RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3343
(274 letters)
>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 = 117 bits (296), Expect = 5e-34
Identities = 47/71 (66%), Positives = 56/71 (78%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
+ILVKNLP TL +L+ LF FG LGRVL+PP GIT +VEFL+ ++AK AF LAY+KF
Sbjct: 2 VILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKLAYSKF 61
Query: 158 KEVPLYLEWAP 168
K VPLYLEWAP
Sbjct: 62 KHVPLYLEWAP 72
>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 = 109 bits (275), Expect = 6e-31
Identities = 43/72 (59%), Positives = 53/72 (73%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
+ILVKNLP+ T +L+ LFE FG LGR+L+PP LVEFL+ + A+ AF SLAY +
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKR 60
Query: 157 FKEVPLYLEWAP 168
FK VPLYLEWAP
Sbjct: 61 FKHVPLYLEWAP 72
Score = 28.3 bits (64), Expect = 0.78
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
T + +KNL F +TE+ +R F+K G + +
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRL 30
>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 = 93.6 bits (233), Expect = 9e-25
Identities = 38/70 (54%), Positives = 46/70 (65%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
ILVKN PY T +L+ LFEP G L RVL+PP G +VEF QA+ AF +LAY +FK
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRRFK 62
Query: 159 EVPLYLEWAP 168
+ LYLE P
Sbjct: 63 DSILYLEKGP 72
>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 = 80.3 bits (199), Expect = 2e-19
Identities = 29/47 (61%), Positives = 42/47 (89%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
TTL++KNLNF +TE+++++HF+KCG + SVT+A+KKDPK PG+ LSM
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSM 47
>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 = 49.7 bits (119), Expect = 3e-08
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAFNS 151
ILV+N+P+ +L+ LF FG+L V +P G V+F+ K AK AF +
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62
Query: 152 LAY-TKFKEVPLYLEWA 167
L + T L LEWA
Sbjct: 63 LCHSTHLYGRRLVLEWA 79
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 48.7 bits (117), Expect = 4e-08
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
TL++ NL ++TE+ +R F K G + SV + R K+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKS 40
Score = 45.3 bits (108), Expect = 9e-07
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ V NLP T +L+ LF FG + V + TG VEF + A+ A +L
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 153 AYTKFKEVPLYL 164
+ PL +
Sbjct: 62 NGKELDGRPLKV 73
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNSLA 153
++V+N+P+ +L+ LF PFG + V +P G VEF+ K +A+ A +L
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62
Query: 154 YTKFKEVPLYLEWA 167
T L LE+A
Sbjct: 63 STHLYGRHLVLEYA 76
Score = 27.6 bits (62), Expect = 1.8
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
T L ++N+ F +T+ +R F G + SV + +K D
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD 37
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 18/40 (45%), Positives = 25/40 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
L++ NL ++TE+ +R F K G I SV + R KD KS G
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKG 40
Score = 44.2 bits (105), Expect = 2e-06
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 153
+ V NLP T DL+ LF FG++ V + VEF A+ A +L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 154 YTKFKEVPLYLE 165
+ L +
Sbjct: 61 GKELDGRKLKVS 72
>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 = 46.8 bits (111), Expect = 4e-07
Identities = 21/46 (45%), Positives = 26/46 (56%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
TL++KNLNF++T + FK V K DPK PGQ LSM
Sbjct: 2 TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSM 47
>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 = 45.0 bits (107), Expect = 1e-06
Identities = 14/41 (34%), Positives = 27/41 (65%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
TL++ NL++++ +D + FK+CG + V +A+ D +S G
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKG 41
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 47.6 bits (112), Expect = 2e-06
Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 8/112 (7%)
Query: 165 EWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE- 223
E E + + + K++ E +EE + E+++ + E E E
Sbjct: 45 ELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSES 104
Query: 224 -------PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
E + TL++ NL ++ TE+ +R FKK GP+ V + R ++
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKS 156
Score = 43.0 bits (100), Expect = 7e-05
Identities = 39/190 (20%), Positives = 65/190 (34%), Gaps = 33/190 (17%)
Query: 88 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQ 141
++ + V NLPY DL+ LF+ FG + RV + TG VEF
Sbjct: 107 SRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFES 166
Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
+ A+ A L + + PL ++ A + + + + K+ +
Sbjct: 167 EESAEKAIEELNGKELEGRPLRVQKA----------QPASQPRSELSNNLDASFAKKLSR 216
Query: 202 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+ E LY+ NL + E+ + FK G I ++
Sbjct: 217 GKALLL-----------------EKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPP 259
Query: 262 KKDPKSPGQF 271
KD K P
Sbjct: 260 SKDGKIPKSR 269
>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 = 43.7 bits (104), Expect = 3e-06
Identities = 14/40 (35%), Positives = 25/40 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
