EE + LA +++ L ++ + + EQQQ
Sbjct: 104 KEESLEEKEKELAARQQQLEEKEEELEELIEEQQQ 138
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 37.4 bits (87), Expect = 0.017
Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 12/90 (13%)
Query: 309 GSRWKQLHELYEHETEMLRKELAQ----REIDRERQK------AEWEMKERQAEELKRRD 358
K+L ELYE E E L +EL++ E+ E ++ E E +
Sbjct: 469 EEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALK 528
Query: 359 EELMKKHAEEMQLRLAQQEEDLRRRQNDNS 388
EEL +K + L ++ E+L+ +
Sbjct: 529 EELEEKLEKLENLL--EELEELKEKLQLQQ 556
Score = 35.1 bits (81), Expect = 0.086
Identities = 17/72 (23%), Positives = 31/72 (43%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+L E E + LR+ + E ++A E E + E+L+ EEL + + +
Sbjct: 497 AELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQ 556
Query: 373 LAQQEEDLRRRQ 384
L ++ L R
Sbjct: 557 LKEELRQLEDRL 568
Score = 32.8 bits (75), Expect = 0.57
Identities = 20/101 (19%), Positives = 36/101 (35%), Gaps = 9/101 (8%)
Query: 307 EYGSRWKQLHELYEHETEMLRKELAQREIDRERQK--------AEWEMKERQAEELKRRD 358
E + +L E E E L +EL + + E Q+ E E E + EL+
Sbjct: 189 ELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEK 248
Query: 359 EELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGRG 399
E L + A +++ + E R + ++
Sbjct: 249 ERLEELKARLLEIESLELEALKIREEELR-ELERLLEELEE 288
Score = 32.0 bits (73), Expect = 0.81
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+ L E E + E L L + E +E+ + + + + +L+ R +EL + E LR
Sbjct: 525 EALKEELEEKLEKLENLLEELEELKEKLQLQ--QLKEELRQLEDRLQELKELLEELRLLR 582
Query: 373 LAQQE-EDLRRRQN 385
++E E+LR R
Sbjct: 583 TRKEELEELRERLK 596
Score = 30.1 bits (68), Expect = 3.4
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 9/93 (9%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKH------- 365
K L E E E L K ++ E E + ++ E + +EL+ R EEL K+
Sbjct: 325 KSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERL 384
Query: 366 --AEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
EE L ++ +L + L E ++
Sbjct: 385 KQLEEAIQELKEELAELSAALEEIQEELEELEK 417
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct 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. Raver-2 contains 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.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 77
Score = 34.1 bits (78), Expect = 0.017
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQA 244
V NL T E E +G+IER ++ E G+SK G VE+ +K +A++A
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKA 57
Score = 28.3 bits (63), Expect = 1.8
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
L + N+ T + EL + YG + F+ K +GF+ K +A KA+ +L
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61
Query: 170 DGHVLKGRSLKIRFA 184
G L +L ++
Sbjct: 62 LGKQLGESTLFAQWM 76
>gnl|CDD|241160 cd12716, RRM1_2_NP220, RNA recognition motif 1 and 2 in vertebrate
nuclear protein 220 (NP220). This subgroup corresponds
to RRM1 and RRM2 of NP220, also termed zinc finger
protein 638 (ZN638), or cutaneous T-cell
lymphoma-associated antigen se33-1, or zinc finger
matrin-like protein, a large nucleoplasmic DNA-binding
protein that binds to cytidine-rich sequences, such as
CCCCC (G/C), in double-stranded DNA (dsDNA). NP220
contains multiple domains, including MH1, MH2, and MH3,
domains homologous to the acidic nuclear protein matrin
3; RS, an arginine/serine-rich domain commonly found in
pre-mRNA splicing factors; PstI-HindIII, a domain
essential for DNA binding; acidic repeat, a domain with
nine repeats of the sequence LVTVDEVIEEEDL; and a
Cys2-His2 zinc finger-like motif that is also present in
matrin 3. It may be involved in packaging, transferring,
or processing transcripts. This subgroup corresponds to
the domain of MH2 that contains two tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 76
Score = 34.0 bits (78), Expect = 0.020
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 126 TENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL--KGRSLKIRF 183
+E +I L KP+G+ +++ I ++ M+ K A+ + + KG+ +KI
Sbjct: 14 SEEEIYNLAKPFGKLKDILILSSHKKAYLEMNNKEAAEAMVKYFETTPVLVKGKQVKISM 73
Query: 184 AP 185
Sbjct: 74 PE 75
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 34.2 bits (78), Expect = 0.020
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 6/55 (10%)
Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMD 157
++ ++ +L++GN+ DI E+++ E F +G EL IN + + FGF+ D
Sbjct: 1 RYPDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFD 55
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 33.8 bits (77), Expect = 0.021
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
L++ N+ +TE + + F +G+ + + K K + FI D + A KA +++G L+
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLER--VKKLKDYAFIHFDERDGAVKAMEEMNGKELE 61
Query: 176 GRSLKIRFA 184
G +++I FA
Sbjct: 62 GENIEIVFA 70
Score = 33.0 bits (75), Expect = 0.035
Identities = 15/25 (60%), Positives = 19/25 (76%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIER 216
V+NL + VT E+LE AFG FG +ER
Sbjct: 6 VRNLANTVTEEILEKAFGQFGKLER 30
>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 = 33.6 bits (77), Expect = 0.021
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDG 171
+Y+GN+ GDI E ++ +LF YG ++ + + + FI + +A+ A DG
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60
Query: 172 HVLKGRSLKI 181
+ G+ L++
Sbjct: 61 YDFDGQRLRV 70
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 37.2 bits (86), Expect = 0.024
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
RW + + E LR EL E+QK E + ++R AEELK + M+ HA
Sbjct: 1055 RWTEAESKWISLAEELRTELDASRALAEKQKHELDTEKRCAEELKEAMQMAMEGHA---- 1110
Query: 371 LRLAQQEEDLRRR 383
R+ +Q DL +
Sbjct: 1111 -RMLEQYADLEEK 1122
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 34.2 bits (78), Expect = 0.024
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKA 167
N L+LGN+ +TE D+ F +G E+ I + +GF++ + A +AK
Sbjct: 7 NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66
Query: 168 KLDGHVLKGRSLKIRF 183
+ G VL+ +KI +
Sbjct: 67 AMSGKVLRRNPIKIGY 82
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 33.7 bits (78), Expect = 0.026
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAK 168
C +++G I D+ E++++ LF+ G EL F + + F+ K A +A +
Sbjct: 2 CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ 61
Query: 169 LDGHVL-KGRSLKI 181
L + + G+ L +
Sbjct: 62 LHNYEIRPGKRLGV 75
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB 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. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 33.4 bits (77), Expect = 0.028
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 116 LYLGNIGGDITENDIIELFKP-YGETQEL--FINKEKMFGFIRMDYKHNADKAKAKLDGH 172
L+L NI +TE D+ ELF G + F KM I+M A +A L +
Sbjct: 2 LHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKM-ALIQMGSVEEAIEALIALHNY 60
Query: 173 VLKGRS-LKIRFA 184
L S L++ F+
Sbjct: 61 QLSESSHLRVSFS 73
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 36.6 bits (84), Expect = 0.029
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 9/97 (9%)
Query: 299 ATVNSFEFEYGSRWKQLHELY---EHETEMLRKELAQREIDRE---RQKAEWEMKERQAE 352
+ VN E + W ++ Y E+ETE R+E Q E + R K + R+ E
Sbjct: 328 SPVNMSALERTAAWVLMNSQYEDIEYETEENREEGTQAEKYEQEIARLKERLRVSVRRLE 387
Query: 353 ELKRR---DEELMKKHAEEMQLRLAQQEEDLRRRQND 386
E +RR E+ M+K +E Q RL EE LRR+Q +
Sbjct: 388 EYERRLLGQEQQMQKLLQEYQARLEDSEERLRRQQEE 424
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 36.1 bits (84), Expect = 0.031
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 331 AQREIDRERQKAEWEMKERQAEELKRRDEELM--------KKHAEEMQLRLAQQEEDLRR 382
++ I+ ER KAE E++ K+++EE M ++H +++ ++ + E L
Sbjct: 202 KEKAIEAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLA 261
Query: 383 RQN 385
Q
Sbjct: 262 EQE 264
Score = 31.5 bits (72), Expect = 0.93
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
E E + E A+ E + R+K + E E+ E +R +E +K+ E+M+ + +
Sbjct: 207 EAERAKAEAAEAEQELLREKQKEE--EQMMEAQERSYQEHVKQLIEKMEAEREKLLAEQE 264
Query: 382 R 382
R
Sbjct: 265 R 265
Score = 30.7 bits (70), Expect = 1.8
Identities = 17/66 (25%), Positives = 31/66 (46%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQ 376
E E E E+LR++ + E E Q+ ++ +Q E + E + E M Q+
Sbjct: 214 EAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLAEQERMLEHKLQE 273
Query: 377 EEDLRR 382
+E+L +
Sbjct: 274 QEELLK 279
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 33.2 bits (76), Expect = 0.034
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 114 CR-LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
R +Y+GN+ +E ++ E + +G ++ I KEK F+ NA K L
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL 59
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 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 = 83
Score = 33.3 bits (76), Expect = 0.034
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 132 ELFKPYGETQELFINKEK-----MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
++F YG+ +E I +++ F F+ M + NA+ A +G + GR + + +A
Sbjct: 20 KIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 77
>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 = 33.1 bits (76), Expect = 0.034
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKL 169
L++GN+ D E+ I E F YGE + + + K FG++ + A A L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 170 DGHVLKGRSLKI 181
G L GR +++
Sbjct: 61 GGTDLLGRPVRL 72
>gnl|CDD|218661 pfam05622, HOOK, HOOK protein. This family consists of several
HOOK1, 2 and 3 proteins from different eukaryotic
organisms. The different members of the human gene
family are HOOK1, HOOK2 and HOOK3. Different domains
have been identified in the three human HOOK proteins,
and it was demonstrated that the highly conserved
NH2-domain mediates attachment to microtubules, whereas
the central coiled-coil motif mediates homodimerisation
and the more divergent C-terminal domains are involved
in binding to specific organelles (organelle-binding
domains). It has been demonstrated that endogenous HOOK3
binds to Golgi membranes, whereas both HOOK1 and HOOK2
are localised to discrete but unidentified cellular
structures. In mice the Hook1 gene is predominantly
expressed in the testis. Hook1 function is necessary for
the correct positioning of microtubular structures
within the haploid germ cell. Disruption of Hook1
function in mice causes abnormal sperm head shape and
fragile attachment of the flagellum to the sperm head.
Length = 713
Score = 36.3 bits (84), Expect = 0.035
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
E L++E + E R+ + + E E++ EL+ R++EL AE L+ E D+ R
Sbjct: 249 EQLQEENFRLEAARDDYRIKCEELEKELAELQHRNDELTSLAAESQALK---DEIDVLRE 305
Query: 384 QND 386
+D
Sbjct: 306 SSD 308
Score = 31.3 bits (71), Expect = 1.3
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE-E 378
+HE +MLR L Q + ER ++ E+ RR+ EL E QLRLA Q
Sbjct: 465 QHENKMLR--LGQEGSENERITE----LQQLLEDANRRNNEL------ETQLRLANQRIL 512
Query: 379 DLRRRQNDNSMFLVEQ 394
+L+++ D L EQ
Sbjct: 513 ELQQQVEDLQKALQEQ 528
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). 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. It 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. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 33.5 bits (76), Expect = 0.036
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAK 166
NC L + + TE D+ E+F YG ++ I + + F F+ + +A +AK
Sbjct: 9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68
Query: 167 AKLDGHVLKGRSLKIRFA 184
+ +G L GR +++ F+
Sbjct: 69 ERANGMELDGRRIRVDFS 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 = 33.9 bits (78), Expect = 0.037
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYG 138
C+++LG + DITE +I FKP+G
Sbjct: 3 CKVFLGGVPWDITEAGLINTFKPFG 27
>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail. The myosin molecule is a
multi-subunit complex made up of two heavy chains and
four light chains it is a fundamental contractile
protein found in all eukaryote cell types. This family
consists of the coiled-coil myosin heavy chain tail
region. The coiled-coil is composed of the tail from two
molecules of myosin. These can then assemble into the
macromolecular thick filament. The coiled-coil region
provides the structural backbone the thick filament.
Length = 859
Score = 36.6 bits (85), Expect = 0.038
Identities = 35/142 (24%), Positives = 51/142 (35%), Gaps = 28/142 (19%)
Query: 278 ERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDR 337
E K+ E R+ + E E + ++ E E R + E++
Sbjct: 1 ELERQKRELENQLYRKESELSQLSSKLEDEQALVAQLQKKIKELEA---RIRELEEELEA 57
Query: 338 E---RQKAEW----------EMKER----------QAEELKRRDEELMK--KHAEEMQLR 372
E R KAE E+ ER Q E K+R+ EL K K EE L+
Sbjct: 58 ERAARAKAEKARADLSRELEELSERLEEAGGATAAQIELNKKREAELAKLRKDLEEANLQ 117
Query: 373 LAQQEEDLRRRQNDNSMFLVEQ 394
+ LR++ D L EQ
Sbjct: 118 HEEALATLRKKHQDAINELSEQ 139
Score = 30.4 bits (69), Expect = 2.8
Identities = 31/131 (23%), Positives = 56/131 (42%), Gaps = 17/131 (12%)
Query: 268 ELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE------- 320
EL E+D N T F + ++ V + E + ++H+L +
Sbjct: 395 ELQAELDTAQREARNLSTELFRLKNELEELKDQVEALRRENKNLQDEIHDLTDQLGEGGR 454
Query: 321 --HETEMLRKELAQREIDRERQKAEWEMKE--RQAEELKR-RDEELMKKHAEEMQLRLAQ 375
HE E R+ L E +++ +A E E + EE K R + + + E++ RLA+
Sbjct: 455 NVHELEKARRRL---EAEKDELQAALEEAEAALELEESKVLRAQVELSQIRSEIERRLAE 511
Query: 376 QEEDL--RRRQ 384
+EE+ R+
Sbjct: 512 KEEEFENTRKN 522
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 32.8 bits (75), Expect = 0.040
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM---FGFIRMDYKHNADKAKAKLDG 171
R+Y+GN+ D+ E D+ +LF YG +++ + + F F+R + +A+ A +G
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNG 60
Query: 172 HVLKGRSLKIRF 183
+ L++ F
Sbjct: 61 YDFGQCRLRVEF 72
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 33.1 bits (75), Expect = 0.042
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 113 NCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
N R+++GN+ + ++D+ +F YG+ ++K F F++ + NA A A DG
Sbjct: 1 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--FAFVQYVNERNARAAVAGEDG 58
Query: 172 HVLKGRSLKIRFA 184
++ G+ L I A
Sbjct: 59 RMIAGQVLDINLA 71
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 32.8 bits (75), Expect = 0.043
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGH 172
L++GN+ T +D+ E F+ +GE ++ I K+ + FI+ + KA K+DG
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDGE 64
Query: 173 VLKGRSLKI 181
L +K+
Sbjct: 65 YLGNNRVKL 73
>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 = 33.2 bits (76), Expect = 0.044
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
V L VT E LE F G ++ ++ + G K VE+ + +A+QA+
Sbjct: 7 VSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAV 60
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 34.5 bits (80), Expect = 0.044
Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 312 WKQLHELYEHETEMLRKELA--QREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM 369
K + E E + + EL ++E+ + ++K + + +++++EL KK +E
Sbjct: 16 GKAAQKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQKK-VQEF 74
Query: 370 QLRLAQQEEDLRRRQNDN 387
Q + + ++DL++RQ +
Sbjct: 75 QRKQQKLQQDLQKRQQEE 92
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 33.0 bits (75), Expect = 0.045
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFIN---KEKMFGFIRMD 157
+L++GN+ D+ ++++ E F+ YG EL IN K FGF+ D
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFD 50
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 32.9 bits (75), Expect = 0.048
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKLD 170
LY+GN+ +TE+ + ++F+ G Q + I NK +GF+ H+A+ A L+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 171 GHVLKGRSLKIRFA 184
G ++ +++ +A
Sbjct: 61 GRQIENNEIRVNWA 74
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 32.6 bits (75), Expect = 0.048
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 202 ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
EL ++ F +GD+ +V+ K IVEFA K AA A+
Sbjct: 20 ELRKI-FSKYGDVS-DVVV---SSKKKGSAIVEFASKKAAEAAVE 59
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that 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.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains 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 = 81
Score = 33.1 bits (75), Expect = 0.049
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-FGFIRMDYKHNADKAKAKLDG 171
+C++Y+GN+G + + ++ F YG + +++ + F F+ + +A A +LDG
Sbjct: 4 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 63
Query: 172 HVLKGRSLKIRFA 184
L G +++ +
Sbjct: 64 RTLCGCRVRVELS 76
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB 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. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 32.9 bits (76), Expect = 0.051
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA 249
+ + NL VT ++L F +G +E+ I+I E+ + +V+F +A A +
Sbjct: 4 VTISNLLYPVTVDVLHQVFSPYGAVEK-ILIF-EKNTG-VQALVQFDSVESAENAKKAL- 59
Query: 250 EGCFFLTQSL 259
G
Sbjct: 60 NGRNIYDGCC 69
Score = 32.1 bits (74), Expect = 0.095
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 120 NIGGDITENDIIELFKPYGETQELFI-NKEKMF-GFIRMDYKHNADKAKAKLDGH 172
N+ +T + + ++F PYG +++ I K ++ D +A+ AK L+G
Sbjct: 8 NLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGR 62
>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM4 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 = 72
Score = 32.7 bits (75), Expect = 0.052
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA 249
I VKNL + L F FG + R V++ G + IVEF A A R+ A
Sbjct: 3 ILVKNLPAGTLTAELRELFSKFGSLGR--VLLPPAGIT---AIVEFLEPSEAKLAFRKLA 57
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 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 homologues 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. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 32.6 bits (75), Expect = 0.052
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA 249
I VKNL T E L F FG + R ++ S+ +VEF A +A + A
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLGRLLL-----PPSRTIALVEFLEPSDARKAFKSLA 57
Score = 28.3 bits (64), Expect = 1.9
Identities = 16/66 (24%), Positives = 27/66 (40%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSL 179
N+ TE ++ ELF+ +G L + + + +A KA L K L
Sbjct: 7 NLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKRFKHVPL 66
Query: 180 KIRFAP 185
+ +AP
Sbjct: 67 YLEWAP 72
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 33.1 bits (76), Expect = 0.053
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH--- 172
+L + D+ E I + F+ +G+++ + +N GF+R + + A+K A + +
Sbjct: 5 FFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISENGLN 64
Query: 173 ---------VLKGRSLKIRFA 184
VL+G L++ +
Sbjct: 65 AGLSRGGLLVLEGCPLRVAWG 85
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 32.8 bits (75), Expect = 0.057
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEK-----MFGFIRMDYKHNADKAKAKLD 170
L++GN+ ITE ++ F+ YG +++ I + + F++ A +AK +
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMS 64
Query: 171 GHVLKGRSLKI 181
G + +KI
Sbjct: 65 GQYIGRNQIKI 75
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 34.5 bits (80), Expect = 0.057
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 326 LRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQN 385
+RK L Q E + + E + E + EEL++R EL K E ++ R ++ + +R
Sbjct: 112 MRKAL-QAEQGKSELEQEIKKLEEEKEELEKRVAELEAK-LEAIEKREEEERQIEEKRHA 169
Query: 386 DNSMFLVEQQQ 396
D FL +Q Q
Sbjct: 170 DEIAFLKKQNQ 180
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 33.8 bits (78), Expect = 0.060
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 328 KELAQREID------RERQKAEWEMKERQAEEL-KRRDEELMKKHAEEMQLRLAQQEEDL 380
K +E+D + + + + E K+ +AE+L K EE + E+++ L + E +L
Sbjct: 6 KTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAEL 65
Query: 381 RRRQNDN 387
RR+
Sbjct: 66 ARRELKA 72
Score = 30.3 bits (69), Expect = 0.98
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 310 SRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM 369
++W++ E + E E L K A+ + + E +K E E++E +A EL RR+ +K A++M
Sbjct: 22 AKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEA-ELARRE---LKAEAKKM 77
>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 = 32.5 bits (74), Expect = 0.062
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
+++GNI + TE + ++F G + K K +GF + A A L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 170 DGHVLKGRSLKIRFA 184
+G+ L GR L++ A
Sbjct: 61 NGYELNGRQLRVDNA 75
>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 = 33.0 bits (76), Expect = 0.065
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDII-ELFKPYGETQ--ELFINKE---KMFGFIRMDYKHNADKAKAKL 169
L++ + + I+ +LF G+ +L I + F F+ +A++A+ L
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64
Query: 170 DGHVLKGRSLKIRF 183
+GH L+G +++ F
Sbjct: 65 NGHSLQGSPIRVSF 78
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 35.6 bits (82), Expect = 0.065
Identities = 13/56 (23%), Positives = 16/56 (28%)
Query: 447 QGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGPTDYQPKRR 502
Q GG G G RR G + + G P Q +RR
Sbjct: 392 QQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRR 447
Score = 32.9 bits (75), Expect = 0.38
Identities = 14/57 (24%), Positives = 16/57 (28%)
Query: 447 QGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGPTDYQPKRRN 503
Q G G G G R EGGA R + Q +RR
Sbjct: 393 QRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRP 449
>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 = 32.3 bits (74), Expect = 0.071
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 117 YLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLD 170
++GN+ T ++ E FK G + I +K F +I K + + A L+
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LN 61
Query: 171 GHVLKGRSLKI 181
+GR +K+
Sbjct: 62 ESEFRGRQIKV 72
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 35.2 bits (81), Expect = 0.074
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDE-ELMKKHAEEM 369
R K+L + E + E + E+QK E K +QA E K + E E KK EE
Sbjct: 90 RQKELEQRAAAEKAAKQAE-QAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEA 148
Query: 370 QLRLAQQEED 379
+ Q EE+
Sbjct: 149 K---KQAEEE 155
Score = 31.3 bits (71), Expect = 1.0
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE 377
E + E Q++ + + K E K + E +++ +E KK AEE A E
Sbjct: 108 EQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAE 163
Score = 30.6 bits (69), Expect = 1.8
Identities = 25/119 (21%), Positives = 39/119 (32%), Gaps = 22/119 (18%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKER-------QAEELKRRDEELMKKHAEEMQLR 372
E E + A+++ ++KAE E K + +AEE K + E K A E
Sbjct: 153 EEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAA-A 211
Query: 373 LAQQEEDLRRR---------QNDNSMFLVE-----QQQGRGGSGGYGSPGQAYGNAIID 417
A+ E +F + ++QG GS Y I
Sbjct: 212 KAEAEAAAAAAAEAERKADEAELGDIFGLASGSNAEKQGGARGNAAGSEVDKYAAIIQQ 270
Score = 29.4 bits (66), Expect = 4.5
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 328 KELAQREIDRERQKAEWEMKE-----RQAEELKRRDEELMKKHAEEMQLRLAQQEE 378
E A+++ +R AE K+ +QAEE +++ EE K A E + + + E
Sbjct: 86 AEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAE 141
Score = 29.0 bits (65), Expect = 5.6
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ 384
++ Q Q+A E +QAE+ ++ EE +K AEE A+Q + + +
Sbjct: 83 QRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEE-KQKQAEE---AKAKQAAEAKAKA 136
Score = 28.6 bits (64), Expect = 7.1
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 313 KQLHEL-YEHETEMLRKELAQRE---IDRERQKAEWEMKERQAEELKRRDEELMKKHAEE 368
KQ E + E K A+ E + +++AE E K + A E K++ E KK E
Sbjct: 119 KQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAE 178
>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 = 32.4 bits (74), Expect = 0.076
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKP-YGETQ--ELFIN---KEKMFGFIRMDYKHNADKAKAK 168
R+++ NI D+ D+ +LF+ GE ELF + K + G + K + KA
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60
Query: 169 LDGHVLKGRSLKIR 182
++ + LKGR L ++
Sbjct: 61 MNRYELKGRKLVVK 74
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM3
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 = 72
Score = 32.0 bits (73), Expect = 0.080
Identities = 20/61 (32%), Positives = 24/61 (39%), Gaps = 5/61 (8%)
Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
I VKN T E L F G + R V++ G IVEFA A A +
Sbjct: 2 TILVKNFPYGTTAEELRDLFEPHGKLTR--VLMPPAGTI---AIVEFANPQQARLAFKAL 56
Query: 249 A 249
A
Sbjct: 57 A 57
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 32.5 bits (74), Expect = 0.082
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKA-KAK 168
+L++G + END+ +F P+G +E + + + F+ + A A KA
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62
Query: 169 LDGHVLKGRS--LKIRFA 184
++G S L ++FA
Sbjct: 63 HHSQTMEGCSSPLVVKFA 80
Score = 30.9 bits (70), Expect = 0.25
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 204 LELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR-----RCAEGC 252
+ + F FG IE V+ D+ G S+ V FA + A A++ + EGC
Sbjct: 18 VRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMHHSQTMEGC 71
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 35.2 bits (81), Expect = 0.082
Identities = 26/70 (37%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
EH E E +RE+ E+ E +ERQAEE +RR+EE K A E A+ E +
Sbjct: 243 EHSFEDFLLEEKRREL--EKLAKEEAERERQAEEQRRREEE---KAAMEADRAQAKAEVE 297
Query: 380 LRRRQNDNSM 389
RR + N +
Sbjct: 298 KRREKLQNLL 307
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 32.2 bits (73), Expect = 0.083
Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKA--KLDGHV 173
+++G + ++E D+ F+ Y + + + K + + + + +D A K++G V
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY-QVSVISLCKLSNYRYASLHFDRASDALLAVKKMNGGV 60
Query: 174 LKGRSLKIRF 183
L G S+K+R
Sbjct: 61 LSGLSIKVRM 70
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 35.5 bits (81), Expect = 0.084
Identities = 27/122 (22%), Positives = 56/122 (45%), Gaps = 9/122 (7%)
Query: 271 DEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHE---TEMLR 327
+E+ L E K E K + + + E E + +QL + E E L+
Sbjct: 1595 EEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAE-EEKKKVEQLKKKEAEEKKKAEELK 1653
Query: 328 KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE---EDLRRRQ 384
K + +I + + E +++AEE K+ +E+ +K A E + A++ E+L++++
Sbjct: 1654 KAEEENKIKAAEEAKKAEEDKKKAEEAKKAEED--EKKAAEALKKEAEEAKKAEELKKKE 1711
Query: 385 ND 386
+
Sbjct: 1712 AE 1713
Score = 34.7 bits (79), Expect = 0.15
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 17/83 (20%)
Query: 310 SRWKQLHELYEHETEM----LRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKH 365
+R +++ +LYE E +M +K + + KAE + ++AEE K++ E+L KK
Sbjct: 1592 ARIEEVMKLYEEEKKMKAEEAKKA------EEAKIKAE---ELKKAEEEKKKVEQLKKKE 1642
Query: 366 AEEM----QLRLAQQEEDLRRRQ 384
AEE +L+ A++E ++ +
Sbjct: 1643 AEEKKKAEELKKAEEENKIKAAE 1665
Score = 34.7 bits (79), Expect = 0.15
Identities = 27/105 (25%), Positives = 49/105 (46%), Gaps = 5/105 (4%)
Query: 283 KKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHE---TEMLRKELAQREIDRER 339
KK E K + + A E E + ++L + E E L+K + +I E
Sbjct: 1675 KKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734
Query: 340 QKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ 384
K E E +++AEE K+ +EE KK ++ ++ E++R+ +
Sbjct: 1735 AKKEAEEDKKKAEEAKKDEEE--KKKIAHLKKEEEKKAEEIRKEK 1777
Score = 33.6 bits (76), Expect = 0.32
Identities = 26/116 (22%), Positives = 52/116 (44%), Gaps = 17/116 (14%)
Query: 284 KTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAE 343
K E K + + + E E + ++L + E ++ ++ + +++KAE
Sbjct: 1621 KAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKK--AEEENKIKAAEEAKKAEEDKKKAE 1678
Query: 344 W-----EMKERQAEELKRRDEE------LMKKHAEEM----QLRLAQQEEDLRRRQ 384
E +++ AE LK+ EE L KK AEE +L+ A++E ++ +
Sbjct: 1679 EAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734
Score = 32.0 bits (72), Expect = 1.0
Identities = 18/73 (24%), Positives = 43/73 (58%), Gaps = 7/73 (9%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
K+ E + E+ + A+++ D ++KAE ++++A+E K++ EE K A+E + +
Sbjct: 1398 KKAEEDKKKADELKKAAAAKKKADEAKKKAE---EKKKADEAKKKAEE--AKKADEAKKK 1452
Query: 373 L--AQQEEDLRRR 383
A++ E+ +++
Sbjct: 1453 AEEAKKAEEAKKK 1465
Score = 30.9 bits (69), Expect = 1.8
Identities = 18/69 (26%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMK----ERQAEELKRRDEELMKKHAEEMQLRLAQQE 377
E +KE A+++ D ++KAE + K +++AEE K++ +EL K A + + A+++
Sbjct: 1367 EAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK 1426
Query: 378 EDLRRRQND 386
+ +++ ++
Sbjct: 1427 AEEKKKADE 1435
Score = 30.9 bits (69), Expect = 2.0
Identities = 13/49 (26%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
+ + +K +++ D ++KAE + ++A+E K++ EE KK A+ +
Sbjct: 1291 KADEAKKAEEKKKADEAKKKAE---EAKKADEAKKKAEE-AKKKADAAK 1335
Score = 29.0 bits (64), Expect = 7.7
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
E +K ++ D ++KAE + ++A+E K++ EE KK A+E +
Sbjct: 1461 EAKKKAEEAKKADEAKKKAE---EAKKADEAKKKAEE-AKKKADEAK 1503
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 32.0 bits (73), Expect = 0.085
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 123 GDITENDIIELFKPYGETQELFI--NKEKMFGFIRMDYKHNADKAKAKLD 170
TE D+ E F +G ++ I +++MFGF+ + NA+ K L
Sbjct: 9 SRFTEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFE---NAETVKRILS 55
>gnl|CDD|241223 cd12779, RRM1_ROD1, RNA recognition motif 1 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM1 of ROD1 coding protein Rod1, a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein that negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It might
play a role controlling differentiation in mammals. Rod1
contains four repeats of RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and does have RNA binding
activities. .
Length = 90
Score = 32.4 bits (73), Expect = 0.087
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRM 156
L+L I D+TE +II L P+G+ L + K K F+ M
Sbjct: 8 LHLRKIPNDVTEAEIISLGLPFGKVTNLLMLKGKSQAFLEM 48
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 32.2 bits (73), Expect = 0.089
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEK-----MFGFIRMDYKHNADKAKAKLD 170
L++GN+ +++E ++ F YG +E+ I + + F++ A +AK +
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMS 70
Query: 171 GHVLKGRSLKIRFA 184
G V+ +KI +
Sbjct: 71 GRVIGRNPIKIGYG 84
>gnl|CDD|222613 pfam14235, DUF4337, Domain of unknown function (DUF4337). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 187 and 201 amino
acids in length. There is a single completely conserved
residue Q that may be functionally important.
Length = 158
Score = 33.7 bits (78), Expect = 0.090
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 11/59 (18%)
Query: 318 LYEHETEMLRKELA------QREIDR-ERQKAEWEMK----ERQAEELKRRDEELMKKH 365
L E ++L E A Q +I R +++KA + + E +A+E + + + +H
Sbjct: 53 LAELAADLLELEAAAPRAELQAKIARYKKEKARYRSEAKELEAKAKEAEAESDHALHQH 111
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 35.0 bits (81), Expect = 0.091
Identities = 28/116 (24%), Positives = 55/116 (47%), Gaps = 12/116 (10%)
Query: 268 ELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLR 327
E+ ++ L+++ I E + + + E E + ++ E E E
Sbjct: 269 EIEQLLEELNKK-IKDLGEEEQLRVK-----EKIGELEAEI-ASLERSIAEKERELEDAE 321
Query: 328 KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
+ LA+ E + ++ AE E ER+ EE ++R ++L +++AE L ++ EDLR
Sbjct: 322 ERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE-----LKEELEDLRAE 372
Score = 34.7 bits (80), Expect = 0.12
Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRR----DEELMKKHAEE 368
K++ +L E E +++++ + E + + KER+ E+ + R + E+ K AE
Sbjct: 279 KKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEI 338
Query: 369 MQLRLAQQEEDLRRRQ 384
+L +EE RR +
Sbjct: 339 EELEREIEEERKRRDK 354
Score = 32.3 bits (74), Expect = 0.76
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 2/82 (2%)
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM--QLRLAQQ 376
E + LR+ L + + ++E E + +EL + + +K E +L Q+
Sbjct: 672 EPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQE 731
Query: 377 EEDLRRRQNDNSMFLVEQQQGR 398
EE L+ R + L +Q
Sbjct: 732 EEKLKERLEELEEDLSSLEQEI 753
Score = 30.8 bits (70), Expect = 2.0
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAE--EMQLRLAQQ 376
E E L +E+ + R++ E+ + + E+L+ EE+ K+ AE + ++
Sbjct: 334 LLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREK 393
Query: 377 EEDLRRRQND 386
E L+R N+
Sbjct: 394 LEKLKREINE 403
Score = 30.0 bits (68), Expect = 4.0
Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 289 YKQRQVGPRFATVNSFEFEYG-SRWKQLHELYEH-ETEMLRKELAQREIDRERQKAEWEM 346
+ + +N E SR ++ E E+ R E REI+++ + E
Sbjct: 769 ELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEK 828
Query: 347 ----KERQAEELKRRDEELMK----KHAEEMQLRLAQQEEDLRRRQN 385
KE Q + +R D + K E + + + EE+L +
Sbjct: 829 EYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEA 875
>gnl|CDD|240879 cd12433, RRM_Yme2p_like, RNA recognition motif in yeast
mitochondrial escape protein 2 (Yme2p) and similar
proteins. This subfamily corresponds to the RRM of
Yme2p, also termed protein RNA12, an inner mitochondrial
membrane protein that plays a critical role in
mitochondrial DNA transactions. It may serve as a
mediator of nucleoid structure and number in
mitochondria of the yeast Saccharomyces cerevisiae.
Yme2p contains an exonuclease domain, an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal domain. .
Length = 86
Score = 32.2 bits (74), Expect = 0.092
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 122 GGDITENDIIELFKPYGETQELFINKEK---MFGFIRMDYKHNADKAKAKLDGHVL--KG 176
G ++++ ++ LF+PYG+ +++ + + A AK L G L
Sbjct: 13 GPELSQEELYSLFRPYGKIKDITPPPPDSLPRYATVTFRRIRGAISAKNCLHGFELNEGK 72
Query: 177 RSLKIRFAPIN 187
L I++ P
Sbjct: 73 TRLHIQYEPKL 83
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 31.6 bits (72), Expect = 0.096
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 123 GDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR 182
G E DI +LF+P+G I K F F+ + +A KA L G + G L +
Sbjct: 10 GTTREEDIEKLFEPFGPLVRCDIRKT--FAFVEFEDSEDATKALEALHGSRIDGSVLTVE 67
Query: 183 FA 184
F
Sbjct: 68 FV 69
>gnl|CDD|146016 pfam03179, V-ATPase_G, Vacuolar (H+)-ATPase G subunit. This family
represents the eukaryotic vacuolar (H+)-ATPase
(V-ATPase) G subunit. V-ATPases generate an acidic
environment in several intracellular compartments.
Correspondingly, they are found as membrane-attached
proteins in several organelles. They are also found in
the plasma membranes of some specialised cells.
V-ATPases consist of peripheral (V1) and membrane
integral (V0) heteromultimeric complexes. The G subunit
is part of the V1 subunit, but is also thought to be
strongly attached to the V0 complex. It may be involved
in the coupling of ATP degradation to H+ translocation.
Length = 105
Score = 32.5 bits (75), Expect = 0.10
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 320 EHETEMLR--KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE 377
+ + L+ KE A++EI+ R + E E KE +AE R EL KK +E + ++ + +
Sbjct: 25 KRRAKRLKQAKEEAEKEIEEYRAQREAEFKEFEAEHSGSR-GELEKKIEKETEEKIDELK 83
Query: 378 EDLRRRQND 386
+ +
Sbjct: 84 RSFNKNKEA 92
>gnl|CDD|151313 pfam10864, DUF2663, Protein of unknown function (DUF2663). Some
members in this family of proteins are annotated as YpbF
however currently no function is known.
Length = 131
Score = 33.1 bits (76), Expect = 0.10
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRR 357
E E LR E+ Q+ D ++ W+ + R E +K+
Sbjct: 86 EKEFHALRCEIIQKSKDLWPKEESWKKRHRVFEMMKKE 123
>gnl|CDD|241132 cd12688, RRM1_PTBP1_like, RNA recognition motif 1 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM1 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
functions at several aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein and negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It may play
a role controlling differentiation in mammals. All
members in this family contain four RNA recognition
motifs (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 81
Score = 32.0 bits (73), Expect = 0.10
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKA 167
L++ NI D TE +II L P+G+ + + K K F+ M AD+ A
Sbjct: 3 LHIRNIPNDATEAEIIALGLPFGKVTNVLMLKGKNQAFLEM-----ADEEAA 49
>gnl|CDD|204935 pfam12474, PKK, Polo kinase kinase. This domain family is found in
eukaryotes, and is approximately 140 amino acids in
length. The family is found in association with
pfam00069. Polo-like kinase 1 (Plx1) is essential during
mitosis for the activation of Cdc25C, for spindle
assembly, and for cyclin B degradation. This family is
Polo kinase kinase (PKK) which phosphorylates Polo
kinase and Polo-like kinase to activate them. PKK is a
serine/threonine kinase.
Length = 142
Score = 33.5 bits (77), Expect = 0.10
Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 320 EHETEMLRKELAQR----EIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQ 375
+ +M ++ L + + E+ +E++ + +K EE +KH ++ + LA+
Sbjct: 62 KTRLKMFKESLKIEKKELKQEVEKLPRF---QEQEKKRMKAEKEEQEQKHQKQEREFLAK 118
Query: 376 QEED----LRRRQNDNSMFLVE 393
QEE+ L++ QN+ L E
Sbjct: 119 QEENLEEALQQLQNEKRHELAE 140
Score = 32.7 bits (75), Expect = 0.15
Identities = 23/119 (19%), Positives = 49/119 (41%), Gaps = 45/119 (37%)
Query: 312 WKQLHELYEHE-TEMLR---KELAQREIDRERQKAEWEMKERQAEELK------------ 355
+QL + + E T++L+ KEL Q E R++++ ++++RQ +EL+
Sbjct: 6 KEQLKDRFFLERTQLLKRHEKELEQLE--RQQKRTIEKLEQRQTQELRRLPKRIRAEQKT 63
Query: 356 ---------------------------RRDEELMKKHAEEMQLRLAQQEEDLRRRQNDN 387
++++ MK EE + + +QE + +Q +N
Sbjct: 64 RLKMFKESLKIEKKELKQEVEKLPRFQEQEKKRMKAEKEEQEQKHQKQEREFLAKQEEN 122
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 32.1 bits (73), Expect = 0.11
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAK 168
+++G I D+ E+ +I LF+ G E F + F + + + A A A
Sbjct: 2 SEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIAT 61
Query: 169 LDGHVL-KGRSLKIR 182
L + L +G L +
Sbjct: 62 LHNYELPEGCCLLVC 76
>gnl|CDD|218452 pfam05130, FlgN, FlgN protein. This family includes the FlgN
protein and export chaperone involved in flagellar
synthesis.
Length = 140
Score = 33.1 bits (76), Expect = 0.11
Identities = 24/116 (20%), Positives = 44/116 (37%), Gaps = 28/116 (24%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+ L EL E + E+L + +++ ERQ+ E+ + +
Sbjct: 33 EALEELTEEKQELLAQ---LEQLEEERQQLLAELGLSP-------GPAGLSELLAAEDEE 82
Query: 373 LAQQEEDLR------RRQNDNSMFLVEQ------------QQGRGGSGGYGSPGQA 410
L + ++L+ + N+ + L+EQ Q R SG YG+ GQ
Sbjct: 83 LRELWQELKELLEELQELNERNGRLLEQSLEFNQRLLNILQGARKPSGTYGADGQT 138
>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 = 31.9 bits (73), Expect = 0.11
Identities = 16/56 (28%), Positives = 26/56 (46%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR 247
V NL V + L F G+I ++ + +G SK VEF + + +AL+
Sbjct: 4 VSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59
>gnl|CDD|225381 COG2825, HlpA, Outer membrane protein [Cell envelope biogenesis,
outer membrane].
Length = 170
Score = 33.5 bits (77), Expect = 0.11
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 6/100 (6%)
Query: 293 QVGPRFATVNSFE--FEYGSRWKQLHELYEHETEMLRKEL--AQREIDRERQKAEWEMKE 348
Q P+ A VN F+ + K++ E E + +KEL Q+E+ + K + + K
Sbjct: 22 QAAPKIAIVN-LGRIFQESPQAKKVSADLESEFKKRQKELQKMQKELKAKEAKLQDDGKM 80
Query: 349 RQAEELKRRDEELMKKHAEEMQLRLAQQ-EEDLRRRQNDN 387
+ + + E+ K+ + Q+ E+DL RR+ +
Sbjct: 81 EALSDRAKAEAEIKKEKLVNAFNKKQQEYEKDLNRREAEE 120
Score = 28.5 bits (64), Expect = 6.0
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 16/82 (19%)
Query: 304 FEFEYGSRWKQLHELYEHETEMLRKEL---AQREIDRERQKAEWE-MKERQA-------- 351
E E+ R K+L ++ + E + +L + E +R KAE E KE+
Sbjct: 49 LESEFKKRQKELQKM-QKELKAKEAKLQDDGKMEALSDRAKAEAEIKKEKLVNAFNKKQQ 107
Query: 352 ---EELKRRDEELMKKHAEEMQ 370
++L RR+ E +K E++Q
Sbjct: 108 EYEKDLNRREAEEEQKLLEKIQ 129
>gnl|CDD|153351 cd07667, BAR_SNX30, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 30. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. The specific function of SNX30 is
still unknown. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 240
Score = 34.2 bits (78), Expect = 0.12
Identities = 35/139 (25%), Positives = 63/139 (45%), Gaps = 26/139 (18%)
Query: 273 IDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEY-----------GSRWKQLHELYEH 321
ID +++R I ++ + R+ GP ++T + E E G+ L EL E
Sbjct: 70 IDRIAQRIIKEEIEYLVELREYGPVYSTWSGLEGELAEPLEGVSACIGNCSTALEELTED 129
Query: 322 ETE----MLRKELAQREI------DRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQL 371
TE +LR+ + E R++ +AE+E K +A L++ + + E+ Q
Sbjct: 130 MTEDFLPVLREYILYSESMKNVLKKRDQVQAEYEAK-LEAVALRKEERPKVPTDVEKCQD 188
Query: 372 RL----AQQEEDLRRRQND 386
R+ A + D+ R QN+
Sbjct: 189 RVECFNADLKADMERWQNN 207
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
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. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR 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 AU-rich RNA element (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. .
Length = 84
Score = 31.9 bits (72), Expect = 0.12
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE--TQELFINK----EKMFGFIRMDYKHNADKAKAKL 169
LY+ + +T+ D+ ++F +G + +++ + FIR D + A++A
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 170 DGHVLKGRS--LKIRFA 184
+GH G S + ++FA
Sbjct: 63 NGHKPPGSSEPITVKFA 79
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 31.5 bits (71), Expect = 0.12
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
+L++GNI T ++ F+ YG E I K+ + F+ M+ +A +A LD
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--YAFVHMERAEDAVEAIRGLDNTEF 59
Query: 175 KGRSLKIR 182
+G+ + ++
Sbjct: 60 QGKRMHVQ 67
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 31.6 bits (72), Expect = 0.12
Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEK-MFGFIRMDYKHNADKAKAKLDGHVL 174
+++ +E +++ F +G + ++K+K ++ + D K DK ++ H L
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSE-PQHTL 63
Query: 175 KGRSLKIR 182
G L++R
Sbjct: 64 NGHRLRVR 71
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which 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 = 84
Score = 31.7 bits (72), Expect = 0.13
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 151 FGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
FGF+ K A A +DG VL G +L ++F+
Sbjct: 49 FGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFS 82
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains 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 effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 32.0 bits (73), Expect = 0.13
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 16/86 (18%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAKAK 168
+L++G I ++ E D+ LF+ +G+ EL + K+K G F+ + +A KA++
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66
Query: 169 L-DGHVLKGRSLKIRFAPINAAIKVK 193
L + L G +N I+VK
Sbjct: 67 LHEQKTLPG---------MNRPIQVK 83
>gnl|CDD|224555 COG1640, MalQ, 4-alpha-glucanotransferase [Carbohydrate transport
and metabolism].
Length = 520
Score = 34.6 bits (80), Expect = 0.13
Identities = 24/161 (14%), Positives = 50/161 (31%), Gaps = 39/161 (24%)
Query: 259 LRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL 318
L P+ ++ L + D L ++ + + + K L +
Sbjct: 79 LNPLYIDVEALPEFQDFLLDKDLQALPQLRALDWV---------DYAKVTALKRKALEKA 129
Query: 319 Y---------EHETEMLRKELAQ--------REIDRERQKAEWEMKERQAEELKRRDEE- 360
+ E + +E + A W++ + +RRD
Sbjct: 130 FANFKKRKEREKDFAAFCQEEGYWLDDYALFMALKEHFHAAGWQVWP---DSYRRRDLSA 186
Query: 361 ---LMKKHAEE------MQLRLAQQEEDLRRRQNDNSMFLV 392
++ HAEE +Q +Q L+R ND + ++
Sbjct: 187 VSAFIELHAEEVDFHRFLQWLFFRQLAALKRYANDMGIGII 227
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 31.6 bits (72), Expect = 0.13
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 115 RLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
RL++GN+ +++ D+ +F YGE + I + +GF++ D + A G +
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQ--IVLKNAYGFVQFDSPESCANAINCEQGKM 58
Query: 174 LKGRSL 179
++GR L
Sbjct: 59 IRGRKL 64
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 34.4 bits (79), Expect = 0.15
Identities = 23/65 (35%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 26 HFKIPEIEDMPF-MSLGGRGGGRGGG--VGGRGGYRGNRPDGRGSDMNESRMGGGGGGDR 82
HF I + P M L G GG GG G+ G R +G + E R GG G G R
Sbjct: 544 HFTRTRILNKPMNMQLLGDAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRR 603
Query: 83 YFTEK 87
+ E+
Sbjct: 604 FSGER 608
Score = 34.4 bits (79), Expect = 0.15
Identities = 21/68 (30%), Positives = 22/68 (32%), Gaps = 8/68 (11%)
Query: 440 GSAMDFDQGGRSGGG----GGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGPT 495
G A G R GGG G RR + RREGG G S G
Sbjct: 561 GDAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGR----RFSGERREGRAPRR 616
Query: 496 DYQPKRRN 503
D RR
Sbjct: 617 DDSTGRRR 624
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 31.8 bits (72), Expect = 0.15
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 116 LYLGNIG--GD---ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD 170
+Y+GN+ GD + E ++ + + YGE + + I +EK FI NA A L+
Sbjct: 5 VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQTLN 64
Query: 171 GHVLKGRSLKIRF 183
G ++I +
Sbjct: 65 GKKPYDTIVRINY 77
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 34.2 bits (79), Expect = 0.15
Identities = 18/72 (25%), Positives = 26/72 (36%), Gaps = 9/72 (12%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQL-------- 371
+ LR L+ E +R R +A + R EL ++ E Q+
Sbjct: 80 QDSVANLRASLSAAEAERSRLQALLAELAGAGAAAEGRAGELAQELDSEKQVSARALAQV 139
Query: 372 -RLAQQEEDLRR 382
L QQ LRR
Sbjct: 140 ELLNQQIAALRR 151
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 34.5 bits (80), Expect = 0.16
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEE------MQLR 372
++ LR ELA E + +A W+ ++ E + EL ++ +
Sbjct: 448 HDERLAELRAELAALEAELAALEARWQQEKELVEAILALRAELEADADAPADDDAALRAQ 507
Query: 373 LAQQEEDLRRRQNDNSM 389
LA+ E L Q + +
Sbjct: 508 LAELEAALASAQGEEPL 524
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 34.3 bits (79), Expect = 0.17
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
E E L EL ++ E E + EE +R E L KK E L ++ E L
Sbjct: 210 EIEALEAELKEQSEKYEDLAQEIAHLRNELEEAQRSLESLEKKFRSE-GGDLFEEREQLE 268
Query: 382 RRQ 384
R+
Sbjct: 269 RQL 271
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which 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 A0 contains 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 = 79
Score = 31.3 bits (71), Expect = 0.18
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQE--LFINKE----KMFGFIRMDYKHNADKAKA 167
C+L++G + +++ + F YG+ E + ++ + FGFI AD+A
Sbjct: 3 CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62
Query: 168 KLDGHVLKGRSLKIR 182
H + G ++++
Sbjct: 63 -AQPHSIDGNQIELK 76
>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 = 31.4 bits (72), Expect = 0.18
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKMFGFIR----MDYKH--NADKAKAKLDGHV 173
+ + E D+ + F +GE + L +N ++ GF++ ++Y+ A A L+G
Sbjct: 13 GVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKE 72
Query: 174 LKGRSLKIRFA 184
L G+++ + +A
Sbjct: 73 LLGQTISVDWA 83
>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 = 31.2 bits (71), Expect = 0.18
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
++++G + + TE I E F +G E+ + NK + F FI D + K +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI-LE 59
Query: 169 LDGHVLKGRSLKIRFA 184
HV+ G+ ++++ A
Sbjct: 60 TQFHVIGGKKVEVKKA 75
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 31.6 bits (71), Expect = 0.18
Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE--TQELFINKE----KMFGFIRMDYKHNADKAKAKL 169
L++ ++ + + D++++F P+G + ++FI+K+ K FGF+ D +A A +
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69
Query: 170 DGHVLKGRSLKIRF 183
+G + + LK++
Sbjct: 70 NGFQIGMKRLKVQL 83
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 31.2 bits (70), Expect = 0.19
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHNADKAKAKLDG 171
LY+GN+ D+TE I++LF G + + + + F+ +A + A ++G
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMNG 61
Query: 172 HVLKGRSLKIRFA 184
+ G+ +K+ +A
Sbjct: 62 RKIMGKEVKVNWA 74
>gnl|CDD|218970 pfam06278, DUF1032, Protein of unknown function (DUF1032). This
family consists of several conserved eukaryotic proteins
of unknown function.