L++ NL ++TE+ ++ F K GPI S+ + R + +S G
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKG 40
Score = 41.8 bits (99), Expect = 1e-05
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 153
+ V NLP T DLK LF FG + + + VEF + A+ A +L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 154 YTKFK 158
+
Sbjct: 61 GKELG 65
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+Y++NL+F ED +R F K G + S+ + +K+D K
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQ 40
Score = 33.4 bits (77), Expect = 0.016
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP 130
R I V+NL ++ DL+ +F FG++ + +P
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPK 34
>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 = 42.8 bits (101), Expect = 7e-06
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 151
+ V+NLPY DL+ LF FG+L V V G V FL A A+
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGF-AYVLFLDPEDAVKAYKE 63
Query: 152 LAYTKFK 158
L F+
Sbjct: 64 LDGKVFQ 70
Score = 28.9 bits (65), Expect = 0.64
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+++NL ++ ED + + F K G ++ V VA K F
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGF 46
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 42.2 bits (100), Expect = 1e-05
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
LY++NL + TE+ +R F G + V + R KD
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPR 38
Score = 40.6 bits (96), Expect = 4e-05
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 4/64 (6%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI----TGLVEFLQKNQAKAAFNSLAY 154
+ V+NLP DL+ F P+G + V + VEF A+AA L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 155 TKFK 158
Sbjct: 61 LVLD 64
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 151
+ ++NL Y DL+ LF +G L V +P P G V ++ A AF
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF-AFVTYMIPEHAVKAFAE 63
Query: 152 LAYTKFK 158
L T F+
Sbjct: 64 LDGTVFQ 70
Score = 31.2 bits (71), Expect = 0.11
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I+NL + TE+ + + F K GP++ V + K K P F
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF 46
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 41.4 bits (98), Expect = 2e-05
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
++++ NL F+ E+ +R+HF+ CG + +V + R D K+
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVR--DRKT 37
>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 = 41.4 bits (98), Expect = 3e-05
Identities = 10/40 (25%), Positives = 22/40 (55%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
T++I+NL F++TE+ ++ F + G + + + K
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHS 41
Score = 32.2 bits (74), Expect = 0.045
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL---VEFLQKNQAKAAFNSL- 152
R + ++NLP+ +LK LF FG++ + +TG F++ ++A L
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 153 AYTKFKEVPLYLE 165
A ++ L L+
Sbjct: 61 AADNAEDSGLSLD 73
>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 = 40.4 bits (95), Expect = 4e-05
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 152
V NL YRT P DL+ +FE +G++G V +P Y V F K A+ A +++
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Score = 31.5 bits (72), Expect = 0.064
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
L + NL + +T D +RR F+K G + V + R +
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDR 34
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in 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 = 78
Score = 40.0 bits (94), Expect = 7e-05
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
L+I L++ +T+DS++ +F + G I V + DP +
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMK--DPNT 37
>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 = 39.8 bits (93), Expect = 8e-05
Identities = 27/75 (36%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAAFNSL 152
ILVKNLP+ D++ LF +G L V VP G VEF +A A N+L
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGF-AFVEFSTAKEALNAMNAL 61
Query: 153 AYTKFKEVPLYLEWA 167
T L L++A
Sbjct: 62 KDTHLLGRRLVLQYA 76
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T+++ NL+++ ED +R+ F KCG I V + + KS G
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKG 41
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 112 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW 166
+L++LF PFG++ V +PP G V+F+ + A+AA L T + L W
Sbjct: 17 ELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLSW 71
Score = 28.8 bits (65), Expect = 0.64
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
+TT+++ L+ TED +R F G I V +
Sbjct: 1 NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI 33
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNS 151
R+I V+NLP++ DLK LF PFG + V +P P G V+F K A+ A
Sbjct: 1 RLI-VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59
Query: 152 LAYTKFKEVPLYLEWA 167
+ K K P+ ++WA
Sbjct: 60 VNGKKIKGRPVAVDWA 75
Score = 36.1 bits (84), Expect = 0.002
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG----QFLSM 274
L ++NL F TE +++ F G + VT+ RK D K G QF S
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSK 50
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V+NLP+ T +L+ LFE FG++ V +P T V F+ A A++ L
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 153 AYTKFK 158
+ F+
Sbjct: 62 DGSIFQ 67
Score = 37.3 bits (87), Expect = 6e-04