Length = 565
Score = 34.2 bits (78), Expect = 0.19
Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 32/133 (24%)
Query: 286 PEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWE 345
+ + R+ GP FA + WK + E E + +MLR+ A+R + E QK
Sbjct: 322 EDARRSRRKGPTFADMEVL------YWKHVKERLETQRQMLRRRGAERWLPDEEQKLWPL 375
Query: 346 MKERQAEELK----------------------RRDEELMKKHAEEMQLRLAQQEEDLRRR 383
++R + ++ ++ AE M L+ E+L RR
Sbjct: 376 EEDRLEDSVEDDGDADDFSDPEDYLEPPEGLDPEEQAFQDLEAEAMPSSLSY--EELVRR 433
Query: 384 QNDNSMFLVEQQQ 396
D +F+ Q+
Sbjct: 434 NVD--LFIANSQK 444
>gnl|CDD|235850 PRK06669, fliH, flagellar assembly protein H; Validated.
Length = 281
Score = 33.5 bits (77), Expect = 0.19
Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 3/91 (3%)
Query: 296 PRFATVNSFEFE-YGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEEL 354
RF ++ E E ++ E E KE+ + + + E +E + E L
Sbjct: 25 YRFKVLSIKEKERLREEEEEQVEQLREEANDEAKEIIEEAEEDAFEIVEAAEEEAKEELL 84
Query: 355 KRRDEELMKKHAEEMQLRLAQQEEDLRRRQN 385
K+ DE E++Q+++ +++E+
Sbjct: 85 KKTDE--ASSIIEKLQMQIEREQEEWEEELE 113
>gnl|CDD|130728 TIGR01667, YCCS_YHJK, integral membrane protein, YccS/YhfK family.
This model represents two clades of putative
transmembrane proteins including the E. coli YccS and
YhfK proteins. The YccS hypothetical equivalog
(TIGR01666) is found in beta and gamma proteobacteria,
while the smaller YhfK group is only found in E. coli,
Salmonella and Yersinia. TMHMM on the 19 hits to this
model shows a consensus of 11 transmembrane helices
separated into two clusters, an N-terminal cluster of 6
and a central cluster of 5. This would indicate two
non-membrane domains one on each side of the membrane.
Length = 701
Score = 34.0 bits (78), Expect = 0.19
Identities = 27/114 (23%), Positives = 40/114 (35%), Gaps = 17/114 (14%)
Query: 286 PEFYKQ-RQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEW 344
P F + G R T++ Y + L H +L ELA E+ + +
Sbjct: 589 PAFNSHYLEDGFRLLTLSHTLLSY------ISALGAHRERLLNPELAA-ELLQACEIVAK 641
Query: 345 EMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGR 398
++ QA DEE + A M+ + Q ED LV QQ
Sbjct: 642 AIQRCQARL--EYDEEALAGDANIMEAQEMQPHEDAAGT-------LVYQQLQL 686
>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 = 31.2 bits (71), Expect = 0.19
Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
L++GN+ + + + F+ +G + + + FG++ + +A KA
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 169 LDGHVLKGRSLKIRFA 184
+DG L GR + + F+
Sbjct: 61 MDGKELDGRPINVDFS 76
Score = 30.0 bits (68), Expect = 0.54
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQA 244
V NL+ V +E L+ F FG + A VI D E G S+ G V+F A +A
Sbjct: 4 VGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA 57
>gnl|CDD|241221 cd12777, RRM1_PTBP1, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM1 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence shows that
the RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 81
Score = 31.1 bits (70), Expect = 0.20
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 123 GDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNAD 163
D+TE ++I L P+G+ L + K K F+ M+ + A+
Sbjct: 10 NDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMNTEEAAN 50
>gnl|CDD|144876 pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain. These
proteins contain several 22 residue repeats which form a
pair of alpha helices. This family includes:
Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein
E.
Length = 191
Score = 33.0 bits (76), Expect = 0.20
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 11/77 (14%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKE------RQAEELKRRDEELMKKHA 366
++ ETE LR+EL Q++++ R + + + E + EEL++R + +A
Sbjct: 26 QEFWARLSKETEALREEL-QKDLEDVRARLQPYLDELKAKVGQNLEELRQR----LAPYA 80
Query: 367 EEMQLRLAQQEEDLRRR 383
EE++ RL + E+LRR+
Sbjct: 81 EELRKRLNRDAEELRRK 97
Score = 31.4 bits (72), Expect = 0.72
Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 14/84 (16%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQA------EELKRR-DEEL---- 361
++L + + E LR++LA + R + ++ +A EEL+++ E L
Sbjct: 81 EELRKRLNRDAEELRRKLAP-YAEELRDRLRQNVEALRARLGPYVEELRQKLAERLEELK 139
Query: 362 --MKKHAEEMQLRLAQQEEDLRRR 383
+ +AEE + +L++Q E+LR +
Sbjct: 140 ESVGPYAEEYKAQLSEQVEELREK 163
Score = 28.3 bits (64), Expect = 7.8
Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 314 QLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRL 373
+L + E L++ + + + Q EEL+ + ++ +AE+++ +L
Sbjct: 126 ELRQKLAERLEELKESVGPYAEEYK------AQLSEQVEELREK----LEPYAEDLREKL 175
Query: 374 AQQEEDLRRR 383
EDL+++
Sbjct: 176 EPYAEDLKKQ 185
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 31.1 bits (71), Expect = 0.21
Identities = 11/23 (47%), Positives = 11/23 (47%)
Query: 162 ADKAKAKLDGHVLKGRSLKIRFA 184
KA LDG KGR L R A
Sbjct: 55 RQKALEILDGFKWKGRVLSARLA 77
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 31.1 bits (71), Expect = 0.21
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGE-TQELFI-----NKEKMFGFIRMDYK-H-NADK 164
NCRL++G I T+ +I+E F E ++ + +K K GF ++Y+ H A
Sbjct: 1 NCRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAM 60
Query: 165 AKAKL 169
A+ KL
Sbjct: 61 ARRKL 65
Score = 27.2 bits (61), Expect = 5.3
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 193 KNLTSCVTNELLELAFGVFGDIERAIVI--VDERGNSKCEGIVEFARKPAAAQALRRCAE 250
K T E+LE V + IV D++ ++ VE+ AAA A R+
Sbjct: 11 KTKTK---EEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARRKLVP 67
Query: 251 G 251
G
Sbjct: 68 G 68
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 30.9 bits (70), Expect = 0.21
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQAL 245
I V +L+ VT+ L AF F A V+ D + G S+ G V F + A A+
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAI 58
>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 = 30.8 bits (70), Expect = 0.23
Identities = 16/67 (23%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGR 177
D+T+ ++ LF+ G + I ++++ +GF+ +++A KA L+G ++ +
Sbjct: 11 DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNK 70
Query: 178 SLKIRFA 184
LK+ +A
Sbjct: 71 RLKVSYA 77
Score = 30.0 bits (68), Expect = 0.57
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 199 VTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQAL 245
+T E L F G IE ++ D G S G V++ + A +A+
Sbjct: 12 MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAI 59
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 33.7 bits (78), Expect = 0.25
Identities = 30/186 (16%), Positives = 45/186 (24%), Gaps = 46/186 (24%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQND 386
R + E+ E + E + RDE Q E + R
Sbjct: 139 RGAARKAGEGGEQPATEARADAAERTEEEERDER-----RRRGDREDRQAEAERGERGRR 193
Query: 387 NSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFD 446
E++ G + + +G D
Sbjct: 194 ------EERGRDGDDRDRRDRREQGDRR----------------------EERGRR---D 222
Query: 447 QGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRG----------GSGGGGPTD 496
G R G R A +R + G G RRG GG G +
Sbjct: 223 GGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNE 282
Query: 497 YQPKRR 502
+P+ R
Sbjct: 283 REPELR 288
>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 = 30.7 bits (70), Expect = 0.26
Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
LY+G + ++ E + F P+G+ +++ I K + F F+ + +A A +
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 170 DGHVLKGRSLKI 181
+ L GR++++
Sbjct: 61 NESELFGRTIRV 72
>gnl|CDD|240963 cd12519, RRM1_SREK1, RNA recognition motif 1 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subgroup corresponds to the RRM1 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), and is
involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 generally contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1; plays a modulatory role controlling SR
domain function by involvement in the inhibition of both
constitutive and alternative splicing and in the
selection of splice-site. .
Length = 80
Score = 30.8 bits (69), Expect = 0.28
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIE 215
I+V NL++ VT++ + FG GDIE
Sbjct: 2 IQVTNLSAAVTSDQMRTLFGFLGDIE 27
>gnl|CDD|179529 PRK03057, PRK03057, hypothetical protein; Provisional.
Length = 180
Score = 32.5 bits (74), Expect = 0.28
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 306 FEYGSRWKQLHELYEHETEMLRKELAQR-EIDRERQKAEWEMKERQAEELKRRDEELMKK 364
FE R KQ + Y ETE + E+ +R E+ R R + + + L R+D E ++
Sbjct: 117 FENVKRHKQ-FQKYAKETEQVLDEVLKRNEVSRLRMQID--------QALDRKDMEEFQR 167
Query: 365 HAEEMQ 370
E+++
Sbjct: 168 LTEKLK 173
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 33.4 bits (76), Expect = 0.28
Identities = 14/33 (42%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESR 73
GGR G GG G G G R DG G+D
Sbjct: 434 GGRSGPGGGSRSGSVG-GGGRRDGAGADGKPRP 465
Score = 30.7 bits (69), Expect = 2.1
Identities = 14/57 (24%), Positives = 15/57 (26%), Gaps = 1/57 (1%)
Query: 43 RGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRYFTEKIMAIQGPTLDLP 99
RGGGR G GG GR R E A G +
Sbjct: 432 RGGGRSGPGGGSRSGSVG-GGGRRDGAGADGKPRPRRKPRVEGEADAAAAGAETPVV 487
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 33.5 bits (77), Expect = 0.28
Identities = 29/90 (32%), Positives = 43/90 (47%), Gaps = 10/90 (11%)
Query: 303 SFEFEYGSRWKQLHELY---------EHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
S E E R K+L Y E E E KEL + E + ++ E E++ EE
Sbjct: 586 SVE-ELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEE 644
Query: 354 LKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
L++ EEL KK++EE L ++ +L R
Sbjct: 645 LRKELEELEKKYSEEEYEELREEYLELSRE 674
Score = 31.2 bits (71), Expect = 1.5
Identities = 27/96 (28%), Positives = 44/96 (45%), Gaps = 14/96 (14%)
Query: 307 EYGSRWKQLHELYEHETEMLR---KELAQREIDR---ERQKAEWEMKERQAEELKRRDEE 360
E + +L E YE + LR K L++ E + E + E E KE + EELK++ +E
Sbjct: 290 EKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKE 349
Query: 361 LMKKHAE--------EMQLRLAQQEEDLRRRQNDNS 388
L K+ E E ++ E L++R +
Sbjct: 350 LEKRLEELEERHELYEEAKAKKEELERLKKRLTGLT 385
Score = 28.5 bits (64), Expect = 9.5
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 310 SRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM 369
K+L EL E E E L KEL E + + + + E + EELK+ EEL +K E
Sbjct: 228 KEVKELEELKE-EIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELK 286
Query: 370 QLR 372
+L+
Sbjct: 287 ELK 289
>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 = 30.7 bits (70), Expect = 0.29
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKL 169
R+++G I D TE ++ + F +G +++ I + K +GF+ + + +A+K A +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILA-M 62
Query: 170 DGHVLKGRSLKIRFA 184
+G+ L I A
Sbjct: 63 GNLNFRGKKLNIGPA 77
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 30.3 bits (69), Expect = 0.30
Identities = 18/69 (26%), Positives = 39/69 (56%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
N +++G + +TE+++ LF P+GE + I K GF++ ++ A+ A +L G
Sbjct: 1 NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60
Query: 173 VLKGRSLKI 181
++ G +++
Sbjct: 61 IIGGSRIRL 69
Score = 28.8 bits (65), Expect = 1.2
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
N + V L VT + L FG FG+I + K G V+F + AA A+
Sbjct: 1 NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP-----GKGCGFVQFVHRAAAEAAI 54
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 33.3 bits (77), Expect = 0.32
Identities = 21/102 (20%), Positives = 49/102 (48%), Gaps = 12/102 (11%)
Query: 305 EFEYGSRWKQLHELYEHETEMLRKELAQR------EIDRERQKAEWEMKERQAEELKRRD 358
E E + ++ L E E L++EL ++ E D+ ++AE E ++ +E K+
Sbjct: 529 ERELEQKAEEAEAL-LKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQA-IKEAKKEA 586
Query: 359 EELMKKHAEEMQLRL----AQQEEDLRRRQNDNSMFLVEQQQ 396
+E++K+ + + A + + R+R N + ++++
Sbjct: 587 DEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKK 628
Score = 30.6 bits (70), Expect = 2.2
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 330 LAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEE 378
L + E + E++ E E ++AE+LK EE +K EE L + E+
Sbjct: 525 LEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEK 573
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 32.3 bits (73), Expect = 0.33
Identities = 14/62 (22%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQND 386
R+EL +R ++ ER++ + + +E Q E+ + R+E+ +++ +++ + + +Q+E +D
Sbjct: 135 REELEER-MEWERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDESETESDDD 193
Query: 387 NS 388
+
Sbjct: 194 KT 195
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC 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 AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. 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. .
Length = 84
Score = 30.9 bits (69), Expect = 0.33
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGR 177
++T+ + LF GE + + ++K+ +GF+ ++ADKA L+G L+ +
Sbjct: 14 NMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTK 73
Query: 178 SLKIRFA 184
++K+ +A
Sbjct: 74 TIKVSYA 80
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 32.8 bits (75), Expect = 0.34
Identities = 10/49 (20%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEE 368
+ + ++ + +++ +RE+++ E E+++R A+E + EE ++ A++
Sbjct: 99 QRQKKLQKLLEEKQKQEREKEREEAELRQRLAKE---KYEEWCRQKAQQ 144
Score = 32.8 bits (75), Expect = 0.37
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 327 RKELAQREIDRERQKA--EWEMKERQAEELKR-RDEELMKKHAEEMQLRLAQQEE 378
+ + E +K EWE+K+ + ++ KR + +K +E + R + EE
Sbjct: 168 SAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEEERKQKAEE 222
>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 = 30.6 bits (69), Expect = 0.35
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAKL 169
++ + N+ + T+ D+ LF YG+ + + F + F F+ A A L
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNAL 61
Query: 170 DGHVLKGRSLKIRFA 184
L GR L +++A
Sbjct: 62 KDTHLLGRRLVLQYA 76
>gnl|CDD|204032 pfam08703, PLC-beta_C, PLC-beta C terminal. This domain
corresponds to the alpha helical C terminal domain of
phospholipase C beta.
Length = 181
Score = 32.1 bits (73), Expect = 0.37
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 15/87 (17%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER---QAEELKRRDEELMKKHAEEM 369
K+L E+ E E KEL ++++DR+R + E K + E K E+ + H +E+
Sbjct: 55 KKLKEISEKEK----KEL-KKKLDRKRLERIQEAKTKEKHAQEREKT---EINRSHIQEV 106
Query: 370 QLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
+ + EE +RRQ L E+Q
Sbjct: 107 VQSIKRLEEAQKRRQEK----LEEKQA 129
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 33.4 bits (76), Expect = 0.37
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQ 376
+ + E E L KEL + EI RE ++ E E E+ E+L++ +EEL+ K E + +
Sbjct: 332 KKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAA 391
Query: 377 EE 378
+
Sbjct: 392 KL 393
Score = 29.9 bits (67), Expect = 4.0
Identities = 19/70 (27%), Positives = 29/70 (41%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
K +L + E E+L K+ + E K + E E + EE K L EE L+
Sbjct: 364 KLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLK 423
Query: 373 LAQQEEDLRR 382
++EE
Sbjct: 424 EEKKEELKIV 433
Score = 28.8 bits (64), Expect = 9.0
Identities = 13/69 (18%), Positives = 27/69 (39%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
E RK + ++ ++ + KE + E+ + + E K E + ++EE
Sbjct: 302 ELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQ 361
Query: 380 LRRRQNDNS 388
L + Q
Sbjct: 362 LEKLQEKLE 370
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, 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 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 30.4 bits (68), Expect = 0.37
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
+ I V NL V + L+ F + G ++RA + D+ G S+ G V F + A QA+
Sbjct: 1 STIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAI 58
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 31.9 bits (73), Expect = 0.37
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 296 PRFATV--NSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRER---QKAEWEMKER- 349
PRF ++ ++ +K L + E E E L K L + + E+ ++ MK R
Sbjct: 36 PRFDSLSGKLNLDKFRKNYKFLDDYREKEIEELEKALKKTKDSEEKEELKRTLQSMKSRL 95
Query: 350 QAEELKRRDEELMKKH-AEEMQLRL 373
+ + K R+ E++K+H +E +L
Sbjct: 96 KTLKNKDREREILKEHKKQEKELIK 120
>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1. This is
the N-terminal 200 residues of a set of proteins
conserved from yeasts to humans. Most of the proteins in
this entry have an RhoGEF pfam00621 domain at their
C-terminal end.
Length = 158
Score = 32.0 bits (73), Expect = 0.37
Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
Q E+ E E+LR++ + ER+K + E++ E E+ +++ +E+Q +
Sbjct: 45 NQELEV---ELELLREDNERLSTQYEREKELRKQAEQKLLEF----EDELEQEKKELQKK 97
Query: 373 LAQQEEDLRRRQNDNS 388
+ EE++R+ +
Sbjct: 98 IEDLEENVRQLELKAK 113
>gnl|CDD|205436 pfam13256, DUF4047, Domain of unknown function (DUF4047). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
130 amino acids in length. There are two conserved
sequence motifs: TEA and FPKT.
Length = 123
Score = 31.4 bits (71), Expect = 0.39
Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKA-EWEMKERQAEELKRRDEELMKKHAEEMQL 371
KQ ++ HE E ++KE+ I+ Q+ W ++ E + E ++K E++
Sbjct: 37 KQHEKVILHEYEGMKKEVKATSIEVLEQRLVSW----KEQREKVAVEREALQKIYTEIED 92
Query: 372 RLAQQEEDLRRRQNDNS 388
Q +E+L+ ++++S
Sbjct: 93 YYNQSQEELKVEKSESS 109
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 30.2 bits (68), Expect = 0.40
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
V NL V+N+ L FG +G+I+ + E N + +EF +A AL+
Sbjct: 6 VFNLDPSVSNDDLHQIFGAYGEIKE----IRETPNKRHHKFIEFYDVRSAEAALK 56
Score = 26.3 bits (58), Expect = 8.8
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKMF-GFIRMDYKHNADKAKAKLDGHVLKGRS 178
N+ ++ +D+ ++F YGE +E+ K FI +A+ A L+ + G+
Sbjct: 8 NLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSEIAGKR 67
Query: 179 LKI 181
+K+
Sbjct: 68 IKL 70
>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 = 30.4 bits (69), Expect = 0.41
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 117 YLGNIGGDITENDIIELFKPYGETQELFIN----KEKMFGFIRMDYKHNADKAKA-KLDG 171
++G I G ++E+D+ E F GE + + F F+ ++ A L G
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFV--EFADAESALSALNLSG 61
Query: 172 HVLKGRSLKI 181
+L G L++
Sbjct: 62 TLLGGHPLRV 71
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is 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 = 83
Score = 30.3 bits (69), Expect = 0.42
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 116 LYLGNIGGDITENDIIELFKPYG---ETQELFINKE----KMFGFIRMDYKHNADKAKAK 168
L++GN+ ++ E + + F +G +T ++ + + K F FI D +D A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 169 LDGHVLKGRSLKIRFA 184
++G L R + + +A
Sbjct: 64 MNGQYLCNRPITVSYA 79
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as
well as induction of apoptosis. .
Length = 75
Score = 30.1 bits (67), Expect = 0.42
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE---TQELF---INKEKMFGFIRMDYKHNADKAKAKL 169
LY+ + T+ D+++L +PYG+ T+ + NK K +GF+ D A KA L
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63
>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 = 30.0 bits (68), Expect = 0.42
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 124 DITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGR 177
TE D+ + F +GE + + K+ K FGF+R + D+ K H++ GR
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVR--FADYEDQVKVLSQRHMIDGR 67
Query: 178 SLKIR 182
++
Sbjct: 68 WCDVK 72
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 30.0 bits (68), Expect = 0.43
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE--TQELFINKE----KMFGFIRMDYKHNADKAKAKL 169
L++ + D+ +LF YG+ ++ N + FGF+ M A K L
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 170 DGHVLKGRSLKI 181
L GR + +
Sbjct: 62 HRTELHGRVISV 73
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 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. 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 = 76
Score = 30.0 bits (68), Expect = 0.44
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQE--LFINKEKM---FGFIRMDYKHNADKAKAKL 169
RL + N+ I E+ + +LF+ +G + L K+ FGF+ + A KA
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHF 61
Query: 170 DG 171
+
Sbjct: 62 NN 63
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM1 of FCA, a gene controlling
flowering time in Arabidopsis, encoding a flowering time
control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains), and
a WW protein interaction domain. .
Length = 80
Score = 30.3 bits (68), Expect = 0.46
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKA 165
+L++G++ ITE ++ +F+ +G E+ I K+K G F++ + AD+A
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA 57
>gnl|CDD|180700 PRK06800, fliH, flagellar assembly protein H; Validated.
Length = 228
Score = 32.2 bits (73), Expect = 0.47
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 305 EFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKK 364
E E ++ HE + + L KEL Q + +E+QK E E ++ A+ + + +E +++
Sbjct: 29 EVEVEEEIQKDHEELLAQQKSLHKELNQ--LRQEQQKLERERQQLLAD--REQFQEHVQQ 84
Query: 365 HAEEMQL-RLAQQEE 378
+E++ R Q+E
Sbjct: 85 QMKEIEAARQQFQKE 99
>gnl|CDD|184064 PRK13461, PRK13461, F0F1 ATP synthase subunit B; Provisional.
Length = 159
Score = 31.6 bits (72), Expect = 0.47
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 321 HETEMLRKELAQREIDRERQKAEWEMKERQAEEL 354
HE L E A+ E RE++KAE+E+K QA +L
Sbjct: 96 HEEADLIIERAKLEAQREKEKAEYEIK-NQAVDL 128
>gnl|CDD|236815 PRK10997, yieM, hypothetical protein; Provisional.
Length = 487
Score = 32.6 bits (75), Expect = 0.48
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 22/82 (26%)
Query: 313 KQLH-ELYEHETEMLRKELAQR-EIDRERQK--AE--------WEMKERQAEELKRRDEE 360
L+ +L E E E L EL QR + + + AE W+M A +LKR D +
Sbjct: 145 TTLNQQLLEQEREQLLAELQQRMTLSGQLEPVLAENDEAAGRLWDM---SAGQLKRGDYQ 201
Query: 361 LMKKHAE------EMQLRLAQQ 376
L+ ++ E E+Q +LA+Q
Sbjct: 202 LIVQYGEFLKQQPELQ-KLAEQ 222
>gnl|CDD|218336 pfam04935, SURF6, Surfeit locus protein 6. The surfeit locus
protein SURF-6 is shown to be a component of the
nucleolar matrix and has a strong binding capacity for
nucleic acids.
Length = 206
Score = 31.9 bits (73), Expect = 0.50
Identities = 14/59 (23%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 323 TEMLRKELAQREIDRERQKAEWEM-----KERQAEELKRRDEELMKKHAEEMQLRLAQQ 376
++L+K L ++E +++ K EW+ ++++AE K+R+E L K+ ++ + +
Sbjct: 141 EKLLKKALKRKEKQKKKSKKEWKERKEKVEKKKAERQKKREENLKKRKDDKKNKKKKKA 199
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 32.0 bits (73), Expect = 0.52
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 310 SRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM 369
RW++L EL E + L + L ++ R+ E ++E++ L D + EE+
Sbjct: 86 QRWEELRELAEERRQRLEEALDLQQFFRDADDLEQWLEEKE-AALASEDLGKDLESVEEL 144
Query: 370 QLRLAQQEEDLRRRQND 386
+ + EE+L +
Sbjct: 145 LKKHKELEEELEAHEPR 161
>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 = 30.0 bits (68), Expect = 0.52
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
LY+ N+ +D+ LF YG +++I + + F +++ + +A+ A L
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 170 DGHVLKGRSLKIRFA 184
D GR ++I+FA
Sbjct: 63 DRTRFLGREIEIQFA 77
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 32.4 bits (74), Expect = 0.52
Identities = 20/121 (16%), Positives = 38/121 (31%), Gaps = 11/121 (9%)
Query: 267 LELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE--HETE 324
+L + L + + V + + +F E L E
Sbjct: 21 RQLLLRLGRLEQM--------LGELAAVLEQLLLLLAFRAEAEQLRTFARSLQALNLELI 72
Query: 325 MLRKELAQREIDRERQKAE-WEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
EL R + Q E ++ +L +EL + EE+ RLA+ + ++
Sbjct: 73 QELNELKARLQQQLLQSREQLQLLIESLAQLSSEFQELANEIFEELNRRLAELNQQNLKQ 132
Query: 384 Q 384
Sbjct: 133 L 133
>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 = 29.9 bits (68), Expect = 0.53
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
+Y+GN+ +TE + ELF G + I K+++ +GF+ + +AD A +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 170 DGHVLKGRSLKIR 182
+ L G+ +++
Sbjct: 61 NMIKLYGKPIRVN 73
>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 = 29.6 bits (67), Expect = 0.53
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAI-VIVDERGNSKCEGIVEFARKPAAAQALRR 247
IK+KN+ VT + F E+ I ++ D+ G + E VEF + A +A R
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERL 60
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It 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. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 30.2 bits (67), Expect = 0.54
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE---TQELF---INKEKMFGFIRMDYKHNADKAKAKL 169
LY+ + T+ D+I+L +PYG+ T+ + N+ K +GF+ D A KA A L
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66
Query: 170 DGHVLKGRSLK 180
+ ++ + K
Sbjct: 67 KANGVQAQMAK 77
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 31.5 bits (72), Expect = 0.55
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 312 WKQLHELYEHETEMLRKEL--AQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEM 369
K + E E + L+ EL ++E+ +E QK + + E K + +EL +K +E+
Sbjct: 33 GKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQK-QQEL 91
Query: 370 QLRLAQQEEDLRRRQN 385
Q + +++L+++Q
Sbjct: 92 QQKQQAAQQELQQKQQ 107
Score = 30.7 bits (70), Expect = 1.1
Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 324 EMLRKELA--QREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
+ L KE Q E+ ++ ++ + E ++ Q + +E + Q L Q++++L+
Sbjct: 38 KQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEA-----RKAKQQELQQKQQELQ 92
Query: 382 RRQNDNSMFLVEQQQ 396
++Q L ++QQ
Sbjct: 93 QKQQAAQQELQQKQQ 107
Score = 29.1 bits (66), Expect = 3.1
Identities = 14/64 (21%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 322 ETEMLRKEL--AQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
E + KEL ++++ ++ E ++ + +EL+++ +EL +K + Q L Q++++
Sbjct: 50 ELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQELQQK-QQAAQQELQQKQQE 108
Query: 380 LRRR 383
L +
Sbjct: 109 LLQP 112
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM3 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB 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. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 29.9 bits (68), Expect = 0.55
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 124 DITENDIIELFKPYGETQE---LFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK 180
+T + + LF YG+ LF K+ I+M A A L+G L G+ L+
Sbjct: 11 MVTPDALFTLFGVYGDVVRVKILFNKKDT--ALIQMADPQQAQTALTHLNGIRLHGKKLR 68
Query: 181 I 181
+
Sbjct: 69 V 69
>gnl|CDD|205150 pfam12925, APP_E2, E2 domain of amyloid precursor protein. The E2
domain is the largest of the conserved domains of the
amyloid precursor protein. The structure of E2 consists
of two coiled-coil sub-structures connected through a
continuous helix, and bears an unexpected resemblance to
the spectrin family of protein structures.E 2 can
reversibly dimerise in solution, and the dimerisation
occurs along the longest dimension of the molecule in an
antiparallel orientation, which enables the N-terminal
substructure of one monomer to pack against the
C-terminal substructure of a second monomer. The high
degree of conservation of residues at the putative dimer
interface suggests that the E2 dimer observed in the
crystal could be physiologically relevant. Heparin
sulfate proteoglycans, the putative ligands for the
precursor present in extracellular matrix, bind to E2 at
a conserved and positively charged site near the dimer
interface.
Length = 193
Score = 31.6 bits (72), Expect = 0.60
Identities = 27/92 (29%), Positives = 36/92 (39%), Gaps = 18/92 (19%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKA---EWEMKERQAEELKRRD---EELMKK----HA 366
E EHE + E RER EWE E Q + L + D +LM+K
Sbjct: 21 EDNEHE-RYKEAKKRLEEKHRERMTQVMKEWEEAESQYKNLPKADPKAAQLMRKELTERF 79
Query: 367 EEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGR 398
+E L Q+ R++ LVE Q R
Sbjct: 80 QETVQTLEQEAAAERQQ-------LVETHQQR 104
>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 = 29.9 bits (67), Expect = 0.61
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
L++ NI D D+ F YG ++++ + + F +++ + +A+ A L
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 170 DGHVLKGRSLKIRFA 184
D + GR ++I+FA
Sbjct: 63 DRKWICGRQIEIQFA 77
>gnl|CDD|188709 cd08755, RGS_p115RhoGEF, Regulator of G protein signaling (RGS)
domain found in the Rho guanine nucleotide exchange
factor (GEF), p115 RhoGEF. The RGS (Regulator of
G-protein Signaling) domain is an essential part of the
p115RhoGEF protein, a member of the RhoGEF (Rho guanine
nucleotide exchange factor) subfamily of the RGS protein
family. The RhoGEFs are peripheral membrane proteins
that regulate essential cellular processes, including
cell shape, cell migration, cell cycle progression of
cells, and gene transcription by linking signals from
heterotrimeric G-alpha12/13 protein-coupled receptors to
Rho GTPase activation, leading to various cellular
responses, such as actin reorganization and gene
expression. The RhoGEF subfamily includes p115RhoGEF,
LARG, PDZ-RhoGEF and its rat specific splice variant
GTRAP48. The RGS domain of RhoGEFs has very little
sequence similarity with the canonical RGS domain of the
RGS proteins and is often refered to as RH (RGS
Homology) domain. In addition to being a G-alpha13/12
effector, the p115RhoGEF protein also functions as a
GTPase-activating protein (GAP) for G-alpha13. RGS
proteins play critical regulatory role as GTPase
activating proteins (GAPs) of the heterotrimeric
G-protein G-alpha-subunits. RGS proteins play critical
regulatory role as GTPase activating proteins (GAPs) of
the heterotrimeric G-protein G-alpha-subunits. RGS
proteins regulate many aspects of embryonic development
such as glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 193
Score = 31.4 bits (71), Expect = 0.62
Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 9/52 (17%)
Query: 328 KELAQREIDRERQKAEWEMKERQ-AEELKRRDEELMKKHAEEMQLRLAQQEE 378
+EL E R + E KE+ AE L L EM + EE
Sbjct: 119 RELNDLESHRPTDRIPMEAKEKAVAESL------LE--KLVEMNPTIVPDEE 162
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 32.3 bits (74), Expect = 0.63
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 7/92 (7%)
Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKH----A 366
+ + E L ++L + + + E +AE E E + EEL+ R EEL ++ +
Sbjct: 327 ELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRS 386
Query: 367 EEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGR 398
+ QL L + + + +E+ + R
Sbjct: 387 KVAQLELQIASLNNEIERLEA---RLERLEDR 415
Score = 32.0 bits (73), Expect = 0.96
Identities = 26/121 (21%), Positives = 44/121 (36%), Gaps = 7/121 (5%)
Query: 278 ERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDR 337
E I + E Y + + + R L E L + ++ +
Sbjct: 280 EEEIEELQKELYALAN---EISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELA 336
Query: 338 ERQKAEWEMKERQAEELKRRDEELMKKHA--EEMQLRLAQQEEDLRRRQNDNSMFLVEQQ 395
E E E EEL+ + EL + A EE++ RL + EE L ++ + +E Q
Sbjct: 337 EELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSK--VAQLELQ 394
Query: 396 Q 396
Sbjct: 395 I 395
Score = 30.4 bits (69), Expect = 2.9
Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 10/94 (10%)
Query: 314 QLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKK--------- 364
++ EL E LRKEL + E + E+ + E E RQ L++ L +
Sbjct: 692 KIAEL-EKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIA 750
Query: 365 HAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGR 398
+ L + E+L R + L E +
Sbjct: 751 QLSKELTELEAEIEELEERLEEAEEELAEAEAEI 784
>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 = 29.5 bits (67), Expect = 0.63
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYG-----ETQELFINKEKMFGFIRMDYKHNADKAKAKLD 170
+++ N+ +T D+ +LF+ G + + + K FG + + +A +A +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 171 GHVLKGRSLKIR 182
G+ L+GR L++R
Sbjct: 61 GYDLEGRELEVR 72
Score = 27.6 bits (62), Expect = 3.5
Identities = 21/57 (36%), Positives = 28/57 (49%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
I V+NL VT + L+ F G++ RA V D G SK G V F A +A+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIE 57
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 30.8 bits (70), Expect = 0.69
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 339 RQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ 384
R+ KE AE+ K ++E MK AE + R +++ +
Sbjct: 73 RRDKLKAKKEE-AEKEKEKEERFMKALAEAEKERAELEKKKAEAKL 117
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
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. MSSP-1 contains 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 as
well as induction of apoptosis. .
Length = 86
Score = 29.8 bits (66), Expect = 0.70
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE---TQELF---INKEKMFGFIRMDYKHNADKAKAKL 169
LY+ + + T+ D+++L +PYG+ T+ + NK K +GF+ D A KA + L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69
Query: 170 DGHVLKGRSLK 180
++ + K
Sbjct: 70 KASGVQAQMAK 80
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 31.9 bits (73), Expect = 0.73
Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 9/95 (9%)
Query: 273 IDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQ 332
+ L E T E Y+ ++ NS E K++HE +E E K+
Sbjct: 272 LQELKETT-ENLLYENYRTEKLSGL---KNSGEPSL----KEIHEARLNEEERELKKKFT 323
Query: 333 REIDRERQKAEWEMKERQAEELKRRDEELMKKHAE 367
+I RE++K E+++ EE K + +L + +
Sbjct: 324 EKI-REKEKRLEELEQNLIEERKELNSKLEEIQKK 357
>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 = 29.6 bits (67), Expect = 0.73
Identities = 19/55 (34%), Positives = 27/55 (49%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
V NL+ + LE F G++ + D+ G SK G VEFA + A +AL
Sbjct: 4 VGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE 58
Score = 29.2 bits (66), Expect = 1.1
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKL 169
L++GN+ ++D+ E FK GE ++ I + K FG + + A KA K
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK- 59
Query: 170 DGHVLKGRSLKIRFA 184
G L GR +++ A
Sbjct: 60 SGEELLGREIRVDLA 74
>gnl|CDD|241129 cd12685, RRM_RBM20, RNA recognition motif of vertebrate RNA-binding
protein 20 (RBM20). This subfamily corresponds to the
RRM of RBM20, an alternative splicing regulator
associated with dilated cardiomyopathy (DCM). It
contains only one copy of RNA-recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 29.6 bits (66), Expect = 0.75
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 123 GDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNAD 163
G TEND+I L P+G+ + K F+ M Y A
Sbjct: 11 GSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQ 51
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48
(RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 30.0 bits (68), Expect = 0.76
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 127 ENDIIELFKPYGETQELFINKE---KMFG---FIRMDYKHNADKAKAKLDGHVLKGRSLK 180
E +++ELF YG +E + E + F I+ + +A AK KLD G L
Sbjct: 24 EKELLELFALYGTIEEYRLLDEYPCEEFTEVYLIKFETIQSARFAKRKLDERSFFGGLLH 83
Query: 181 IRFAP 185
+ +AP
Sbjct: 84 VCYAP 88
>gnl|CDD|147523 pfam05384, DegS, Sensor protein DegS. This is small family of
Bacillus DegS proteins. The DegS-DegU two-component
regulatory system of Bacillus subtilis controls various
processes that characterize the transition from the
exponential to the stationary growth phase, including
the induction of extracellular degradative enzymes,
expression of late competence genes and down-regulation
of the sigma D regulon. The family also contains one
sequence from Thermoanaerobacter tengcongensis which is
described as a sensory transduction histidine kinase.
Length = 159
Score = 31.0 bits (71), Expect = 0.77
Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 17/92 (18%)
Query: 322 ETEMLRKELAQ--REIDRERQKAE-WEMKERQA--------EELKRRDEELMKK---HAE 367
E E L +EL + E+ ++ + E +ER+A + EE +++ A
Sbjct: 28 EYERLEQELEEVKEEVSEVIKEVDKLEKQERRARKRLAEVSRNFDKYSEEDIREAYEKAH 87
Query: 368 EMQLRLA---QQEEDLRRRQNDNSMFLVEQQQ 396
++Q++LA Q+E+ LR+R+++ L ++
Sbjct: 88 DLQVKLALLRQEEKQLRKRRDELERRLKNLKE 119
Score = 28.7 bits (65), Expect = 4.6
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 11/78 (14%)
Query: 317 ELYEHETEMLRKELAQREIDRERQK-AEWEMKE--RQAEEL------KRRDEELMKKHAE 367
+ E + RK LA E+ R K +E +++E +A +L R++E+ ++K +
Sbjct: 51 DKLEKQERRARKRLA--EVSRNFDKYSEEDIREAYEKAHDLQVKLALLRQEEKQLRKRRD 108
Query: 368 EMQLRLAQQEEDLRRRQN 385
E++ RL +E + R +N
Sbjct: 109 ELERRLKNLKETIERAEN 126
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 29.4 bits (66), Expect = 0.79
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD 170
++ GN D +++I LF YG ++ + F F+ M+ + +A+ A LD
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDR--VDMKSGFAFVYMEDERDAEDAIRGLD 55
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 31.8 bits (72), Expect = 0.84
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 314 QLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMK-KHAEEMQLR 372
+L EL E E + L EL + + ++E+ + E R+ R + +L + E+Q
Sbjct: 85 ELEEL-EKEDDDLDGELVELQEEKEQLENEELQYLREYNLFDRNNLQLEDNLQSLELQYE 143
Query: 373 LAQQEEDLRRRQN 385
+ + D R+ N
Sbjct: 144 YSLNQLDKLRKTN 156
Score = 30.2 bits (68), Expect = 2.5
Identities = 20/70 (28%), Positives = 28/70 (40%), Gaps = 7/70 (10%)
Query: 320 EHETEMLRKELAQ--REIDRERQKAEWEMKERQ--AEELKRRDEELMKKHAEEMQLRLAQ 375
E L EL + +E +R + E KE EL EE + EE+Q
Sbjct: 62 ISNYEALDSELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENEELQY---L 118
Query: 376 QEEDLRRRQN 385
+E +L R N
Sbjct: 119 REYNLFDRNN 128
Score = 29.1 bits (65), Expect = 5.7
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMK-KHAEEMQL 371
+L EL + E +L + E+++E + E+ E Q E+ + +EEL +
Sbjct: 70 SELDELKKEEERLLDELE---ELEKEDDDLDGELVELQEEKEQLENEELQYLREYNLFDR 126
Query: 372 RLAQQEEDLR 381
Q E++L+
Sbjct: 127 NNLQLEDNLQ 136
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 29.2 bits (66), Expect = 0.85
Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 129 DIIE-LFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR 182
I+E +F +G ++++ K +G+ + + +A++A L G + G LK+
Sbjct: 14 YILEDVFCRFGGLIDVYLVPGKNYGYAKYADRESAERAITTLHGKEVNGVKLKVM 68
>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 = 31.5 bits (72), Expect = 0.86
Identities = 15/47 (31%), Positives = 16/47 (34%), Gaps = 7/47 (14%)
Query: 448 GGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGP 494
GGR GGG R +SS G G G G G P
Sbjct: 5 GGRIGGGSFRAPSRSSSSPRSSSPGGG-------GYYGSPGGGFGFP 44
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a 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. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
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 AU-rich RNA element (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. .
Length = 81
Score = 29.3 bits (65), Expect = 0.88
Identities = 15/67 (22%), Positives = 38/67 (56%), Gaps = 6/67 (8%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGR 177
++T++++ LF GE + + ++K+ +GF+ +A++A L+G L+ +
Sbjct: 12 NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSK 71
Query: 178 SLKIRFA 184
++K+ +A
Sbjct: 72 TIKVSYA 78
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 29.5 bits (67), Expect = 0.89
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 116 LYLGNIGGDITENDIIELFKPY-GETQELFINKEKM-FGFIRMDYKHNADKAKAKLDGHV 173
L++ N+G + TE ++ +LF G + NK F+ + A +A L G V
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPVCFVEFEDVSFATQALNSLQGAV 64
Query: 174 L 174
L
Sbjct: 65 L 65
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 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 the 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. Also included in this subfamily is 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 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 RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 29.5 bits (66), Expect = 0.90
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE--TQELFINK----EKMFGFIRMDYKHNADKAKAKL 169
LY+ + +T+ ++ +LF YG T + ++ + GFIR D + A++A L
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 170 DGHVLKGRS--LKIRFA 184
+G +G S + ++FA
Sbjct: 63 NGQKPEGASEPITVKFA 79
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 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 = 80
Score = 29.2 bits (66), Expect = 0.90
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 190 IKVKNLTSCVTNELLELAF-GVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQALRR 247
I V +L VT+ +L+ F + + A V++D G SK G V F + +AL
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 248 CAEGCFFLTQSLRPVIVEP 266
G + S RP+ V P
Sbjct: 64 M-NGVYC---SSRPMRVSP 78
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form of
the carboxy-terminal domain (CTD) of the largest subunit
of RNA polymerase II (pol II). The pol II CTD plays a
role in coupling transcription and pre-mRNA processing.
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 29.2 bits (65), Expect = 0.91
Identities = 16/69 (23%), Positives = 35/69 (50%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
L++G + T+ D+ LF+ +G+ + + + + ++ M ++ +A +A KL K
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSSGSYK 64
Query: 176 GRSLKIRFA 184
S I+ A
Sbjct: 65 IGSKVIKIA 73
>gnl|CDD|227900 COG5613, COG5613, Uncharacterized conserved protein [Function
unknown].
Length = 400
Score = 31.5 bits (71), Expect = 0.94
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 323 TEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLA 374
T L E AQ + D + A+ + +R E LK + ++K EEM+ A
Sbjct: 325 TTALNAEAAQLQADSQLAAADVQNLQRIIERLKEELKLELEKAQEEMENIFA 376
>gnl|CDD|146261 pfam03528, Rabaptin, Rabaptin.
Length = 106
Score = 29.9 bits (67), Expect = 0.99
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 319 YEHETEMLRKELAQREIDRE---RQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
YE + +L++E Q +E R+ + + + RQA E + ++ + KK E +L+
Sbjct: 40 YETQWNLLQQERLQWIQYQEAEEREVKKLQRRLRQANEEDQLEKTMKKKKELEDKLK 96
>gnl|CDD|221514 pfam12297, EVC2_like, Ellis van Creveld protein 2 like protein.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 571 and 1310 amino
acids in length. There are two conserved sequence
motifs: LPA and ELH. EVC2 is implicated in Ellis van
Creveld chondrodysplastic dwarfism in humans. Mutations
in this protein can give rise to this congenital
condition. LIMBIN is a protein which shares around 80%
sequence homology with EVC2 and it is implicated in a
similar condition in bovine chondrodysplastic dwarfism.
Length = 429
Score = 31.7 bits (72), Expect = 1.0
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 18/83 (21%)
Query: 313 KQLHELYEHETEMLRKELA---QREIDRERQKAEWEMKERQAEELKRRDEE--------- 360
++L E YE + L E +++++ + Q+ EM+ QAEEL +R E
Sbjct: 209 RRLQEEYERKMVALTAECNLETRKKMEAQHQREMAEME--QAEELLKRAPEREAVECSSL 266
Query: 361 LMKKHA---EEMQLRLA-QQEED 379
L H E +Q L QQEED
Sbjct: 267 LDTLHGLEQEHLQRSLLLQQEED 289
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 31.5 bits (71), Expect = 1.0
Identities = 37/147 (25%), Positives = 63/147 (42%), Gaps = 9/147 (6%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAK 168
C +++G I D+ E++++ LF+ G EL F + + + F+ K A +A
Sbjct: 59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKL 118
Query: 169 LDGHVLK-GRSLKIRFAPINAAIKVKNLTSCVTNE-LLELAFGVFGDIERAIVIVDERGN 226
L+ + ++ GR L + + N + V + E +LE V + IV
Sbjct: 119 LNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADK 178
Query: 227 SKCEG--IVEFARKPAAAQALRRCAEG 251
K G VE+ AAA A R+ G
Sbjct: 179 KKNRGFAFVEYESHRAAAMARRKLMPG 205
Score = 31.1 bits (70), Expect = 1.4
Identities = 41/157 (26%), Positives = 70/157 (44%), Gaps = 30/157 (19%)
Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKA 165
+NCRL++G I + +I+E F E I +K+K GF ++Y+ + A
Sbjct: 137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAA 196
Query: 166 KAK---LDGHV-LKGRSLKIRFAP--------INAAIK---VKNLTSCVTNELLELAFGV 210
A+ + G + L G + + +A + A +K V+NL + T E++E +F
Sbjct: 197 MARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSE 256
Query: 211 F--GDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
F G +ER I D V F + A +A+
Sbjct: 257 FKPGKVERVKKIRD-------YAFVHFEDREDAVKAM 286
>gnl|CDD|220844 pfam10675, DUF2489, Protein of unknown function (DUF2489). This is
a bacterial family of uncharacterized proteins.
Length = 131
Score = 30.2 bits (69), Expect = 1.1
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 13/52 (25%)
Query: 315 LHELYE-------HETEMLRKELAQREI---DRERQKAEWEMKERQAEELKR 356
+ELYE H+ RK L ++E D ER+K E E+++ EE K
Sbjct: 82 FYELYEVVKHMPTHDA---RKALPKKERMKLDLEREKLEAELEDAILEEAKA 130
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 29.1 bits (66), Expect = 1.1
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGN-SKCEGIVEFARKPAAAQALR 246
I V +L + VT+E+L AF + ++A V+ D+R SK G V F+ +A++
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMK 66
Score = 27.2 bits (61), Expect = 5.6
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKA 165
N+ R+++G++G ++T+ + F Y Q+ + K K +GF+ + D
Sbjct: 5 NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFV--SFSDPNDYL 62
Query: 166 KA--KLDGHVLKGRSLKIR 182
KA +++G + R +K+R
Sbjct: 63 KAMKEMNGKYVGNRPIKLR 81
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that 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. 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. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, 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 = 77
Score = 28.8 bits (64), Expect = 1.2
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-FGFIRMDYKHNADKAKAKLDGHV 173
++Y+GN+G + ++ F YG + ++I + F F+ + +A+ A LDG V
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60
Query: 174 LKGRSLKIRFA 184
+ G +++ +
Sbjct: 61 ICGSRVRVELS 71
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM2 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed
BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-1 is strongly expressed in all adult
and fetal tissues tested. Human CELF-1 is a nuclear and
cytoplasmic RNA-binding protein that regulates multiple
aspects of nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic dystrophy
protein kinase) gene; it preferentially targets UGU-rich
mRNA elements. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
binds specifically to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contains 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 two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it preferentially binds
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contains three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are also
important for localization in the cytoplasm. The
splicing activation or repression activity of CELF-2 on
some specific substrates is mediated by RRM1/RRM2. Both,
RRM1 and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 29.3 bits (65), Expect = 1.2
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQE 142
+L++G + ENDI +F P+G+ +E
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEE 30
>gnl|CDD|220979 pfam11101, DUF2884, Protein of unknown function (DUF2884). Some
members in this bacterial family of proteins are
annotated as YggN which currently has no known function.