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
L+++NL F +TE+ +R F+ G I+ V + K+ K
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRS 40
>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 = 37.7 bits (88), Expect = 4e-04
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 231 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
++ N+++ +T + ++ HFK CG I +T+ K P
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQP 40
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
LY+KNL+ + ++ +R F G I S V + +S G
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKG 43
>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 = 37.4 bits (87), Expect = 5e-04
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L++ NL+F +TED +R HF + G I V + +D
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFED 35
>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 = 40.9 bits (96), Expect = 5e-04
Identities = 48/211 (22%), Positives = 78/211 (36%), Gaps = 44/211 (20%)
Query: 75 AFLEENGVQLDAFNQVVE---ARSKRI---------ILVKNLPYRTLPTDLKALFEPFGD 122
A + NG+ L+ V + +R + VKNL L+ LF FG
Sbjct: 145 AIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFG- 203
Query: 123 LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGK 182
IT + F + + K E A+A E+ GK
Sbjct: 204 ---------EITSAAVMKDGSGRSRGFAFVNFEK-----------HEDA-AKAVEEMNGK 242
Query: 183 EKEKNEEGE----GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN 238
+ +EG+ G +K+ E ++ EE +E + + + LY+KNL+
Sbjct: 243 KIGLAKEGKKLYVGRAQKRAEREAELRRK----FEELQQERKMKAQGVN--LYVKNLDDT 296
Query: 239 STEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T++ +R F +CG I S V + S G
Sbjct: 297 VTDEKLRELFSECGEITSAKVMLDEKGVSRG 327
Score = 28.2 bits (63), Expect = 5.0
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+LY+ +L+ + TE + FK GP+ SV V R
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCR 34
>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 = 37.6 bits (88), Expect = 6e-04
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T +Y+KNL + ++ ++ F K G I S V + + KS G
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKG 43
>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 = 37.5 bits (88), Expect = 6e-04
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
LY+ NL+F +TE+ I F +CG I + + + K+P F
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGF 42
Score = 28.3 bits (64), Expect = 1.0
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 18/80 (22%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------------VEFLQKNQAK 146
+ V NL + T + LF GD+ R+ I GL VE+ + A+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRI------IMGLDRFTKTPCGFCFVEYYTREDAE 54
Query: 147 AAFNSLAYTKFKEVPLYLEW 166
A L TK + + ++W
Sbjct: 55 NAVKYLNGTKLDDRIIRVDW 74
>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 = 37.6 bits (88), Expect = 7e-04
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
T LY+ NLN TE+ + + F + GP+ASV
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASV 31
Score = 26.8 bits (60), Expect = 3.5
Identities = 18/78 (23%), Positives = 24/78 (30%), Gaps = 9/78 (11%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRV---------LVPPYGITGLVEFLQKNQAKAAF 149
+ V NL + L F FG L V G V F+ + A+ A
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 150 NSLAYTKFKEVPLYLEWA 167
+ L L L W
Sbjct: 64 DELDGKDVMGYELKLGWG 81
>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 = 37.1 bits (86), Expect = 8e-04
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
L+I L+F++ E S+ + F K G I+ V V + ++ +
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQ 39
>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 = 36.9 bits (86), Expect = 0.001
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
L++ NL +++T + + HFK G SV + K
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKS 41
>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 = 36.3 bits (85), Expect = 0.001
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 113 LKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
L LF PFG++ ++ + VEF + A+ A L F PL ++++
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. 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 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.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 36.2 bits (84), Expect = 0.002
Identities = 17/57 (29%), Positives = 23/57 (40%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
++ V+ LP DL FG + V + P LVEF + AKA N
Sbjct: 3 PVVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNHAQ 59
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 36.5 bits (85), Expect = 0.002
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
TL++ LN+++TE +RR F++ GPI + + R K P
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKP 42
>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 = 35.6 bits (83), Expect = 0.003
Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNS 151
I V NL DL+ LF PFG + RV + TG V F + A+ A
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 152 LAYTKFKEVPLYLEWA 167
L + + L +EWA
Sbjct: 61 LNGFGYDNLILSVEWA 76
Score = 30.6 bits (70), Expect = 0.15
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
T+ + NL+ ++ ED +R F+ GPI+ V +A+ K+
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKE 36
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is 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 = 81