Length = 228
Score = 30.8 bits (70), Expect = 1.2
Identities = 10/46 (21%), Positives = 24/46 (52%), Gaps = 10/46 (21%)
Query: 348 ERQAEELKRRDEELMKKHAEEMQLR----------LAQQEEDLRRR 383
E++ + L + EE M+ ++ ++ + L +QE+ L++R
Sbjct: 172 EQRMDGLGQEIEEEMESQSQALEAKADELCDRLEGLDEQEQQLQQR 217
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 31.3 bits (71), Expect = 1.2
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 321 HETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQ 376
HE+E +++E+ + E + ++E + +E +A + E +K E+ ++A Q
Sbjct: 279 HESEHVQEEITKLEGQIIQLRSEAQDREAEA----SGEAESFRKQPRELSQQIAPQ 330
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 31.1 bits (71), Expect = 1.2
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 10/68 (14%)
Query: 326 LRKELAQREIDRERQKAEWE----MKERQAEEL--KRRDEELMKKHAEEMQLRLAQQ--- 376
L E R++D+ R++ E + +E + EE K+ +++ ++ A+ +L +Q
Sbjct: 253 LSPE-VLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKL 311
Query: 377 EEDLRRRQ 384
EE R++Q
Sbjct: 312 EEKERKKQ 319
Score = 29.5 bits (67), Expect = 4.0
Identities = 10/53 (18%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 313 KQLHELYEHETEMLRKE-LAQREIDRERQKAEWEMKERQAEELKRRDEELMKK 364
++ E E R+E +++ ++++++ E ++ + EE ++ +E+ KK
Sbjct: 266 EEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKK 318
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 28.9 bits (64), Expect = 1.3
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 113 NCRLYLGNIGGDITE-NDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
N R+++GN+ + + +D+ +F YG ++K + F++ + +A A +G
Sbjct: 1 NSRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSVHKG--YAFVQYSNERHARGAVIGENG 58
Query: 172 HVLKGRSLKIRFA 184
VL G++L I A
Sbjct: 59 RVLAGQTLDINMA 71
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 31.6 bits (72), Expect = 1.3
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQ 376
+E E L++E+ E ER E + + +EL+ EEL + EE+ L +
Sbjct: 393 AEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEEL-QTELEELNEELEEL 451
Query: 377 EEDLRRRQNDNS 388
EE L ++
Sbjct: 452 EEQLEELRDRLK 463
Score = 30.1 bits (68), Expect = 3.5
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 315 LHELYEHETEMLRKELAQREIDRERQKAEW--EMKERQAEELKRRDEELMK--KHAEEMQ 370
EL + E+ E E+ R+ ++ E E +R+ L+ E+L + EE
Sbjct: 687 EEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEEL 746
Query: 371 LRLAQQEEDLRRRQNDNSMFLVEQQQ 396
L ++ E+L+ R + L ++
Sbjct: 747 EELEEELEELQERLEELEEELESLEE 772
Score = 29.3 bits (66), Expect = 6.4
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAE-EMQLRLAQQE 377
E E L +L + E + + K E E EEL+R+ EEL ++ E + +L ++E
Sbjct: 672 LEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEE 731
Query: 378 -EDLRRR 383
E L+ R
Sbjct: 732 LEQLQSR 738
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which 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 the 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. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. 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. .
Length = 78
Score = 28.9 bits (65), Expect = 1.3
Identities = 17/66 (25%), Positives = 37/66 (56%), Gaps = 6/66 (9%)
Query: 125 ITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGRS 178
+T+++I LF GE + + ++K+ +GF+ +A+KA L+G L+ ++
Sbjct: 13 MTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72
Query: 179 LKIRFA 184
+K+ +A
Sbjct: 73 IKVSYA 78
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 31.2 bits (71), Expect = 1.3
Identities = 17/75 (22%), Positives = 26/75 (34%), Gaps = 14/75 (18%)
Query: 317 ELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRR--DEELMKKHAEEMQ---- 370
E E E L++EL E K E E E + E +R D+ +
Sbjct: 432 ERLEEENSELKREL-------EELKREIEKLESELERFRREVRDKVRKDREIRARDRRIE 484
Query: 371 -LRLAQQEEDLRRRQ 384
L +E+ R +
Sbjct: 485 RLEKELEEKKKRVEE 499
Score = 28.5 bits (64), Expect = 8.9
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 17/71 (23%)
Query: 317 ELYEHETEMLRKELAQ--RE------IDRERQKAEWEM---------KERQAEELKRRDE 359
E + E E L EL + RE DRE + + + K+++ EEL+R+
Sbjct: 446 EELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLA 505
Query: 360 ELMKKHAEEMQ 370
EL K E+
Sbjct: 506 ELRKMRKLELS 516
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 31.3 bits (71), Expect = 1.3
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
E RK+ Q++ + +QK E + + E +R + KK AEE + A ++
Sbjct: 78 EEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEE-AAKQAALKQK 132
Score = 30.2 bits (68), Expect = 2.9
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 20/84 (23%)
Query: 320 EHETEMLRKELA----QREIDRERQKAEWEMKE------------RQAEELKRRDEELMK 363
+ E+ +K+ A +++++ER A+ + K+ +QAEE + K
Sbjct: 87 QQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAK 146
Query: 364 KHAEEMQLRLA----QQEEDLRRR 383
AE R A + + +++
Sbjct: 147 AKAEAEAKRAAAAAKKAAAEAKKK 170
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 31.2 bits (71), Expect = 1.3
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ 384
RK AQR ++ R++ E E KE + + K +K+ A+E+ + + +R+
Sbjct: 277 RKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQRK 334
>gnl|CDD|220410 pfam09798, LCD1, DNA damage checkpoint protein. This is a family
of proteins which regulate checkpoint kinases. In
Schizosaccharomyces pombe this protein is called Rad26
and in Saccharomyces cerevisiae it is called LCD1.
Length = 648
Score = 31.3 bits (71), Expect = 1.3
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 15/73 (20%)
Query: 325 MLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ 384
MLR +L + ++ ++ + K R EL +KH +E+Q L Q+ + L
Sbjct: 1 MLRDKLDMLQQQKQEER----------NKQKSRVNELKEKHDQELQK-LKQELQSLE--- 46
Query: 385 NDNSMFLVEQQQG 397
D FLV +Q+G
Sbjct: 47 -DERKFLVLEQRG 58
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 30.2 bits (68), Expect = 1.4
Identities = 15/46 (32%), Positives = 15/46 (32%), Gaps = 5/46 (10%)
Query: 448 GGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGG 493
GR GGGG G G G GPS GGG
Sbjct: 115 DGRGEGGGGGGGGDDGGG-----GDFGSSGPSRGGPRPASSGGGGN 155
Score = 29.0 bits (65), Expect = 3.5
Identities = 15/41 (36%), Positives = 17/41 (41%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGD 81
G GGG GG GG G + + P G S GG D
Sbjct: 119 EGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSRD 159
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 30.9 bits (70), Expect = 1.4
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 307 EYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHA 366
E R K L E + E + + Q E+ R+R + E E + RQ EEL + EE + +
Sbjct: 90 EAEERRKTLQEQTQQEQQRAQ---YQDELARKRYQKELEQQRRQNEELLKMQEESVLRQ- 145
Query: 367 EEMQLRLAQQEEDLRRRQ 384
E M+ ++ ++RR
Sbjct: 146 EAMRRATEEEILEMRRET 163
Score = 29.0 bits (65), Expect = 6.0
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWE-----MKERQAEELKR---RDEELMKKHAEEMQL 371
E E ++ E Q + ER + E E ++E+ +E +R +DE K++ +E++
Sbjct: 67 ELEAKIKEYEAQQAQAKLERARVEAEERRKTLQEQTQQEQQRAQYQDELARKRYQKELEQ 126
Query: 372 RLAQQEEDLRR 382
+ Q EE L+
Sbjct: 127 QRRQNEELLKM 137
Score = 28.6 bits (64), Expect = 7.9
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
+Q + +++ E+ RK + + RQ E + EE R E + + EE+
Sbjct: 103 QQEQQRAQYQDELARKRYQKELEQQRRQNEELL---KMQEESVLRQEAMRRATEEEILEM 159
Query: 373 LAQQ--EEDLRRRQND 386
+ EE R+N
Sbjct: 160 RRETIEEEAELERENI 175
>gnl|CDD|221049 pfam11262, Tho2, Transcription factor/nuclear export subunit
protein 2. THO and TREX form a eukaryotic complex which
functions in messenger ribonucleoprotein metabolism and
plays a role in preventing the transcription-associated
genetic instability. Tho2, along with four other
subunits forms THO.
Length = 296
Score = 30.8 bits (70), Expect = 1.4
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 316 HELYEHETEMLRKELAQREIDRERQKAEWEMKER-QAEELKRRDEELMKKHAE 367
ELY+ E E L K++ +E+D + + KE+ + + L ++ EE +KKH E
Sbjct: 26 KELYDKEIERLEKQI--KELDSSSSGIDKKKKEKKRLKSLIKKLEEELKKHIE 76
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryote. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAF orthologs
and paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 30.4 bits (69), Expect = 1.5
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 14/67 (20%)
Query: 326 LRKELAQREIDRERQKAEWEMKERQAEELKRR------DEELMKKHAEEMQLRLAQQEED 379
+RK+L E + ++ E E ++ + E R ++ +K+ A+EM Q+EED
Sbjct: 112 VRKQLRFLE---QLEREEEEKRDEEERERLLRAAKSRSEQSRLKQKAKEM-----QKEED 163
Query: 380 LRRRQND 386
R
Sbjct: 164 EEMRHRA 170
Score = 28.8 bits (65), Expect = 5.6
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE------ELKRRDEELMKKHAEEMQLRL 373
+ ++ E +RE + +R + E E R A+ LK++ +E+ K+ EEM+ R
Sbjct: 111 DVRKQLRFLEQLEREEEEKRDEEERERLLRAAKSRSEQSRLKQKAKEMQKEEDEEMRHRA 170
Query: 374 A 374
A
Sbjct: 171 A 171
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 31.5 bits (71), Expect = 1.5
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 9/80 (11%)
Query: 314 QLHELYEHETEMLRKELAQREIDRERQKAEW-------EMKERQAEELKRRDEELMKKHA 366
+ E + E Q I+R R+ A E+QA+ + + M+ A
Sbjct: 265 LRARIEELRAQEAVLEETQERINRARKAAPLAAHIKAVTQIEQQAQRIHTELQSKMRSRA 324
Query: 367 EEMQLR--LAQQEEDLRRRQ 384
+ + R +Q+ + ++
Sbjct: 325 KLLMKRAAHVKQQSSIEEQR 344
Score = 29.9 bits (67), Expect = 4.4
Identities = 14/86 (16%), Positives = 27/86 (31%), Gaps = 5/86 (5%)
Query: 305 EFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQ-KAEWEMKERQAEE----LKRRDE 359
E + +R H A + AE + R EE LK +
Sbjct: 747 ELMHQARTVLKARTEAHFNNNEEVTAALQTGAELSHLAAEIQFFNRLREEDTHLLKTLEA 806
Query: 360 ELMKKHAEEMQLRLAQQEEDLRRRQN 385
E+ ++ + + Q E ++ +
Sbjct: 807 EIGQEIPSDEDILNLQCETLVQEEEQ 832
Score = 28.8 bits (64), Expect = 9.7
Identities = 22/165 (13%), Positives = 44/165 (26%), Gaps = 23/165 (13%)
Query: 243 QALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVN 302
+ +T L+ + + E D + + K PE Q +
Sbjct: 580 NRSKEDIPNLQNITVRLQDLTEKLSEAEDMLACEQHALLRKLQPEQDLQDVR----LHLQ 635
Query: 303 SFEFEYGSRWKQLHELYEHETEMLRKELAQREID------RERQKAEWEMKERQAEELKR 356
E L H ++ L Q + R K ++ ++++
Sbjct: 636 QCSQE-----LALKLTALHALQL---TLTQERVREHALSIRVLPKELLASRQLALQKMQS 687
Query: 357 RDEEL-----MKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
E+L M + + L E+ R N+
Sbjct: 688 EKEQLTYWKEMLAQCQTLLRELETHIEEYDREFNEIENASSSLGS 732
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 30.7 bits (69), Expect = 1.5
Identities = 20/54 (37%), Positives = 22/54 (40%)
Query: 440 GSAMDFDQGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGG 493
GSA GG +G GG G + G G G S GS GGS GG
Sbjct: 78 GSADKDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGS 131
Score = 30.7 bits (69), Expect = 1.9
Identities = 22/69 (31%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 425 VGNAVVGNVTGVDNK-GSAMDFDQGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHG 483
G+A G + GS D GG + GGG D+ SG +GG G G S
Sbjct: 77 TGSADKDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGG-GSEGGSTGKS 135
Query: 484 SRRGGSGGG 492
+ G G G
Sbjct: 136 LTKEGVGAG 144
Score = 28.3 bits (63), Expect = 8.1
Identities = 14/40 (35%), Positives = 16/40 (40%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG G G G G GG G DG GS+ + G
Sbjct: 101 GGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEG 140
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 31.0 bits (70), Expect = 1.5
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
RK+ A+ +++RER+ E K+R+A E +R L A E Q++ QQ ++
Sbjct: 19 RKQRAKLKLERERKAKEEAAKQREAIEAAQRSRRL---DAIEAQIKADQQMQE 68
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 31.2 bits (70), Expect = 1.5
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 6/93 (6%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
K++ L E E L +E +R ER++ E E ER+ E R + + + + E R
Sbjct: 458 KRIERLEREERERLERERMER---IERERLERERLERERLERDRLERDRLDRLERERVDR 514
Query: 373 LAQQEEDLRRRQNDNSMFLVEQQQGRGGSGGYG 405
L + + RR NS FL + G GG G
Sbjct: 515 LERDRLEKARR---NSYFLKGMENGLSAGGGPG 544
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
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. It 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). .
Length = 76
Score = 28.8 bits (64), Expect = 1.6
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
+ + V NL V + L+ F + G + RA ++ D+ G S+ G V F + A QA+
Sbjct: 1 STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAI 58
>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 = 28.5 bits (64), Expect = 1.6
Identities = 15/76 (19%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
++++G + ++TE D+ + F +G E+ + + + FGFI + + + D+ +
Sbjct: 4 KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63
Query: 169 LDGHVLKGRSLKIRFA 184
H + G+ ++++ A
Sbjct: 64 -HFHDINGKKVEVKRA 78
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 28.5 bits (64), Expect = 1.6
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI---NKEKMFGFIRMDYKHNADKAKAKLDG 171
++ + NI + D+ L YG + E + + A +A KL+G
Sbjct: 2 KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNG 61
Query: 172 HVLKGRSLKIRFAP 185
H +G LK+ + P
Sbjct: 62 HEYEGSKLKVSYIP 75
>gnl|CDD|132534 TIGR03495, phage_LysB, phage lysis regulatory protein, LysB family.
Members of this protein family are phage lysis
regulatory protein, including the well-studied protein
LysB (lysis protein B) of Enterobacteria phage P2. For
members of this family, genes are found in phage or in
prophage regions of bacterial genomes, typically near a
phage lysozyme or phage holin.
Length = 135
Score = 29.7 bits (67), Expect = 1.6
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 6/76 (7%)
Query: 318 LYEHETEMLRKELAQREIDRERQKAEWEMKERQAEEL------KRRDEELMKKHAEEMQL 371
R +L + + Q+AE K Q L + +++ + +
Sbjct: 16 WQSQRLRNARADLERANRVLKAQQAELASKANQLIVLLALAKRNEEAQAQLRQQLAQARA 75
Query: 372 RLAQQEEDLRRRQNDN 387
LAQ+E+ + R + +N
Sbjct: 76 LLAQREQRIERLKREN 91
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 31.0 bits (69), Expect = 1.6
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL----D 170
RL++G +G + +D++++F P G + + K F +D+ ++ + KL +
Sbjct: 12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYN 71
Query: 171 GHVLKGRSLKIRFA 184
G V KG L++ A
Sbjct: 72 GCVWKGGRLRLEKA 85
>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 = 28.5 bits (64), Expect = 1.6
Identities = 14/76 (18%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAK 168
++++G + D+TE + E F +G+ + + ++ FGF+ D + ++ +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 169 LDGHVLKGRSLKIRFA 184
L G+ ++++ A
Sbjct: 61 -GMLELGGKQVEVKRA 75
>gnl|CDD|206035 pfam13864, Enkurin, Calmodulin-binding. This is a family of
apparent calmodulin-binding proteins found at high
levels in the testis and vomeronasal organ and at lower
levels in certain other tissues. Enkurin is a scaffold
protein that binds PI3 kinase to sperm transient
receptor potential (canonical) (TRPC) channels. The
mammalian transient receptor potential (canonical)
channels are the primary candidates for the Ca(2+) entry
pathway activated by the hormones, growth factors, and
neurotransmitters that exert their effect through
activation of PLC. Calmodulin binds to the C-terminus of
all TRPC channels, and dissociation of calmodulin from
TRPC4 results in profound activation of the channel.
Length = 98
Score = 29.1 bits (66), Expect = 1.7
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 26/81 (32%)
Query: 327 RKELAQREIDRERQKAEWEMK---------ERQA--EELKRRDEEL-------------- 361
++E+A+ + +RERQ+ + + ER LK+ +EL
Sbjct: 11 KEEIAEEKEERERQEEDPDCPPGHRLLSEEERLELLNGLKKNWDELNKEYQKLPVVIDTP 70
Query: 362 -MKKHAEEMQLRLAQQEEDLR 381
K+ EE++ LA+ EED++
Sbjct: 71 SKKRRKEELEKELAEIEEDIK 91
>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 = 28.5 bits (64), Expect = 1.7
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
L++GN+ D T D++ FK G + + K K F+ D KA KL
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA-LKL 61
Query: 170 DGHVLKGRSLKI 181
+LKGR KI
Sbjct: 62 HHTLLKGR--KI 71
>gnl|CDD|213755 TIGR02977, phageshock_pspA, phage shock protein A. Members of this
family are the phage shock protein PspA, from the phage
shock operon. This is a narrower family than the set of
PspA and its homologs, sometimes several in a genome, as
described by pfam04012. PspA appears to maintain the
protonmotive force under stress conditions that include
overexpression of certain phage secretins, heat shock,
ethanol, and protein export defects [Cellular processes,
Adaptations to atypical conditions].
Length = 219
Score = 30.3 bits (69), Expect = 1.7
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 327 RKELAQREIDR-ERQKAEWEMK-----ERQAEELKRRDEELMKKH-----AEEMQLRLAQ 375
+KEL +R + R E Q A+W+ K + E+L R L++K AE ++ LA
Sbjct: 54 KKEL-ERRVSRLEAQVADWQDKAELALSKGREDLAR--AALIEKQKAQELAEALERELAA 110
Query: 376 QEEDLRRRQND 386
EE L + Q D
Sbjct: 111 VEETLAKLQED 121
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 30.8 bits (69), Expect = 1.7
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRE--RQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
QL L E + E E +RE R + + +ER+A + A++
Sbjct: 81 PQLRALRT-ELGTAQGEKRAAETEREAARSELQKARQEREAVRQELAAARQNLAKAQQEL 139
Query: 371 LRLAQQEEDLRRR 383
RL +Q +DL+ R
Sbjct: 140 ARLTKQAQDLQTR 152
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 28.7 bits (65), Expect = 1.7
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCE-------GIVEFARKPAAA 242
+ VKNL T E L+ F G + R++ I ++ G VEF K AA
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGV-RSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61
Query: 243 QALRR 247
+AL+R
Sbjct: 62 KALKR 66
>gnl|CDD|201951 pfam01749, IBB, Importin beta binding domain. This family consists
of the importin alpha (karyopherin alpha), importin beta
(karyopherin beta) binding domain. The domain mediates
formation of the importin alpha beta complex; required
for classical NLS import of proteins into the nucleus,
through the nuclear pore complex and across the nuclear
envelope. Also in the alignment is the NLS of importin
alpha which overlaps with the IBB domain.
Length = 97
Score = 28.9 bits (65), Expect = 1.8
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 347 KERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSM 389
K R AEE++RR EE ++LR ++EE L +R+N
Sbjct: 16 KGRDAEEMRRRREE------VGVELRKNKREEQLLKRRNVGLP 52
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect
modulator 6, a member of a family of transcription
coactivators that plays a central role in the regulation
of cellular energy metabolism. As an inducible
transcription coactivator, PGC-1alpha can interact with
a broad range of transcription factors involved in a
wide variety of biological responses, such as adaptive
thermogenesis, skeletal muscle fiber type switching,
glucose/fatty acid metabolism, and heart development.
PGC-1alpha stimulates mitochondrial biogenesis and
promotes oxidative metabolism. It participates in the
regulation of both carbohydrate and lipid metabolism and
plays a role in disorders such as obesity, diabetes, and
cardiomyopathy. PGC-1alpha is a multi-domain protein
containing an N-terminal activation domain region, a
central region involved in the interaction with at least
a nuclear receptor, and a C-terminal domain region. The
N-terminal domain region consists of three leucine-rich
motifs (L1, NR box 2 and 3), among which the two last
are required for interaction with nuclear receptors,
potential nuclear localization signals (NLS), and a
proline-rich region overlapping a putative repression
domain. The C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 28.8 bits (64), Expect = 1.8
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGH 172
+Y+G I D T ++ + F+ +GE +E +N +GFI Y++ D A +G+
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRDDGDSYGFI--TYRYTCDAFAALENGY 62
Query: 173 VLK 175
L+
Sbjct: 63 TLR 65
>gnl|CDD|113902 pfam05149, Flagellar_rod, Paraflagellar rod protein. This family
consists of several eukaryotic paraflagellar rod
component proteins. The eukaryotic flagellum represents
one of the most complex macromolecular structures found
in any organism and contains more than 250 proteins. In
addition to its locomotive role, the flagellum is
probably involved in nutrient uptake since receptors for
host low-density lipoproteins are localised on the
flagellar membrane as well as on the flagellar pocket
membrane.
Length = 289
Score = 30.4 bits (69), Expect = 1.8
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 12/82 (14%)
Query: 316 HELYEHETE-MLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLA 374
+ E+E L++ + E+Q+A W R +EL+R +L ++ EE++ R+
Sbjct: 43 YSAQRRESEKFLQQ-------NVEQQQACW----RAIQELERELRDLAEERREEVERRIE 91
Query: 375 QQEEDLRRRQNDNSMFLVEQQQ 396
E + +RR + S Q
Sbjct: 92 AVEREEQRRTDYESFLNFAAQH 113
>gnl|CDD|241159 cd12715, RRM2_MATR3, RNA recognition motif 2 in vertebrate
matrin-3. This subgroup corresponds to the RRM2 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated by
the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is responsible
for the activation of the N-methyl-d-aspartic acid
(NMDA) receptor. Furthermore, MATR3 has been identified
as both a Ca2+-dependent CaM-binding protein and a
downstream substrate of caspases. Additional research
indicates that matrin 3 also binds Rev/Rev responsive
element (RRE)-containing viral RNA and functions as a
cofactor that mediates the post-transcriptional
regulation of HIV-1. .
Length = 80
Score = 28.3 bits (63), Expect = 1.9
Identities = 16/71 (22%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 116 LYLGNI---GGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKA--KAKLD 170
++L N+ G +++ +++L +PYG+ + + + K FI M+ + +A+ K +
Sbjct: 3 IHLSNLPHSGY--SDSAVLKLAEPYGKIKNYILMRMKNQAFIEMETREDAEAMVDHCKKN 60
Query: 171 GHVLKGRSLKI 181
+G+ LK+
Sbjct: 61 ALWFQGKCLKV 71
>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein
ArcB; Provisional.
Length = 779
Score = 31.1 bits (71), Expect = 1.9
Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 12/73 (16%)
Query: 314 QLHELYEHETEM---LRKELAQ--REIDRERQKAEWEMKERQAEELKRRDEELMKKHAEE 368
+L E+ E + E+ L+ +AQ +EI ER+KAE E ++ E+LK E+ K EE
Sbjct: 93 KLEEMRERDLELNVQLKDNIAQLNQEIA-EREKAE-EARQEAFEQLK---NEI--KEREE 145
Query: 369 MQLRLAQQEEDLR 381
Q+ L QQ LR
Sbjct: 146 TQIELEQQSSLLR 158
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 28.4 bits (64), Expect = 1.9
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 189 AIKVKNLTSCVTNELLELAFG-VFGDIERAIVIVDERGNSKCEGIVEF 235
++ V +LT V + L F + + A V++D+ GNS+ G V F
Sbjct: 3 SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRF 50
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 31.0 bits (71), Expect = 2.0
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 17/86 (19%)
Query: 319 YEHETEMLRKELAQ-----REIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRL 373
+ ETE L+++LAQ R+ E + +K+ EE + E L +++ RL
Sbjct: 78 QKEETEQLKQQLAQAPAKLRQAQAELEA----LKDDNDEETR---ETLSTLSLRQLESRL 130
Query: 374 AQQEEDLRRRQND----NSMFLVEQQ 395
AQ + L+ QND NS LV Q
Sbjct: 131 AQTLDQLQNAQNDLAEYNSQ-LVSLQ 155
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 28.5 bits (64), Expect = 2.0
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM---FGFIRMDYKHNADKAKAKLDGHVLKGRSLK 180
D E + E F YG + + ++ + F++ +A A AK G +L GR ++
Sbjct: 17 DELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAKGQGTILDGRHIR 76
Query: 181 IRFAPIN 187
A +N
Sbjct: 77 CERAKVN 83
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 28.0 bits (63), Expect = 2.0
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 120 NIGGDITENDIIELFKPYGETQELFINKE 148
N+ D TEN I + FK GE +E+ I +
Sbjct: 7 NLPKDTTENKIRQFFKDCGEIREVKIVES 35
>gnl|CDD|239497 cd03403, Band_7_stomatin_like, Band_7_stomatin_like: A subgroup of
the band 7 domain of flotillin (reggie) like proteins
similar to stomatin and podicin (two lipid
raft-associated integral membrane proteins). Individual
proteins of this band 7 domain family may cluster to
form membrane microdomains which may in turn recruit
multiprotein complexes. Stomatin is widely expressed
and, highly expressed in red blood cells. It localizes
predominantly to the plasma membrane and to
intracellular vesicles of the endocytic pathway, where
it is present in higher order homo-oligomeric complexes
(of between 9 and 12 monomers). Stomatin interacts with
and regulates members of the degenerin/epithelia Na+
channel family in mechanosensory cells of Caenorhabditis
elegans and vertebrate neurons and, is implicated in
trafficking of Glut1 glucose transporters. Prohibitin is
a mitochondrial inner-membrane protein hypothesized to
act as a chaperone for the stabilization of
mitochondrial proteins. Podicin localizes to the plasma
membrane of podocyte foot processes and, is found in
higher order oligomers. Podocin plays a role in
regulating glomerular permeability. Mutations in the
podicin gene give rise to autosomal recessive steroid
resistant nephritic syndrome. This group also contains
proteins similar to three Caenorhabditis elegans
proteins: UNC-1, UNC-24 and, MEC-2. Mutations in the
unc-1 and unc-24 genes result in abnormal motion and
altered patterns of sensitivity to volatile anesthetics.
MEC-2 and UNC-24 proteins interact with MEC-4 which is
part of the degenerin channel complex required for
response to gentle body touch.
Length = 215
Score = 30.2 bits (69), Expect = 2.0
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 331 AQREIDRERQ----KAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQN 385
Q E +RE++ +AE ERQA L + + +QLR + E++ +
Sbjct: 152 KQAEAEREKRAKIIEAE---GERQAAILLAEAAKQAAINPAALQLRELETLEEIAKEAA 207
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 28.2 bits (63), Expect = 2.1
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKL 169
R+++G I END+ + F YG +E+ I K +GF+ + + +A K +
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63
Query: 170 DGHVLKGRSLKI 181
+ + + L I
Sbjct: 64 NRLCFRDKKLNI 75
>gnl|CDD|218657 pfam05615, THOC7, Tho complex subunit 7. The Tho complex is
involved in transcription elongation and mRNA export
from the nucleus.
Length = 132
Score = 29.2 bits (66), Expect = 2.1
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEEL------MKKHAEEMQLRLAQQE 377
E L ELAQ E+ R + EM ER+ E ++ EE+ K EE++ L + +
Sbjct: 42 EDLLAELAQLELSMLRLQFVLEMNERERENYEQEKEEIETTIENAKDEIEELKKELEEAK 101
Query: 378 EDLRRRQ 384
+ R+
Sbjct: 102 RIRKNRK 108
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 30.6 bits (69), Expect = 2.2
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 13/63 (20%)
Query: 26 HFKIPEIEDMPFMSLGGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRYFT 85
+ + ++ G GGG GGG GG GG G GGGGGG R++
Sbjct: 62 LVANGAVALLSASAISGGGGGGGGGFGGFGGGGGG-------------GGGGGGGWRFWL 108
Query: 86 EKI 88
Sbjct: 109 RLF 111
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 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 = 77
Score = 28.4 bits (64), Expect = 2.2
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAK 168
++++G + ++E+ + EL + +G+ + + K+ K + F D+A A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 169 LDGHVLKGRSLKIRFA 184
L+G L + L ++ A
Sbjct: 62 LNGMQLGDKKLTVQRA 77
>gnl|CDD|232786 TIGR00021, rpiA, ribose 5-phosphate isomerase. This model
describes ribose 5-phosphate isomerase, an enzyme of the
non-oxidative branch of the pentose phosphate pathway
[Energy metabolism, Pentose phosphate pathway].
Length = 218
Score = 29.9 bits (68), Expect = 2.2
Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 23/85 (27%)
Query: 215 ERAIVIVDERGNSKCEG-------IVEFARKPAAAQ--------ALRRCAEGCFFLTQS- 258
+R IVI DE G +V FA K A + LR+ +G +T +
Sbjct: 109 KRFIVIADESKLVDKLGKFPLPVEVVPFAWKAVARKLEKLGGEPTLRQGNKGGPVVTDNG 168
Query: 259 -------LRPVIVEPLELTDEIDGL 276
+I +P L +E+ +
Sbjct: 169 NYILDCHFGKIIPDPEALEEELKSI 193
>gnl|CDD|189476 pfam00261, Tropomyosin, Tropomyosin.
Length = 237
Score = 30.3 bits (69), Expect = 2.2
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 322 ETEMLRKELAQREI-DRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDL 380
E+E RK L R + D E+ E E Q +E K EE +K+ EE+ +L E DL
Sbjct: 75 ESERGRKVLENRSLKDDEKM----EQLEAQLKEAKEIAEEADRKY-EEVARKLVVVEGDL 129
Query: 381 RR 382
R
Sbjct: 130 ER 131
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 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). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 28.0 bits (63), Expect = 2.2
Identities = 14/57 (24%), Positives = 28/57 (49%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
C L+ +G + D+ E F+ +GE + + + G++R ++ A +A KL
Sbjct: 1 GCVLHFSGVGEQTSREDLKEAFEEFGEVAWVDFARGQTEGYVRFKEENAAKEALEKL 57
>gnl|CDD|220597 pfam10139, Virul_Fac, Putative bacterial virulence factor. Members
of this family of prokaryotic proteins include various
putative virulence factor effector proteins. Their exact
function is, as yet, unknown.
Length = 852
Score = 30.8 bits (70), Expect = 2.3
Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 297 RFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKR 356
ATV E + G +QL EL E L Q + + ER + K R AE+L R
Sbjct: 543 WLATVALPEQKQGRIQEQLDELQRELGENLLANYYQADDEDERAE-----KRRIAEQLLR 597
Query: 357 RDEELMKKHAEEMQLRLAQQEEDLRR 382
+E +H E ++ L + LRR
Sbjct: 598 ALQERAHRHGELLE-GLLPPRDQLRR 622
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 30.4 bits (68), Expect = 2.3
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 309 GSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEE 368
G+ Q+ E E +++ A E++ ++K E K + EE +R+ EE +K EE
Sbjct: 190 GAEGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREE 249
Query: 369 MQLRLAQQEEDLRRR 383
+ R +EE RRR
Sbjct: 250 EEKR-RLKEEIERRR 263
>gnl|CDD|234796 PRK00571, atpC, F0F1 ATP synthase subunit epsilon; Validated.
Length = 135
Score = 29.3 bits (67), Expect = 2.4
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 342 AEW--EMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
AE ++ E +AEE K R EE ++ +++ AQ L R
Sbjct: 83 AERADDIDEARAEEAKERAEEALENKHDDVDYARAQAA--LAR 123
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 28.4 bits (64), Expect = 2.4
Identities = 16/89 (17%), Positives = 39/89 (43%), Gaps = 24/89 (26%)
Query: 116 LYLGNIGGDITENDIIELFKPYGE----------------TQELFINKEK-------MFG 152
+++GN+ + D+ +LFK +G +++ K+K +
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 153 FIRMDYKHNADKAKAKLDGHVLKGRSLKI 181
++ + +A+KA KL+G +G +++
Sbjct: 63 YVVFKEEESAEKA-LKLNGTEFEGHHIRV 90
>gnl|CDD|218174 pfam04612, T2SM, Type II secretion system (T2SS), protein M. This
family of membrane proteins consists of Type II
secretion system protein M sequences from several
Gram-negative (diderm) bacteria. The precise function of
these proteins is unknown, though in Vibrio cholerae,
the T2SM (EpsM) protein interacts with the T2SL (EpsL)
protein, and also forms homodimers.
Length = 159
Score = 29.5 bits (67), Expect = 2.4
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRD 358
R+ AQR + RQ W ++E QA E++
Sbjct: 42 RRARAQRRLQAARQLLAW-LQE-QAPEIRALR 71
>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 379
Score = 30.3 bits (69), Expect = 2.4
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 318 LYEHETEMLRKELAQREIDRERQKAEWEMKERQAE-ELKRRDEELMKKHAEEMQLRLAQQ 376
L E E E LR+E + + E +K WE +++ E + K+ ++ + A +L +
Sbjct: 63 LEEIEEE-LREEYEEELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLELEA 121
Query: 377 EED---LRRR 383
EE LR R
Sbjct: 122 EEPEPPLRPR 131
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD 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. .
Length = 81
Score = 28.1 bits (62), Expect = 2.5
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGE--TQELFINK----EKMFGFIRMDYKHNADKAK 166
+ LY+ + +T+ ++ +LF YG T + +++ + GFIR D + A++A
Sbjct: 2 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
Query: 167 AKLDGHVLKGRS--LKIRFA 184
L+G G + + ++FA
Sbjct: 62 KGLNGQKPSGAAEPITVKFA 81
>gnl|CDD|181423 PRK08433, PRK08433, flagellar motor switch protein; Validated.
Length = 111
Score = 28.9 bits (65), Expect = 2.5
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 130 IIELFKPYGETQELFINKEKMFG 152
+I+L KP GE+ EL+IN ++ G
Sbjct: 58 VIDLEKPAGESVELYING-RIIG 79
>gnl|CDD|192481 pfam10197, Cir_N, N-terminal domain of CBF1 interacting
co-repressor CIR. This is a 45 residue conserved region
at the N-terminal end of a family of proteins referred
to as CIRs (CBF1-interacting co-repressors). CBF1
(centromere-binding factor 1) acts as a transcription
factor that causes repression by binding specifically to
GTGGGAA motifs in responsive promoters, and it requires
CIR as a co-repressor. CIR binds to histone deacetylase
and to SAP30 and serves as a linker between CBF1 and the
histone deacetylase complex.
Length = 37
Score = 26.8 bits (60), Expect = 2.5
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 340 QKAEWEMKERQAEELKRRDEELMKKHAEE 368
Q+ W E++A E +++ EEL K+ EE
Sbjct: 10 QEKVW-EAEQKALEEQKKIEELRKEIEEE 37
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 27.9 bits (63), Expect = 2.5
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI--NKEKM----FGFIRMDYKHNADKAKAKL 169
LY+GN+ TE I ELF G+ + + + ++ F F+ + +A+ A L
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 170 DGHVLKGRSLKI 181
+G L R +++
Sbjct: 61 NGTKLDDRIIRV 72
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 29.2 bits (66), Expect = 2.5
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 324 EMLRKELAQREIDRERQKAEWEMK----ERQAEE--LKRRDEELMKKHAEEM 369
E R EL + +E + E++ K +R+ EE K+R + KK ++
Sbjct: 48 EYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQKKKK 99
>gnl|CDD|220614 pfam10174, Cast, RIM-binding protein of the cytomatrix active zone.
This is a family of proteins that form part of the CAZ
(cytomatrix at the active zone) complex which is
involved in determining the site of synaptic vesicle
fusion. The C-terminus is a PDZ-binding motif that binds
directly to RIM (a small G protein Rab-3A effector). The
family also contains four coiled-coil domains.
Length = 774
Score = 30.4 bits (68), Expect = 2.6
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 20/94 (21%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWE--------MK---ERQAEELKRRDEELMKKHAE- 367
E+E L+ E DR R E E MK +R A+EL R+ EL+ E
Sbjct: 251 ENEIYRLQSRCDTSEADRNRLDKEVEAERSALAAMKAKCDRAAQELSRKKTELLGLQTEL 310
Query: 368 --------EMQLRLAQQEEDLRRRQNDNSMFLVE 393
+M+ L + +EDL R + + ++ E
Sbjct: 311 ETLANQDSDMRQHLDKLKEDLTRAEQEKAILQTE 344
Score = 30.0 bits (67), Expect = 3.3
Identities = 26/119 (21%), Positives = 55/119 (46%), Gaps = 18/119 (15%)
Query: 285 TPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKEL-AQREIDRERQ--- 340
+PE ++R + A + E ++ ++ + + L++EL +QRE++R +Q
Sbjct: 38 SPELKRERALRKDEAARITVWKEQLRVTQEENQHAQLTVQALQEELKSQRELNRLQQKLE 97
Query: 341 -------------KAEWEMKERQAE-ELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQN 385
K+E + QAE E + + L++ E++QLR+ + ++ L R
Sbjct: 98 KSGNETGELQQLEKSEGQFSRIQAERERQAMELFLLRDTLEKLQLRMERLQQTLDARDE 156
>gnl|CDD|216807 pfam01956, DUF106, Integral membrane protein DUF106. This
archaebacterial protein family has no known function.
Members are predicted to be integral membrane proteins.
Length = 168
Score = 29.5 bits (67), Expect = 2.6
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 9/67 (13%)
Query: 323 TEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
+E+L+ L IDR+ +K ++R+ E KR EL K + + +++E+L
Sbjct: 30 SELLQWLL----IDRKMEKY----QKREKEIQKRA-RELRKNGDKLSPKKFEKRQEELME 80
Query: 383 RQNDNSM 389
Q + M
Sbjct: 81 DQKEMMM 87
>gnl|CDD|167649 PRK03963, PRK03963, V-type ATP synthase subunit E; Provisional.
Length = 198
Score = 29.7 bits (67), Expect = 2.7
Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 325 MLRKELAQREIDRE-RQKAEWEMKE--RQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
M EL +EI+RE QK E+ ++E ++AE++K + + AE + LR A+ + +L
Sbjct: 1 MEGAELIIQEINREAEQKIEYILEEAQKEAEKIKEEARKRAESKAEWI-LRKAKTQAELE 59
Query: 382 RRQ 384
+++
Sbjct: 60 KQR 62
>gnl|CDD|224340 COG1422, COG1422, Predicted membrane protein [Function unknown].
Length = 201
Score = 29.6 bits (67), Expect = 2.7
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 335 IDRER----QKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQ 375
ID+E+ QK E ++ E + D + +KK +E Q+ +
Sbjct: 69 IDQEKMKELQKMMKEFQKEFREAQESGDMKKLKK-LQEKQMEMMD 112
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 27.9 bits (62), Expect = 2.7
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERG 225
I ++NL+S +++ L+ F VFG+IE V++ RG
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRG 40
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding
protein with multiple splicing (RBP-MS). This subfamily
corresponds to the RRM of RBP-MS, also termed heart and
RRM expressed sequence (hermes), an RNA-binding proteins
found in various vertebrate species. It contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). RBP-MS
physically interacts with Smad2, Smad3 and Smad4 and
plays a role in regulation of Smad-mediated
transcriptional activity. In addition, RBP-MS may be
involved in regulation of mRNA translation and
localization during Xenopus laevis development. .
Length = 76
Score = 27.7 bits (61), Expect = 2.9
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 116 LYLGNIGGDITENDIIELFKPYG--ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
L++ + DI ++ LF+P+ E + + ++ GF+ D + A+ AK L+G
Sbjct: 4 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG-- 61
Query: 174 LKGRSLKIRFAP 185
IRF P
Sbjct: 62 -------IRFDP 66
>gnl|CDD|147845 pfam05914, RIB43A, RIB43A. This family consists of several
RIB43A-like eukaryotic proteins. Ciliary and flagellar
microtubules contain a specialised set of
protofilaments, termed ribbons, that are composed of
tubulin and several associated proteins. RIB43A was
first characterized in the unicellular biflagellate,
Chlamydomonas reinhardtii although highly related
sequences are present in several higher eukaryotes
including humans. The function of this protein is
unknown although the structure of RIB43A and its
association with the specialised protofilament ribbons
and with basal bodies is relevant to the proposed role
of ribbons in forming and stabilising doublet and
triplet microtubules and in organising their
three-dimensional structure. Human RIB43A homologues
could represent a structural requirement in centriole
replication in dividing cells.
Length = 379
Score = 30.0 bits (68), Expect = 2.9
Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 15/82 (18%)
Query: 311 RWK-----QLHELYEHETEMLRKELAQREIDRERQKAEWE----MKERQAEELKRRDEEL 361
RWK QL + + + + L+++ +RE ++ R+K EW+ + R A L+R++ L
Sbjct: 273 RWKGMSPEQLAAIRKGQEQQLQEKERRREEEQLREK-EWDRQAINQARAAVLLERQERRL 331
Query: 362 MKKHAEEM-----QLRLAQQEE 378
K+ +++ QL Q+ +
Sbjct: 332 RKELRKQLDSANQQLAKEQKAQ 353
Score = 29.6 bits (67), Expect = 4.2
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 8/59 (13%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
E R+ L Q+ +ERQ+A+ E+QA+ L + + A+E LA EE+ RR
Sbjct: 158 EQQREWLEQQV--QERQQAKAA--EKQADTLHDQLRVELDHRAQE----LASLEEECRR 208
>gnl|CDD|220915 pfam10961, DUF2763, Protein of unknown function (DUF2763). This
eukaryotic family of proteins has no known function.
Length = 91
Score = 28.1 bits (63), Expect = 3.0
Identities = 10/36 (27%), Positives = 10/36 (27%), Gaps = 3/36 (8%)
Query: 42 GRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGG 77
G G G GG G S M GG
Sbjct: 59 DGGRGGPGPPGGGRRMGRIGGGGGPSRPP---MAGG 91
>gnl|CDD|178701 PLN03156, PLN03156, GDSL esterase/lipase; Provisional.
Length = 351
Score = 30.1 bits (68), Expect = 3.0
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 16 YQARLRSYTGHFKIPEI--EDMPFMSLG 41
YQ +LR+Y G K EI E + +S+G
Sbjct: 139 YQTKLRAYLGEEKANEIISEALYLISIG 166
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 30.2 bits (68), Expect = 3.0
Identities = 14/36 (38%), Positives = 24/36 (66%), Gaps = 6/36 (16%)
Query: 350 QAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQN 385
A+EL+RR EE ++++LR ++EE L +R+N
Sbjct: 21 SADELRRRREE------QQVELRKQKREELLNKRRN 50
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome partitioning].
Length = 1480
Score = 30.2 bits (68), Expect = 3.1
Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQL--RLAQQEEDLR 381
E LR+ L Q E +R R + + + Q + + L + + +L L Q+ +D+
Sbjct: 987 EKLRQRLEQAEAERTRAREQLRQHQAQLSQYNQVLASLKSSYDTKKELLNELQQELQDIG 1046
Query: 382 RRQNDNS 388
R + +
Sbjct: 1047 VRADSGA 1053
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 29.9 bits (67), Expect = 3.1
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 307 EYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEM-----KERQAEELKRRDEEL 361
+YG Q + E + +KE E + +Q AE E KER + +++ E
Sbjct: 63 QYGRIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEE 122
Query: 362 MKKHAEEMQLRLAQQEEDLRR 382
+K A+ Q QQEE R+
Sbjct: 123 AEKQAQLEQ---KQQEEQARK 140
Score = 28.4 bits (63), Expect = 9.9
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 315 LHELYEHETEMLRKELAQREIDRERQKAEWEMKE---RQAEELKRRDEELMKKHAEE 368
L +L + + ++ E +++ Q + + +E + A E K++ E K A E
Sbjct: 103 LKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAE 159
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains 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 effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 27.8 bits (62), Expect = 3.2
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQE 142
+L++G + TE+D+ LF+P+G +E
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEE 30
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 29.2 bits (66), Expect = 3.2
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRL 373
E+ +E +++E K + KRR+ E +K + Q+++
Sbjct: 111 VEELDEEEQIDELLEKELAKLK---------REKRRENERKQKEILKEQMKM 153
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 27.6 bits (62), Expect = 3.2
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 23/79 (29%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHN------------AD 163
L + N+ I++ ++ LF +GE ++ IR A+
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKD-----------IRETPLRPSQKFVEFYDIRAAE 52
Query: 164 KAKAKLDGHVLKGRSLKIR 182
A L+G G LK++
Sbjct: 53 AALDALNGRPFLGGRLKVK 71
>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3. This family
consists of several radial spoke protein 3 (RSP3)
sequences. Eukaryotic cilia and flagella present in
diverse types of cells perform motile, sensory, and
developmental functions in organisms from protists to
humans. They are centred by precisely organised,
microtubule-based structures, the axonemes. The axoneme
consists of two central singlet microtubules, called the
central pair, and nine outer doublet microtubules. These
structures are well-conserved during evolution. The
outer doublet microtubules, each composed of A and B
sub-fibres, are connected to each other by nexin links,
while the central pair is held at the centre of the
axoneme by radial spokes. The radial spokes are T-shaped
structures extending from the A-tubule of each outer
doublet microtubule to the centre of the axoneme. Radial
spoke protein 3 (RSP3), is present at the proximal end
of the spoke stalk and helps in anchoring the radial
spoke to the outer doublet. It is thought that radial
spokes regulate the activity of inner arm dynein through
protein phosphorylation and dephosphorylation.
Length = 288
Score = 29.6 bits (67), Expect = 3.2
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 329 ELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDN 387
E A E+ E + AE ++++Q + +RR+ EL E Q RL + E RRR+ +
Sbjct: 142 EQALLEVLEEEELAE--LRQQQRQFEQRRNAELA-----ETQ-RLEEAE---RRRREEK 189
Score = 29.3 bits (66), Expect = 4.3
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 318 LYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE 377
L E E LR++ Q E R + A E + + E +RR+E K+ ++ Q+E
Sbjct: 149 LEEEELAELRQQQRQFEQRRNAELA--ETQRLEEAERRRREE---KERRKKQDKERKQRE 203
Query: 378 EDLRRR 383
++ +
Sbjct: 204 KETAEK 209
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB 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 AU-rich RNA element (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. .
Length = 90
Score = 28.2 bits (62), Expect = 3.2
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGE--TQELFINK----EKMFGFIRMDYKHNADKAK 166
+ LY+ + +T+ ++ +LF YG T + +++ + GFIR D + A++A
Sbjct: 5 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
Query: 167 AKLDGHVLKGRS--LKIRFA 184
L+G G + + ++FA
Sbjct: 65 KGLNGQKPPGATEPITVKFA 84
>gnl|CDD|218703 pfam05700, BCAS2, Breast carcinoma amplified sequence 2 (BCAS2).
This family consists of several eukaryotic sequences of
unknown function. The mammalian members of this family
are annotated as breast carcinoma amplified sequence 2
(BCAS2) proteins. BCAS2 is a putative spliceosome
associated protein.