Score = 35.5 bits (81), Expect = 0.003
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
L+I L+F +T+DS+R HF+K G + V R DP++
Sbjct: 5 LFIGGLSFETTDDSLREHFEKWGTLTDCVVMR--DPQT 40
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 35.6 bits (83), Expect = 0.003
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKK 263
P TL ++ L+ +TE+ I + PI V + R K
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDK 40
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 37.4 bits (87), Expect = 0.004
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
A+ +E K ++E E E +EE+KE ED + +E+ E +EE E E + +
Sbjct: 46 ADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEES 102
Score = 32.8 bits (75), Expect = 0.13
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 169 EGVFAEAKEKSKGKEKEKN----EEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
E V E KE + ++KE +E E EE+ E EE + + E EE E + E+E
Sbjct: 63 EEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKE 121
>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 = 35.0 bits (81), Expect = 0.004
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L++ NL+F++ EDSI F + G I+SV + D P F
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGF 42
Score = 27.3 bits (61), Expect = 2.3
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 151
+ V NL + + F +G++ V +P P G G VEF + A+AA ++
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGF-GYVEFSSQEAAQAALDA 59
Query: 152 L 152
L
Sbjct: 60 L 60
>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 = 35.3 bits (82), Expect = 0.004
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TT+Y+ NL TE+ ++R F G I V V + K
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK 36
>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 = 35.2 bits (82), Expect = 0.004
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
LY+ +L+ + TE + F GP+ S+ V R
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCR 33
Score = 28.3 bits (64), Expect = 1.3
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 135 GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW 166
V F A+ A ++L + K P+ + W
Sbjct: 44 AYVNFQNPADAERALDTLNFDVIKGKPIRIMW 75
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 34.9 bits (80), Expect = 0.004
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+++ NL F E+ + R F KCG I V + R DPK+
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVR--DPKT 37
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 35.3 bits (81), Expect = 0.006
Identities = 12/28 (42%), Positives = 21/28 (75%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPI 254
D TL+++NL +++TE+S+ HF K G +
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSV 28
Score = 31.1 bits (70), Expect = 0.18
Identities = 16/57 (28%), Positives = 20/57 (35%), Gaps = 8/57 (14%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAA 148
+ V+NLPY L F FG + L G TG V F + A
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKG-TGFVCFKDQYTYNAC 59
>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 = 34.9 bits (81), Expect = 0.006
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASV---TVARKKDPKSP 268
T+++ NL + + +++ FK+ GPI SV +V K+
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPK 44
Score = 29.5 bits (67), Expect = 0.42
Identities = 23/68 (33%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGD-----LGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
R + V NLP T DLK LF+ FG V V + V ++K N
Sbjct: 1 RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60
Query: 152 LAYTKFKE 159
AY FKE
Sbjct: 61 NAYVVFKE 68
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 34.5 bits (79), Expect = 0.006
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
++Y+ N+++ ST + + HF CGPI VT+
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTI 31
>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 = 34.5 bits (80), Expect = 0.006
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TTLY+ L TE +R HF + G I S+TV ++
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ 37
>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 = 34.1 bits (79), Expect = 0.008
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+ + +KNL TED +R HF+ G + V V R +D KS
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKS 40
>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 = 33.9 bits (78), Expect = 0.010
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
T+YI NL ++ TED +R F K I SV +A K+
Sbjct: 1 TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKE 35
>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 = 33.7 bits (78), Expect = 0.013
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
+Y+ NL +T+ + F+K GP+ SV VAR
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN 34
>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 = 33.8 bits (78), Expect = 0.015
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+P TL++ L+ +TE+++R F + G I + + R
Sbjct: 1 DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVR 37
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 33.5 bits (77), Expect = 0.016
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
T+Y++ L N+T + ++ F K G + V++ R K F
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGF 43
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 36.0 bits (83), Expect = 0.017
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