Length = 221
Score = 29.4 bits (66), Expect = 3.3
Identities = 24/89 (26%), Positives = 49/89 (55%), Gaps = 15/89 (16%)
Query: 307 EYG-SRWKQLHELYEHETEMLRKELAQ-----REIDRERQKAEWEMKERQAEELKRRDEE 360
+YG + W +E E + L KELA+ E++R+R+ ++ E E+ L++R +
Sbjct: 128 KYGKNAWLVYNEQLEALLKRLEKELAELKEEIEEVNRQRKYSQEEAGEKLR-SLEQRWVD 186
Query: 361 LMKKHAEEMQLRLA-----QQEEDLRRRQ 384
L+ K+ +++ +A Q+ E L+R++
Sbjct: 187 LVSKN---LEIEVACAELEQEIEQLKRKK 212
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 29.9 bits (67), Expect = 3.4
Identities = 24/112 (21%), Positives = 40/112 (35%), Gaps = 10/112 (8%)
Query: 265 EPLE--LTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYG--SRWKQLHELYE 320
EPL ++ DG S + + PR + V+ + +
Sbjct: 378 EPLVYDMSAVFDGTSPELMGASALSPSGK----PRHSGVSVPASTSAMTHSFDDNTSKHA 433
Query: 321 HETEMLRKELAQREI-DRERQKAEWEMKER-QAEELKRRDEELMKKHAEEMQ 370
M K + + + +R + K R Q EE+KR E L KK + M+
Sbjct: 434 DPCAMGVKRMDEGILDERLGRLQALSEKLRTQHEEIKRCREALQKKESIVME 485
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 28.0 bits (63), Expect = 3.4
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRC 248
V L+ T E L F +GDI R ++ D G SK VE+ + A +A R
Sbjct: 8 VGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
>gnl|CDD|219083 pfam06548, Kinesin-related, Kinesin-related. This family
represents a region within kinesin-related proteins from
higher plants. Many family members also contain the
pfam00225 domain. Kinesins are ATP-driven microtubule
motor proteins that produce directed force. Some family
members are associated with the phragmoplast, a
structure composed mainly of microtubules that executes
cytokinesis in higher plants.
Length = 488
Score = 29.9 bits (67), Expect = 3.4
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 12/80 (15%)
Query: 307 EYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHA 366
E S+W L TE LR EL E+ + E E +++ EELK + M+ HA
Sbjct: 288 EAESKWISL-------TEELRVELEANRSLAEKLEMELESEKKCTEELKDALQRAMQGHA 340
Query: 367 EEMQLRLAQQEEDLRRRQND 386
R+ +Q +L+ + ND
Sbjct: 341 -----RIIEQYAELQEKYND 355
>gnl|CDD|115307 pfam06637, PV-1, PV-1 protein (PLVAP). This family consists of
several PV-1 (PLVAP) proteins which seem to be specific
to mammals. PV-1 is a novel protein component of the
endothelial fenestral and stomatal diaphragms. The
function of this family is unknown.
Length = 442
Score = 30.0 bits (67), Expect = 3.4
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 328 KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR--------LAQQEED 379
+ +A+ D +RQK E E + A+E K + E+ + A E +L+ LA +E+
Sbjct: 295 ERVARENADLQRQKLEAEQAAQAAQEAKAKAEK--EAQAREAKLQAECARQTQLALEEKA 352
Query: 380 LRRRQNDN 387
R + DN
Sbjct: 353 ALRAERDN 360
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 29.8 bits (67), Expect = 3.7
Identities = 11/67 (16%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
+ + K+L ++ ++ + + E + E K ++E+L ++ E+ Q A ++++
Sbjct: 368 QELLKEYNKKL--QDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKE 425
Query: 380 LRRRQND 386
R++
Sbjct: 426 KRQKDER 432
>gnl|CDD|223173 COG0095, LplA, Lipoate-protein ligase A [Coenzyme metabolism].
Length = 248
Score = 29.3 bits (66), Expect = 3.7
Identities = 20/84 (23%), Positives = 26/84 (30%), Gaps = 11/84 (13%)
Query: 281 INKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQ 340
I K + ++R N E S E E E K L + E
Sbjct: 176 IKSKGIKSVRERVA-------NLEELLKISVE----EFLEALLEAFFKVLGVELEEYELT 224
Query: 341 KAEWEMKERQAEELKRRDEELMKK 364
E E+ E+ AEE E K
Sbjct: 225 PEELELAEKLAEEKYSSWEWNFGK 248
>gnl|CDD|200948 pfam00038, Filament, Intermediate filament protein.
Length = 312
Score = 29.5 bits (67), Expect = 3.7
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
+ E LR+++ EI+ + K + ERQ EL+ R E + + Q +++ EE+
Sbjct: 215 KEEITELRRQIQSLEIELQSLKKQKASLERQLAELEERYELELADY----QDTISELEEE 270
Query: 380 LRRRQNDNSMFLVEQQQ 396
L++ + + + L E Q+
Sbjct: 271 LQQLKAEMARQLREYQE 287
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, 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 A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains 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 = 80
Score = 27.7 bits (61), Expect = 3.8
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
+L++G I D E+ + + F+ YG+ + I K++ FGF+ D DK +
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
Query: 169 LDGHVLKGRSLKIRFA 184
H + G + ++R A
Sbjct: 62 -KYHTINGHNAEVRKA 76
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 30.0 bits (67), Expect = 3.9
Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQL- 371
+ + Y+ + +R ++ +E E + + E + + LK R +E+ ++ M+L
Sbjct: 209 LKYLKQYKEKACEIRDQITSKEAQLESSREIVKSYENELDPLKNRLKEIEHNLSKIMKLD 268
Query: 372 -RLAQQEEDLRRRQNDNS 388
+ + ++ + DNS
Sbjct: 269 NEIKALKSRKKQMEKDNS 286
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 27.6 bits (62), Expect = 3.9
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 117 YLGNIGGDITENDIIELFKPYGETQELFI----NKEKMFGFIRMDYKHNADKAKAKLDGH 172
Y+GN+ T + ++E F GE + + + + + F+ + + A KL+G
Sbjct: 8 YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINA-LKLNGA 66
Query: 173 VLKGRSLKIRFAPINAAIK 191
+ GR LK+ + NA +K
Sbjct: 67 MFGGRPLKVNHS-NNAIVK 84
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 27.7 bits (61), Expect = 4.0
Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKA 167
C++++G + T+ + E F +GE +E + ++ + FGF+ + DK A
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 168 K 168
+
Sbjct: 61 Q 61
>gnl|CDD|227468 COG5139, COG5139, Uncharacterized conserved protein [Function
unknown].
Length = 397
Score = 29.7 bits (66), Expect = 4.0
Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 3/78 (3%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEM---KERQAEELKRRDEELMKKHAEEM 369
K L M ++ Q + + + + A RR E+L+++ +E+
Sbjct: 98 KNDQSLQPTREPMDSRDSGQDFTEAQSGELGDTGDRQLKAPAASRARRKEDLLEQTVDEI 157
Query: 370 QLRLAQQEEDLRRRQNDN 387
LRL ++ +D ++ N N
Sbjct: 158 SLRLKKRMQDAAKKDNAN 175
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 29.2 bits (66), Expect = 4.0
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 328 KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
K L + ++E+ K E E K + E ++ + AE+++LR Q+E DL
Sbjct: 60 KALKAKIEEKEKAKREKEEKGLRELE----EDTPEDELAEKLRLRKLQEESDLN 109
>gnl|CDD|149160 pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein. The sequences
featured in this family are similar to a region of human
TPR protein and to yeast myosin-like proteins 1 (MLP1)
and 2 (MLP2). These proteins share a number of features;
for example, they all have coiled-coil regions and all
three are associated with nuclear pores. TPR is thought
to be a component of nuclear pore complex- attached
intra-nuclear filaments, and is implicated in nuclear
protein import. Moreover, its N-terminal region is
involved in the activation of oncogenic kinases,
possibly by mediating the dimerisation of kinase domains
or by targeting these kinases to the nuclear pore
complex. MLP1 and MLP2 are involved in the process of
telomere length regulation, where they are thought to
interact with proteins such as Tel1p and modulate their
activity.
Length = 132
Score = 28.4 bits (64), Expect = 4.1
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWE----MKERQAEELKRRDEEL 361
KQL+EL + E L+ E + + + WE M E + EL++R EEL
Sbjct: 66 KQLNELKK-EIAQLKAEAESAQAELSEAEESWEEQKKMLEDELSELEKRIEEL 117
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 29.5 bits (67), Expect = 4.1
Identities = 26/116 (22%), Positives = 34/116 (29%), Gaps = 25/116 (21%)
Query: 397 GRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFDQGGRSGGGGG 456
RGG+ G AY AA G+ G G+ A G +
Sbjct: 310 ARGGAAAAGGASSAYS--------AGAAGGSGAAGVAAGLGGVARA-----GASAAASPL 356
Query: 457 RRNDSASSG---WSRREGGAGRWGPSVDHGSRRGGSGGGGPTDYQP------KRRN 503
RR S ++ S R G G + G + G P KRR
Sbjct: 357 RRAASRAAESMKSSFRAGARSTGGGA---GGAAAAAAAGAAAAGPPAWAKRMKRRQ 409
>gnl|CDD|117516 pfam08949, DUF1860, Domain of unknown function (DUF1860). This
domain has no known function. It is predominantly found
in the C-terminus of bacteriophage spike proteins.
Length = 220
Score = 29.3 bits (65), Expect = 4.2
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 14/89 (15%)
Query: 398 RGGSGGYGSPGQAYGNAIID------FEAL---AAAVGNAVVGNVTG-----VDNKGSAM 443
+G G G+PG A G +++ E+L A+ G +V ++ + + G +
Sbjct: 5 KGDKGDPGAPGPAGGTVVVEDSGASFGESLLDTASDPGKILVKRISAGSGITLTDYGDEI 64
Query: 444 DFDQGGRSGGGGGRRNDSASSGWSRREGG 472
+ + G GGGGG D+ S +S GG
Sbjct: 65 EIEASGGGGGGGGGVTDALSLFYSTSSGG 93
>gnl|CDD|219581 pfam07795, DUF1635, Protein of unknown function (DUF1635). The
members of this family include sequences that are parts
of hypothetical proteins expressed by plant species. The
region in question is about 170 amino acids long.
Length = 214
Score = 29.1 bits (65), Expect = 4.2
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 12/77 (15%)
Query: 323 TEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
E LR+ L + E+ K EEL++ DE+++ ++ L+ +E D
Sbjct: 3 IEELRQSLQYTTFELEQTKMV------ANEELRKHDEQVI--QLLDL-LKKTIKERDEAL 53
Query: 383 RQNDNSMF---LVEQQQ 396
Q +F ++Q Q
Sbjct: 54 EQLQRLLFDTNFLQQHQ 70
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB 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 AU-rich RNA element (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. .
Length = 83
Score = 27.4 bits (60), Expect = 4.3
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 6/66 (9%)
Query: 125 ITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGRS 178
+T+ ++ LF GE + + ++K+ +GF+ +A+KA L+G L+ ++
Sbjct: 16 MTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 75
Query: 179 LKIRFA 184
+K+ +A
Sbjct: 76 IKVSYA 81
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 29.2 bits (66), Expect = 4.3
Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 10/43 (23%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRY 83
G G G GG GG+ G G GS GGGG +
Sbjct: 239 GSGGSGGSGGGSSGGGFSG----GGGSS------GGGGASGSW 271
Score = 28.9 bits (65), Expect = 6.2
Identities = 18/83 (21%), Positives = 24/83 (28%), Gaps = 12/83 (14%)
Query: 414 AIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFDQGGRSGGGGGRRNDSASSGWSRREGGA 473
A+ F A + G + G D+ G RR+ +
Sbjct: 193 AVWVFILFGGATRAIISGPMFGRSLYLGRQP-DRWLNGVLGRRRRSSGSGGSGGS----- 246
Query: 474 GRWGPSVDHGSRRGG---SGGGG 493
G G GG SGGGG
Sbjct: 247 GGGSSG---GGFSGGGGSSGGGG 266
>gnl|CDD|227780 COG5493, COG5493, Uncharacterized conserved protein containing a
coiled-coil domain [Function unknown].
Length = 231
Score = 29.1 bits (65), Expect = 4.3
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 312 WKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKK 364
W+QL + + E LRKE QR+ + +K E ++ E+LK ++
Sbjct: 39 WQQLAT--KQDVEELRKETEQRQKELADEKLEVRKQKATKEDLKLLQRFQEEE 89
>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869). This
bacterial family of proteins has no known function.
Length = 131
Score = 28.3 bits (64), Expect = 4.4
Identities = 14/74 (18%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAE-ELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
E L+ EL ++ E++ + E + ++A E++++ + E++Q ++ Q+
Sbjct: 19 EELQAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQ----QIEQIQQQVEQERAKRLE 74
Query: 383 RQNDNSMFLVEQQQ 396
++N L + +Q
Sbjct: 75 QKN---QLLFQIEQ 85
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 27.7 bits (62), Expect = 4.4
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 7/85 (8%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGI--VEFA----RKPAAAQ 243
I + L+ T + + + F FG+IE + + + GI V F R AA +
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIE-ESELKLDPRTGQSLGICRVTFRGDPLRPSAAHE 59
Query: 244 ALRRCAEGCFFLTQSLRPVIVEPLE 268
A + +G + V VE
Sbjct: 60 AAKAAVDGLNGRRIGGKRVRVELDR 84
>gnl|CDD|114015 pfam05266, DUF724, Protein of unknown function (DUF724). This
family contains several uncharacterized proteins found
in Arabidopsis thaliana and other plants. This region is
often found associated with Agenet domains and may
contain coiled-coil.
Length = 190
Score = 29.0 bits (65), Expect = 4.4
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 13/79 (16%)
Query: 310 SRWKQLHELYEHETEMLR------KELAQREIDR---ERQKAEWEMKERQAEELKRRDEE 360
SR +L L + +T+ L KE+A++EI R + + AE E K + +R
Sbjct: 93 SRLNKLLSLKDDQTKKLEERKGLEKEIAEKEISRQELDSEIAELERKILE----LQRQAA 148
Query: 361 LMKKHAEEMQLRLAQQEED 379
L+K+ E +A+ + +
Sbjct: 149 LLKEKKEAEDKEIARLKSE 167
>gnl|CDD|218380 pfam05010, TACC, Transforming acidic coiled-coil-containing protein
(TACC). This family contains the proteins TACC 1, 2 and
3 the genes for which are found concentrated in the
centrosomes of eukaryotic and may play a conserved role
in organising centrosomal microtubules. The human TACC
proteins have been linked to cancer and TACC2 has been
identified as a possible tumour suppressor (AZU-1). The
functional homologue (Alp7) in Schizosaccharomyces pombe
has been shown to be required for organisation of
bipolar spindles.
Length = 207
Score = 28.9 bits (65), Expect = 4.4
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 11/81 (13%)
Query: 307 EYGSRWKQLHELYE----HETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELM 362
EY R K+ + Y+ H E L E+A EI + R KA+ E QA L++ E M
Sbjct: 122 EYLDRLKKEEQRYQALKAHAEEKL--EIANEEIAQVRSKAKAETAALQA-SLRK---EQM 175
Query: 363 KKHAEEMQLRLAQQE-EDLRR 382
K + E L +E E+L +
Sbjct: 176 KVQSLEETLEQKNKENEELTK 196
>gnl|CDD|113514 pfam04747, DUF612, Protein of unknown function, DUF612. This
family includes several uncharacterized proteins from
Caenorhabditis elegans.
Length = 517
Score = 29.6 bits (65), Expect = 4.5
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
+HE E +K A++ ++E ++AE E K+R A+E + + K E +Q ++E D
Sbjct: 85 DHEAE--QKVNAKKAAEKEARRAEAEAKKRAAQE---EEHKQWKAEQERIQKEQEKKEAD 139
Query: 380 LRRRQ 384
L++ Q
Sbjct: 140 LKKLQ 144
>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 = 27.1 bits (61), Expect = 4.6
Identities = 12/68 (17%), Positives = 26/68 (38%), Gaps = 7/68 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQE----LFINKEKMFG--FIRMDYKHNADKAKAKL 169
+ L + TE DI + F + ++ + + G ++ +A +A K
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61
Query: 170 DGHVLKGR 177
+ + GR
Sbjct: 62 NNK-MGGR 68
Score = 26.8 bits (60), Expect = 5.5
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIV-DERGNSKCEGIVEFARKPAAAQALRRC 248
++++ L T E + F I IV D+ G E VEFA A +ALR+
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains 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 = 80
Score = 27.3 bits (60), Expect = 4.6
Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
++++G I D E + + F+ YG+ + + + K++ F F+ D DK +
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61
Query: 169 LDGHVLKGRSLKIRFA 184
H + G + +++ A
Sbjct: 62 -KYHTINGHNCEVKKA 76
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 27.1 bits (60), Expect = 4.7
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 10/69 (14%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKA---- 165
+++G + D T+ D+ E F +GE + I + + FGF+ + +K
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 166 KAKLDGHVL 174
+ KLDG V+
Sbjct: 61 EHKLDGRVI 69
>gnl|CDD|176190 cd05288, PGDH, Prostaglandin dehydrogenases. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 29.4 bits (67), Expect = 4.8
Identities = 22/86 (25%), Positives = 32/86 (37%), Gaps = 22/86 (25%)
Query: 117 YLGNIGGDITENDIIELFKPYG-------------------ETQELFINKE-KMFGFIRM 156
Y N+GG+I + + L G + I K M GFI
Sbjct: 218 YFDNVGGEILD-AALTLLNKGGRIALCGAISQYNATEPPGPKNLGNIITKRLTMQGFIVS 276
Query: 157 DYKHNADKAKAKLDGHVLKGRSLKIR 182
DY +A A+L + +G+ LK R
Sbjct: 277 DYADRFPEALAELAKWLAEGK-LKYR 301
>gnl|CDD|215901 pfam00401, ATP-synt_DE, ATP synthase, Delta/Epsilon chain, long
alpha-helix domain. Part of the ATP synthase CF(1).
These subunits are part of the head unit of the ATP
synthase. This subunit is called epsilon in bacteria and
delta in mitochondria. In bacteria the delta (D) subunit
is equivalent to the mitochondrial Oligomycin sensitive
subunit, OSCP (pfam00213).
Length = 48
Score = 26.3 bits (59), Expect = 4.9
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 13/50 (26%)
Query: 333 REIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRR 382
+ID ER AEE K R EE + K + + A+ L+R
Sbjct: 1 EDIDLER-----------AEEAKERAEEALAKAEGDKEYIRAEAA--LKR 37
>gnl|CDD|226213 COG3688, COG3688, Predicted RNA-binding protein containing a PIN
domain [General function prediction only].
Length = 173
Score = 28.5 bits (64), Expect = 5.0
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 306 FEYGSRWKQLHELY-EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKR 356
F G+ ELY E ET R + R+I +E+ + E+L++
Sbjct: 116 FGQGALRMSARELYQEVETIEARISKSSRKISKEKPLTRIALDPEILEKLEK 167
>gnl|CDD|114908 pfam06216, RTBV_P46, Rice tungro bacilliform virus P46 protein.
This family consists of several Rice tungro bacilliform
virus P46 proteins. The function of this family is
unknown.
Length = 392
Score = 29.2 bits (65), Expect = 5.0
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 303 SFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELM 362
+F + R ++LH + +H + +E + E K E E Q LK+++EEL
Sbjct: 47 TFSSDNTERVRKLHIIADH--------IYLKEFEIESYKLECEKLNDQVSHLKKQNEEL- 97
Query: 363 KKHAEEMQLRLAQQEEDLRR 382
K EM+ + E L++
Sbjct: 98 KAQIAEMKDIIEGLREPLKK 117
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 29.3 bits (66), Expect = 5.2
Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 28/97 (28%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEEL-KRRDEELMK-------K 364
K+ H + H+ E L++EL + E E KA+ E + E+L +RR EE M K
Sbjct: 229 KKYHRV--HKKEKLKEELKEFE---ELVKADPEAALEELEKLERRRAEERMTLKHKNTSK 283
Query: 365 HAEEMQLR---------------LAQQEEDLRRRQND 386
A+ M +Q E+LRR+
Sbjct: 284 WAKSMLKTGRAKYDEEARKALEEQLRQGEELRRKIEG 320
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 27.0 bits (60), Expect = 5.3
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQEL----FINKEKMFGFIRMDYKHNADKAKAKLDG 171
L++GN+ + TE+++ F G + + F + K GF +D++ + A L G
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE-EIEFATNALKG 59
Query: 172 HVLKGRSLKIRFA 184
L GR+L++ +
Sbjct: 60 KHLNGRALRVEYG 72
>gnl|CDD|224202 COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and
metabolism].
Length = 533
Score = 29.5 bits (67), Expect = 5.3
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 10/80 (12%)
Query: 302 NSFEFEYGSRWKQLHELYEHETEMLRKELAQREID-RERQKAEWEMKERQAEELKRRDEE 360
N F ++L L+ E LR LA + + + A ++ + + ++R +
Sbjct: 432 NGRAFS-EDGLEELDALFALTLENLR--LAISVLVTGDLELARRLVERK--KRVRRLERR 486
Query: 361 LMKKHAEEMQLRLAQQEEDL 380
K+H + RL +
Sbjct: 487 SSKRHLD----RLRDGAASV 502
>gnl|CDD|218534 pfam05278, PEARLI-4, Arabidopsis phospholipase-like protein (PEARLI
4). This family contains several phospholipase-like
proteins from Arabidopsis thaliana which are homologous
to PEARLI 4.
Length = 234
Score = 29.0 bits (65), Expect = 5.3
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 17/91 (18%)
Query: 316 HELYEHETEMLRKELAQREI-----DRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
+ ET ++ KE +R++ + E+Q+AE KE++ +E + + EEM
Sbjct: 148 EYFDQQETAVVEKERHERDVLLKKQEMEKQEAELVRKEKEVKEFREK--------VEEMA 199
Query: 371 LRLAQQEEDLRRRQNDNSMFL---VEQQQGR 398
RL + E R R FL VE+ +G+
Sbjct: 200 GRLGELEMK-RLRLEKRLDFLGSKVEKFKGK 229
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD 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. .
Length = 83
Score = 27.4 bits (60), Expect = 5.3
Identities = 16/67 (23%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGR 177
++T+ + LF GE + + ++K+ +GF+ +A+KA L+G L+ +
Sbjct: 13 NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72
Query: 178 SLKIRFA 184
++K+ +A
Sbjct: 73 TIKVSYA 79
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 29.4 bits (66), Expect = 5.4
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 40 LGGRGGGRGGGVGGRGGYRGNRPDGRG 66
LGG GGG+G G GG +G RP G
Sbjct: 52 LGGLGGGKGTGSGGGSSSQGPRPQLGG 78
>gnl|CDD|187733 cd09764, Csb3_I-U, CRISPR/Cas system-associated RAMP superfamily
protein Csb3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; Might be a catalytically
active RNA endoribonuclease.
Length = 341
Score = 29.0 bits (65), Expect = 5.4
Identities = 17/58 (29%), Positives = 22/58 (37%), Gaps = 20/58 (34%)
Query: 312 WKQLHELYEHETEMLRKELAQREID-----------------RERQK---AEWEMKER 349
WK+L + EH + LR EL R I +E + WEMK R
Sbjct: 100 WKRLQKDREHAIDSLRTELDYRYIGALGSPGYWSGWFPEKNKKEYPDHGASRWEMKTR 157
>gnl|CDD|221283 pfam11875, DUF3395, Domain of unknown function (DUF3395). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 147 to 176 amino acids in length. This domain is
found associated with pfam00226.
Length = 144
Score = 28.5 bits (64), Expect = 5.4
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 325 MLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKH 365
++E + EI +++Q+AE + ++ E K
Sbjct: 12 ERQREKNKTEIAKKKQEAESAVSLMGDVVERKLTREEEKGG 52
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 27.1 bits (60), Expect = 5.5
Identities = 15/76 (19%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 116 LYLGNIGGDITENDIIELFK-PYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
+++G++ ++ E+D++ LF+ + + I + +GF+R +++ +A +
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Query: 169 LDGHVLKGRSLKIRFA 184
+ G GR ++I A
Sbjct: 64 MQGVYCGGRPMRISTA 79
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 29.2 bits (66), Expect = 5.5
Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 13/72 (18%)
Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
K L+E LR +L I + ++ E E+ QA + A Q
Sbjct: 127 LIKGQQSLFESRKSTLRAQLEL--ILAQIKQLEAELAGLQA-----------QLQALRQQ 173
Query: 371 LRLAQQEEDLRR 382
L + +E + RR
Sbjct: 174 LEVISEELEARR 185
>gnl|CDD|115072 pfam06391, MAT1, CDK-activating kinase assembly factor MAT1. MAT1
is an assembly/targeting factor for cyclin-dependent
kinase-activating kinase (CAK), which interacts with the
transcription factor TFIIH. The domain found to the
N-terminal side of this domain is a C3HC4 RING finger.
Length = 200
Score = 28.6 bits (64), Expect = 5.5
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
E K+ R ++ R E E E QA E ++ +E + H ++ +QE+ + +
Sbjct: 74 EKENKDSIMR--NKRRLTREQEELE-QALEEEKEMKEEKRLHLQKE-----EQEQKMAKE 125
Query: 384 QN 385
++
Sbjct: 126 KD 127
>gnl|CDD|222142 pfam13455, MUG113, Meiotically up-regulated gene 113. This is a
family of fungal proteins found to be up-regulated in
meiosis.