P E++E+ +E+E+ EE E EEE++ E ++++ EVE + +EE E +
Sbjct: 432 PSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSE 491
Score = 32.6 bits (74), Expect = 0.26
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 186 KNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
++E E EE +E EE+ ++ + E E ++E E E
Sbjct: 435 ASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEA 478
Score = 31.8 bits (72), Expect = 0.45
Identities = 15/55 (27%), Positives = 23/55 (41%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 228
+ + E E E ++E EE+ ++ E EE EDEE E E +
Sbjct: 424 ASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEA 478
Score = 29.9 bits (67), Expect = 1.7
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
+E+ + +E+E+ EE E EEE+ E+ EE+ + EE +E E + + +
Sbjct: 444 SVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGE 497
Score = 27.6 bits (61), Expect = 8.9
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
E +E+ + +E+E +E E EE + +N +EE+ + E + + EE EE +
Sbjct: 455 EEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGS-SEGDGDGEEPEEDAERRN 507
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 36.1 bits (83), Expect = 0.017
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 230
A+ + + K+ EK +G G + ++ EE+ ++ E EE EE+EE E E + L
Sbjct: 837 LNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPL 894
Score = 35.0 bits (80), Expect = 0.042
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 174 EAKEKSKGKEKEKNEEG-EGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 230
EAK+ KG + +G + EEE++E EE+ ++ EE EE+EE E E +L
Sbjct: 844 EAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEE-----EEEEEEEEEEENEEPLSL 896
Score = 31.1 bits (70), Expect = 0.74
Identities = 21/74 (28%), Positives = 34/74 (45%)
Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
T+ +EV E EG E + ++ + +E +EGEGE E K E +++ E
Sbjct: 710 TEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGE 769
Query: 215 NVEEDEEREPEPDT 228
E +E E E +
Sbjct: 770 TEAEGKEDEDEGEI 783
Score = 30.0 bits (67), Expect = 1.6
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 168 PEGVFAEAKEKSKGK---EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVE-EDEERE 223
+ + +S+G+ E++ +EGEGE E KE + + + E E E E E E
Sbjct: 670 EGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDE 729
Query: 224 PEPDT 228
E +T
Sbjct: 730 GEIET 734
Score = 29.6 bits (66), Expect = 2.1
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 173 AEAKEKSKGKEKEKNEEGEGE--EEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
AE + G+E E+ E EGE EE +E + E E E ER+ E
Sbjct: 638 AEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGE 692
Score = 27.7 bits (61), Expect = 9.5
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQ-------QGVPEVEENVEED 219
V E K E E EG+ +E++ E A ED + +G E E E
Sbjct: 751 GKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAG 810
Query: 220 EEREPEPDT 228
E+ E E +
Sbjct: 811 EKDEHEGQS 819
>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 = 33.4 bits (77), Expect = 0.019
Identities = 14/49 (28%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQ-FLSM 274
T +++ L +++T+DS+R++F + G I +V + ++ KS G F++
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTF 49
Score = 32.6 bits (75), Expect = 0.026
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAF 149
I V LPY T L+ F FG++ +V TG V F K A+ A
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59
>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 = 33.1 bits (76), Expect = 0.019
Identities = 13/42 (30%), Positives = 18/42 (42%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T LYI NL + E + K G + S + R +S G
Sbjct: 1 TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRG 42
>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 = 33.0 bits (76), Expect = 0.023
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
LY+ NL+FN TED +R F+ G I V + R
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQR 32
Score = 28.0 bits (63), Expect = 1.3
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
V NL + DL+ +FEPFG++ V + TG ++F AK A L
Sbjct: 3 VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
>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 = 33.0 bits (75), Expect = 0.024
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 218 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
ED++R L+I NL+ N +E +RR F K G I V + R
Sbjct: 2 EDDQRATR---NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKR 42
>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 = 33.1 bits (76), Expect = 0.026
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
T+LY++N+ + D +RR F K GPI V +
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYI 32
Score = 31.6 bits (72), Expect = 0.086
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 151
+ V+N+ T P DL+ LF +G + V +P P G V+F A+ A
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGF-AYVQFEDVRDAEDALYY 61
Query: 152 LAYTKFKEVPLYLEWA 167
L T+F + +++A
Sbjct: 62 LDRTRFLGREIEIQFA 77
>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 = 32.7 bits (75), Expect = 0.027
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
+ + +L + DLK LFE +G++ + ++PP G V + A A L
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRG-CAYVCMETRQDAHRALQKLRNV 61
Query: 156 KFKEVPLYLEWAP 168
K + + WAP
Sbjct: 62 KLAGKKIKVAWAP 74
Score = 32.7 bits (75), Expect = 0.032
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