Length = 76
Score = 26.9 bits (60), Expect = 5.6
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 321 HETE-MLRKELAQREIDRERQKAEW-EMKERQAEELKRR 357
+ E +L KELA +++ + EW E+ + +E+ RR
Sbjct: 37 RKLERLLHKELADYRVNKVKCDREWFEVSLEEIKEVIRR 75
>gnl|CDD|130217 TIGR01147, V_ATP_synt_G, vacuolar ATP synthase, subunit G. This
model describes the vacuolar ATP synthase G subunit in
eukaryotes and includes members from diverse groups
e.g., fungi, plants, parasites etc. V-ATPases are
multi-subunit enzymes composed of two functional
domains: A transmembrane Vo domain and a peripheral
catalytic domain V1. The G subunit is one of the
subunits of the catalytic domain. V-ATPases are
responsible for the acidification of endosomes and
lysosomes, which are part of the central vacuolar system
[Energy metabolism, ATP-proton motive force
interconversion].
Length = 113
Score = 27.9 bits (62), Expect = 5.7
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 328 KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEE 378
KE AQ+E+++ +Q+ E E KE +A+ L +K E Q ++ + ++
Sbjct: 37 KEEAQKEVEKYKQQREKEFKEFEAKHLGGN-GAAEEKAEAETQAKIREIKK 86
>gnl|CDD|218852 pfam06008, Laminin_I, Laminin Domain I. coiled-coil structure. It
has been suggested that the domains I and II from
laminin A, B1 and B2 may come together to form a triple
helical coiled-coil structure.
Length = 263
Score = 28.9 bits (65), Expect = 5.8
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLR 372
L + ML E+ +R+ ++ Q AE E+K AEEL R + + EE +
Sbjct: 122 SALSRMLAEAQRMLG-EIRERDFQKQLQNAEAELKA--AEELLNRVQTWFQTPQEENEGL 178
Query: 373 LAQQEEDLRRRQND 386
E LR N+
Sbjct: 179 F----EALRDDLNE 188
>gnl|CDD|131526 TIGR02473, flagell_FliJ, flagellar export protein FliJ. Members of
this family are the FliJ protein found, in nearly every
case, in the midst of other flagellar biosynthesis genes
in bacgterial genomes. Typically the fliJ gene is found
adjacent to the gene for the flagellum-specific ATPase
FliI. Sequence scoring in the gray zone between trusted
and noise cutoffs include both probable FliJ proteins
and components of bacterial type III secretion systems.
Length = 141
Score = 28.0 bits (63), Expect = 5.8
Identities = 11/67 (16%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 330 LAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSM 389
+ Q + ++Q+ E + +++ E + R L++ E L ++++ R +
Sbjct: 70 IRQLDQRIQQQQQELALLQQEVEAKRER---LLEARRELKALEKLKEKKQKEYRAEEA-- 124
Query: 390 FLVEQQQ 396
EQ++
Sbjct: 125 -KREQKE 130
>gnl|CDD|151173 pfam10669, Phage_Gp23, Protein gp23 (Bacteriophage A118). This is
the highly conserved family of the major tail subunit
protein.
Length = 121
Score = 27.8 bits (61), Expect = 5.8
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 329 ELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDN 387
++ + E+ ER K E E ++R E + RD+ + + ++ RL ++ D+ +Q +
Sbjct: 42 KIVRVEMKEERDKMETEREKRDKESKEERDKFISTMNEQQ---RLMDKQNDMMGQQQQS 97
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 29.2 bits (66), Expect = 5.8
Identities = 27/152 (17%), Positives = 53/152 (34%), Gaps = 13/152 (8%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
E + LRK LA+ + E KAE E +++ + + ++ ++ ++ +E+ + Q + + +
Sbjct: 67 EVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQ 126
Query: 382 RRQNDNSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGS 441
+ Q L++Q Q R G G L +G G G
Sbjct: 127 QLQG-----LIDQLQRRLAGVLTGPSGGG--------SDLPVGLGLDPGGGAQFEGGGGV 173
Query: 442 AMDFDQGGRSGGGGGRRNDSASSGWSRREGGA 473
Q G + + A
Sbjct: 174 VWVEPQDALPTDRNGNSGAPSKFSFPTSFDNA 205
>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 = 27.0 bits (60), Expect = 6.1
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 117 YLGNIGGDITENDIIELFK 135
YLGN+ D+TE DI E F+
Sbjct: 5 YLGNLPYDVTEEDIKEFFR 23
>gnl|CDD|192292 pfam09429, Wbp11, WW domain binding protein 11. The WW domain is a
small protein module with a triple-stranded beta-sheet
fold. This is a family of WW domain binding proteins.
Length = 78
Score = 26.9 bits (60), Expect = 6.1
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 16/65 (24%)
Query: 327 RKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ---LRLAQQEED--LR 381
RKE ++E+ + + ERQ RR+ +L KK+ + +Q +L QEE LR
Sbjct: 11 RKEQKKKELKKNK-------AERQ----ARREAKLAKKNPDRLQRELDKLKAQEESGKLR 59
Query: 382 RRQND 386
+
Sbjct: 60 PVEKQ 64
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 29.0 bits (65), Expect = 6.3
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 303 SFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
SFE + +R Q +YE + E R Q IDR R KA K +QA+
Sbjct: 233 SFEVQRATRLAQQQAMYESQQE--RVAHLQSYIDRFRAKAT---KAKQAQ 277
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC 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 AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. 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. .
Length = 81
Score = 26.9 bits (59), Expect = 6.3
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGE--TQELFINK----EKMFGFIRMDYKHNADKAK 166
+ LY+ + +++ ++ +LF YG T + +++ + GFIR D + A++A
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60
Query: 167 AKLDGHVLKGRS--LKIRFA 184
L+G G + + ++FA
Sbjct: 61 KGLNGQKPLGAAEPITVKFA 80
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 27.4 bits (61), Expect = 6.3
Identities = 18/40 (45%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG GG GGG G GG G G GGGGGG
Sbjct: 55 GGGGGYGGGGYYGGGGGYGGGGGGYP--------GGGGGG 86
Score = 27.0 bits (60), Expect = 6.7
Identities = 20/40 (50%), Positives = 20/40 (50%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
GG GGG GGG GG G Y G G G GGG GG
Sbjct: 50 GGYGGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGG 89
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 29.2 bits (65), Expect = 6.4
Identities = 10/57 (17%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 328 KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ 384
E ++ ++KER+++E +R ++L K+ ++ Q+ + ++ Q
Sbjct: 185 ALREDNEKGVNFRRDMTDLKERESQEDAKRAQQL-KEELDKKQIDADKAQQKADFAQ 240
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 28.4 bits (64), Expect = 6.4
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 23/92 (25%)
Query: 277 SERTINKKTPEFYKQRQVGP----RFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQ 332
+E ++KK + K ++ G + ++ S E R +L + +E +E+++ EL +
Sbjct: 120 AESELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEVSELIKSELER 179
Query: 333 REIDR----------------ERQK---AEWE 345
E +R E QK WE
Sbjct: 180 FERERVEDFRNSVEIYLESAIESQKELIELWE 211
>gnl|CDD|226883 COG4477, EzrA, Negative regulator of septation ring formation [Cell
division and chromosome partitioning].
Length = 570
Score = 29.3 bits (66), Expect = 6.4
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQ 376
HE + L KEL++ I+ E A ++ L+ EE+++ LA+Q
Sbjct: 453 GHEIQDLMKELSEVPINMEAVSALVDIATEDMNTLEDETEEVVE------NAVLAEQ 503
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 28.6 bits (64), Expect = 6.6
Identities = 29/107 (27%), Positives = 39/107 (36%), Gaps = 10/107 (9%)
Query: 397 GRGGSG-GYGSPGQAYGNAI---------IDFEALAAAVGNAVVGNVTGVDNKGSAMDFD 446
GRGG+G G S G G+ I I+ A G G +G+ +
Sbjct: 116 GRGGNGSGSNSAGSNGGHCIQNDIGGRLRINNGGAIAGGGGGGGGASLKNSWRGNGVCGG 175
Query: 447 QGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGG 493
GGR G GG+ S G + G G +G GG+ G
Sbjct: 176 GGGRPFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYGGGNGGNVGAA 222
>gnl|CDD|173197 PRK14735, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 139
Score = 28.0 bits (62), Expect = 6.7
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 329 ELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
E+ + ++ R +AE +ERQ+E+ E +++ ++LR+AQ + RR+
Sbjct: 86 EIDEARAEQARAEAEQRRRERQSEQDLALAEAKLRR--AMVRLRVAQLHKIRRRQ 138
>gnl|CDD|216292 pfam01086, Clathrin_lg_ch, Clathrin light chain.
Length = 225
Score = 28.6 bits (64), Expect = 6.7
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 343 EWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE-EDLRRRQND 386
+W +ER+ ++ RDE KK E ++ AQ+E +D N+
Sbjct: 116 KW--RERRDLRIEERDEASEKKKEELIE--KAQKEIDDFYENYNE 156
>gnl|CDD|221433 pfam12130, DUF3585, Protein of unknown function (DUF3585). This
domain is found in eukaryotes. This domain is typically
between 135 and 149 amino acids in length and is found
associated with pfam00307.
Length = 142
Score = 28.0 bits (63), Expect = 6.7
Identities = 23/69 (33%), Positives = 29/69 (42%), Gaps = 11/69 (15%)
Query: 329 ELAQREIDRERQKAEWEMKERQAEELKRRDEELM--------KKHA---EEMQLRLAQQE 377
EL Q E++ E E R EE +EELM +K+A E +L QE
Sbjct: 13 ELEQELDQLEQRGVELEKALRGCEEGDEEEEELMVEWFKLVREKNALVRRESELMYLAQE 72
Query: 378 EDLRRRQND 386
L RQ D
Sbjct: 73 LQLEERQAD 81
>gnl|CDD|191114 pfam04859, DUF641, Plant protein of unknown function (DUF641).
Plant protein of unknown function.
Length = 132
Score = 27.7 bits (62), Expect = 6.8
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKK 364
E + R L EI ++ +AE K+ + + L+ + EEL+
Sbjct: 82 EIQEQRSLLKTYEIMVKKLEAEVRAKDSEIDSLREKLEELLVA 124
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 28.7 bits (64), Expect = 6.9
Identities = 19/43 (44%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRY 83
GG GG GGG GG G G P G G MG G G+ Y
Sbjct: 192 GGGGGMGGGGGGGMGEMGGMGPQGGGGGY--GGMGAPGQGNAY 232
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 26.7 bits (59), Expect = 6.9
Identities = 14/67 (20%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINK-EKMFGFIRMDYKHNADKAKAKLDGHVL 174
L + N+ ++ + +F+ YG+ +EL ++ F+ +A KA ++G +
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKEI 63
Query: 175 KGRSLKI 181
G+ + I
Sbjct: 64 SGKPVVI 70
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 28.1 bits (62), Expect = 7.0
Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
+ +Q E + + R+EL +R ER + E E + ++ E R EE K+ AEE +
Sbjct: 41 QEEQERREQEEQDRLEREELKRRA-AEERLRREEEARRQEEER-AREKEEKAKRKAEEEE 98
Query: 371 LRLAQQEEDLRRRQ 384
+ +++E +++++
Sbjct: 99 KQEQEEQERIQKQK 112
>gnl|CDD|221526 pfam12316, Dsh_C, Segment polarity protein dishevelled (Dsh) C
terminal. This domain family is found in eukaryotes,
and is typically between 177 and 207 amino acids in
length. The family is found in association with
pfam00778, pfam02377, pfam00610, pfam00595. The segment
polarity gene dishevelled (dsh) is required for pattern
formation of the embryonic segments. It is involved in
the determination of body organisation through the
Wingless pathway (analogous to the Wnt-1 pathway).
Length = 202
Score = 28.4 bits (63), Expect = 7.1
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 461 SASSGWSRREGGAGRWGPSVDHGSRRGGSG 490
S SSG +R +G R + G + GGSG
Sbjct: 74 SRSSGSNRSDGERSRAADGREGGRKSGGSG 103
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 29.1 bits (65), Expect = 7.2
Identities = 27/122 (22%), Positives = 47/122 (38%), Gaps = 15/122 (12%)
Query: 277 SERTINKKTPEFYKQRQVGPRFATVNSFEFEYGS--------RWKQLHELY-----EHET 323
E + +K E + + R A+ + +E R K L EL E
Sbjct: 73 LENELMQKELEHKRAQIELERKASTLAENYERELDRNLELEVRLKALEELEKKAENEAAE 132
Query: 324 EMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
+L + ++D E K + E KE Q +E + +K EMQ R + +L+
Sbjct: 133 AEEEAKLLKDKLDAESLKLQNE-KEDQLKE-AKESISRIKNDLSEMQCRAQNADTELKLL 190
Query: 384 QN 385
++
Sbjct: 191 ES 192
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 28.1 bits (62), Expect = 7.2
Identities = 20/44 (45%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 204 LELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
L AF FGD+ A VIVD E G S+ G V F + AA A+
Sbjct: 51 LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 28.9 bits (65), Expect = 7.3
Identities = 18/38 (47%), Positives = 21/38 (55%)
Query: 42 GRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGG 79
G GG GGG GG GG+ G+ G D+ S GGGG
Sbjct: 72 GANGGFGGGAGGFGGFDGSGGFGGFEDIFSSFFGGGGA 109
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 28.9 bits (65), Expect = 7.4
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 12/67 (17%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
E ++ + ELA E +Q+AE +L++ D +L K+ E+ Q L ++D
Sbjct: 664 EQQSLKDKLELAIAE---RKQQAE--------TQLRQLDAQL-KQLLEQQQAFLEALKDD 711
Query: 380 LRRRQND 386
R + +
Sbjct: 712 FRELRTE 718
>gnl|CDD|215964 pfam00513, Late_protein_L2, Late Protein L2.
Length = 466
Score = 28.8 bits (65), Expect = 7.4
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 40 LGGRGGGRGGGVGGRGGY 57
GG G G G G GGR GY
Sbjct: 50 FGGLGIGTGSGSGGRTGY 67
>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 28.8 bits (65), Expect = 7.6
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 333 REIDRERQKAEWEMKERQAEELKRRDEELMKKHAE---EMQLRLAQQEEDLRRRQND 386
R R R E + ++ R +L + +A E+ R Q E LRR Q++
Sbjct: 319 RRRARLRLAELQEARAELERRVEERTADLTRANARLQAEIAER-EQAEAALRRAQDE 374
>gnl|CDD|220098 pfam09057, Smac_DIABLO, Second Mitochondria-derived Activator of
Caspases. Second Mitochondria-derived Activator of
Caspases promotes apoptosis by activating caspases in
the cytochrome c/Apaf-1/caspase-9 pathway, and by
opposing the inhibitory activity of inhibitor of
apoptosis proteins (XIAP-BIR3). The protein assumes an
elongated three-helix bundle structure, and forms a
dimer in solution.
Length = 234
Score = 28.3 bits (63), Expect = 7.7
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 329 ELAQREIDRERQ---KAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
++AQ +++ RQ +AE ++ E +AEE++R E E++
Sbjct: 180 QVAQSQVEEVRQLSKEAEKKLAESKAEEIQRMAEYASSIDLSELE 224
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 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 = 26.6 bits (59), Expect = 7.7
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM--------FGFIRMDYKHNADKA 165
++ + NI + T ++ ELF +GE + + + K KM FGF+ K +A +A
Sbjct: 1 SKILVRNIPFEATVKELRELFSTFGELKTVRLPK-KMTGTGSHRGFGFVDFITKQDAKRA 59
Query: 166 -KAKLDGHVLKGRSLKIRFA 184
KA L GR L + +A
Sbjct: 60 FKALCHSTHLYGRRLVLEWA 79
>gnl|CDD|218517 pfam05236, TAF4, Transcription initiation factor TFIID component
TAF4 family. This region of similarity is found in
Transcription initiation factor TFIID component TAF4.
Length = 255
Score = 28.5 bits (64), Expect = 7.7
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 326 LRKELAQREIDRERQKAEWE--MKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRR 383
+R++L ++QK E E ++ R+ L+ ++ +K+ A+E Q + E+ R R
Sbjct: 111 VRRQLRFLA---QKQKEEEERRVERRRELGLEDPEQLRLKQKAKEEQ---KAESEETRHR 164
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 26.6 bits (59), Expect = 8.0
Identities = 12/57 (21%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKA 165
++++G + + TE+D+ + F +G+ ++ + N+ + FGF+ + + DK
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
>gnl|CDD|221016 pfam11180, DUF2968, Protein of unknown function (DUF2968). This
family of proteins has no known function.
Length = 192
Score = 28.2 bits (63), Expect = 8.0
Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 15/70 (21%)
Query: 329 ELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNS 388
+LA EI R + +A+ ERQ +E RL DL+ Q
Sbjct: 99 QLADVEIRRAQLEAQKAQLERQIAA------------SEARAERLQA---DLQLAQAQEQ 143
Query: 389 MFLVEQQQGR 398
QQQ R
Sbjct: 144 QVAARQQQAR 153
>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 = 26.7 bits (59), Expect = 8.3
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAI-VIVDERGNSKCEGIVEFARKPAAAQALR 246
I +N VT ++ F F E I ++ D++G E +V+F + A +A R
Sbjct: 3 IYARNFPFDVTKVEVQKFFAPFNIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAER 60
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the family
being composed of Afadin- and alpha -Actinin-Binding
Proteins Localised at Cell-Cell Adherens Junctions.
Length = 149
Score = 27.6 bits (62), Expect = 8.4
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 320 EHETEMLRK--ELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQE 377
E + + E+ + + ER K + E ER+ L+ ++ +L KK Q L ++
Sbjct: 54 SLEETLRKLEAEIERLQNTIERLKTQLEDLERELALLQAKERQLEKKLKTLEQK-LKNEK 112
Query: 378 EDLRRRQNDN 387
E+++R +N
Sbjct: 113 EEVQRLKNII 122
>gnl|CDD|184697 PRK14475, PRK14475, F0F1 ATP synthase subunit B; Provisional.
Length = 167
Score = 28.0 bits (62), Expect = 8.8
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 322 ETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
E + LR+E AQ + KAE E ERQA + + ++ E + +L EE ++
Sbjct: 52 EAQRLREE-AQALL--ADVKAEREEAERQAAAMLAAAKADARRMEAEAKEKL---EEQIK 105
Query: 382 RRQ 384
RR
Sbjct: 106 RRA 108
>gnl|CDD|197397 cd10149, ClassIIa_HDAC_Gln-rich-N, Glutamine-rich N-terminal
helical domain of various Class IIa histone deacetylases
(HDAC4, HDAC5 and HDCA9). This superfamily consists of
a glutamine-rich N-terminal helical extension to certain
Class IIa histone deacetylases (HDACs), including HDAC4,
HDAC5 and HDAC9; it is missing in HDAC7. It is referred
to as the glutamine-rich domain, and confers
responsiveness to calcium signals and mediates
interactions with transcription factors and cofactors.
This domain is able to repress transcription
independently of the HDAC's C-terminal, zinc-dependent
catalytic domain. It has many intra- and inter-helical
interactions which are possibly involved in reversible
assembly and disassembly of proteins. HDACs regulate
diverse cellular processes through enzymatic
deacetylation of histone as well as non-histone
proteins, in particular deacetylating N(6)-acetyl-lysine
residues.
Length = 90
Score = 27.0 bits (59), Expect = 9.0
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 326 LRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQN 385
LR++ Q+E+ +Q+ + + K+ E +++ E L ++H ++Q + QQ+E L +Q
Sbjct: 4 LREQQLQQELLALKQQQQIQ-KQLLIAEFQKQHENLTRQHEAQLQEHIKQQQEMLAIKQQ 62
Query: 386 DNSMFLVEQQQGR 398
L+E+Q+
Sbjct: 63 QE---LLEKQRKL 72
>gnl|CDD|218446 pfam05120, GvpG, Gas vesicle protein G. These proteins are
involved in the formation of gas vesicles.
Length = 80
Score = 26.6 bits (59), Expect = 9.2
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 321 HETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED 379
+ E LRKELA+ + + +M E EE RR+EEL+ + + + E
Sbjct: 28 DDPENLRKELAELQR-------QLDMGEISEEEFDRREEELLDRLEALKRAEAESEGEA 79
>gnl|CDD|218704 pfam05701, DUF827, Plant protein of unknown function (DUF827).
This family consists of several plant proteins of
unknown function. Several sequences in this family are
described as being "myosin heavy chain-like".
Length = 484
Score = 28.4 bits (63), Expect = 9.3
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 307 EYGSRWKQLHELYEHETEMLRKEL--AQREIDRERQKAEWEMKERQAEELKRRDEELMKK 364
E ++ K+ E+ E E + KEL +R ++ + K E K + E+ ++D EL K
Sbjct: 43 EEANKLKKELEVAEKEKLQVLKELESTKRTVEDLKLKLE---KAEKEEQQAKQDSELAKL 99
Query: 365 HAEEMQLRLAQQE 377
AEE++ + + E
Sbjct: 100 RAEELEQGIQELE 112
>gnl|CDD|221518 pfam12301, CD99L2, CD99 antigen like protein 2. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 165 and 237 amino acids in length.
CD99L2 and CD99 are involved in trans-endothelial
migration of neutrophils in vitro and in the recruitment
of neutrophils into inflamed peritoneum.
Length = 154
Score = 27.8 bits (62), Expect = 9.3
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDM 69
+G G GGG GG GG G G +
Sbjct: 84 PDKGKGGGGGGGGGGGTDGGPEGGAETGT 112
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 28.1 bits (63), Expect = 9.4
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 325 MLRKEL--AQREIDRERQKAEWEMK-ERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLR 381
ML + + Q E+ + RQ + ++Q E +E KK + + L + E+L
Sbjct: 27 MLEQAIRDMQSELGKARQALAQVIARQKQLERKLEEQKEQAKKLENKARAALTKGNEELA 86
Query: 382 R 382
R
Sbjct: 87 R 87
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 28.6 bits (64), Expect = 9.4
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQ-AEELKRRDEELMKKHAE-EMQLRLAQQE 377
+ E L KE+ ++++A+ +KER E + EEL + L LA +E
Sbjct: 29 KARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEELKNSLEDLSELLELAVEE 88
Query: 378 ED 379
+D
Sbjct: 89 DD 90
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 28.7 bits (65), Expect = 9.7
Identities = 24/117 (20%), Positives = 43/117 (36%), Gaps = 29/117 (24%)
Query: 367 EEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGR---GGSGGYGSPGQAYGNAIIDFEALAA 423
+ Q LA++++ LR + +Q+G G + A G A A+
Sbjct: 656 QGGQGSLAERQQALRDE--------LGRQRGGLPGMGGEAGEAARDALGRA---GRAMGG 704
Query: 424 AVGNAVVGNVTG-VDNKGSAMDF--------------DQGGRSGGGGGRRNDSASSG 465
A G++ VD +G A++ QG + GG G ++ +G
Sbjct: 705 AEEALGQGDLAEAVDRQGRALEALREGARALGEAMAQQQGQQQGGQGQQQGRQGGNG 761
>gnl|CDD|217223 pfam02775, TPP_enzyme_C, Thiamine pyrophosphate enzyme, C-terminal
TPP binding domain.
Length = 151
Score = 27.5 bits (62), Expect = 9.7
Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 385 NDNSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVG 426
N+ + QQ G G Y P + DF LA A G
Sbjct: 81 NNGGYGMTRGQQTPFGGGRYSGPDGKDLPPV-DFAKLAEAYG 121
>gnl|CDD|219385 pfam07352, Phage_Mu_Gam, Bacteriophage Mu Gam like protein. This
family consists of bacterial and phage Gam proteins. The
gam gene of bacteriophage Mu encodes a protein which
protects linear double stranded DNA from exonuclease
degradation in vitro and in vivo.
Length = 147
Score = 27.6 bits (62), Expect = 9.8
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 315 LHELYEHETEMLR-KELAQREIDRERQKAEWEMKERQAE 352
L ++ E + E+ + A EI R ++ E++ + E
Sbjct: 9 LRKIGELKREIEEIETEANDEIARIKEWYAPELEPLKDE 47
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
0.316 0.137 0.403
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,143,327
Number of extensions: 2823969
Number of successful extensions: 5677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4801
Number of HSP's successfully gapped: 944
Length of query: 503
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 402
Effective length of database: 6,457,848
Effective search space: 2596054896
Effective search space used: 2596054896
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: 42 (22.0 bits)
S2: 61 (27.1 bits)