TTL+I +L+ TE+ ++ F++ G I S+ +
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDM 34
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 32.7 bits (75), Expect = 0.028
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+Y+ + + STED IR +F CG I + + D
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPD 35
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 35.4 bits (81), Expect = 0.030
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 6/69 (8%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIK 233
E + GKE E EE EE+ E ++D+ + + +++ +ED+E E + D+TL+
Sbjct: 35 ENAIRKLGKEAE--EEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLH-- 90
Query: 234 NLNFNSTED 242
+ +S +D
Sbjct: 91 --DDSSADD 97
>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 = 32.6 bits (75), Expect = 0.033
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGD 122
R + V+N+ +L+ALFE FGD
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGD 27
Score = 28.0 bits (63), Expect = 1.5
Identities = 9/29 (31%), Positives = 20/29 (68%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
TL+++N+N N ++ +R F++ G I ++
Sbjct: 3 TLFVRNINSNVEDEELRALFEQFGDIRTL 31
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing 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. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 32.2 bits (74), Expect = 0.035
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
+I+ ++NLP T L+ LF F V LVP GI VEF + QA A +L
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGI-AFVEFETEEQATVALQALQGF 61
Query: 156 K 156
K
Sbjct: 62 K 62
>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 = 34.9 bits (80), Expect = 0.041
Identities = 25/102 (24%), Positives = 46/102 (45%), Gaps = 8/102 (7%)
Query: 57 GAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKAL 116
++ +G IV+ ++A E+N A +Q + + + V NL + +L+ +
Sbjct: 149 ALTGQMLLGRPIIVQSSQA--EKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQI 206
Query: 117 FEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 152
FEPFGD+ V + P G ++F +AK A +
Sbjct: 207 FEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248
Score = 31.4 bits (71), Expect = 0.47
Identities = 34/177 (19%), Positives = 55/177 (31%), Gaps = 48/177 (27%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDL-------GRVLVPPYGITGLVEFLQKNQ 144
R R + V L + DL F G + R G+ VEF
Sbjct: 85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGV-AYVEFYDVES 143
Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED 204
A +L P+ ++ + EK++ + ++ G+ K
Sbjct: 144 VIKAL-ALTGQMLLGRPIIVQ-------SSQAEKNRAAKAATHQPGDIPNFLK------- 188
Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
LY+ NL+FN TE +R+ F+ G I V + R
Sbjct: 189 -------------------------LYVGNLHFNITEQELRQIFEPFGDIEDVQLHR 220
Score = 29.9 bits (67), Expect = 1.6
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 5/78 (6%)
Query: 180 KGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNS 239
+G+ + ++ + +D + G E + ER+ D T+++ L +
Sbjct: 47 RGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEP--LTEAERD---DRTVFVLQLALKA 101
Query: 240 TEDSIRRHFKKCGPIASV 257
E + F K G + V
Sbjct: 102 RERDLYEFFSKVGKVRDV 119
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 32.2 bits (74), Expect = 0.042
Identities = 13/38 (34%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
L+I L++++TE+S+R +F K G + + KDP +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVI--MKDPIT 36
>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 = 32.2 bits (74), Expect = 0.043
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
L++ L+ +TE + F K G + V + KDP++
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLM--KDPET 39
Score = 26.4 bits (59), Expect = 5.6
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
+ V L RT +L+ALF FG + VL+
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLL 33
>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 = 32.0 bits (73), Expect = 0.050
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
D L++ L+ TED +RR F+ G I T+ R D S G
Sbjct: 1 DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKG 43
Score = 26.2 bits (58), Expect = 5.8
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 112 DLKALFEPFGDLGR--VLVPPYGIT---GLVEFLQKNQAKAAFNSL 152
D++ LFEPFG + +L P G + V+F +A+AA N+L
Sbjct: 17 DVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINAL 62
>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 = 31.9 bits (73), Expect = 0.051
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+T+Y+ NL F+ T + + + F K G + VT+ + K+
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKE 38
Score = 28.4 bits (64), Expect = 0.98
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAF 149
K + V NLP+ DL +F +G + +V + T + FL + A
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60
Query: 150 NSL 152
+L
Sbjct: 61 KAL 63
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 34.6 bits (80), Expect = 0.057
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYI 232
E +E+ E E E +G ++++E + EED P + +ED ++ + D +
Sbjct: 232 TEEREEETDVEIETTSETKGTKQEQEGSTEED-----PSLFSEEKEDPDKTEDLDKLEIL 286
Query: 233 KNLNFNS 239
K
Sbjct: 287 KEKKDEE 293
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 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 = 76
Score = 31.8 bits (72), Expect = 0.060
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
++I LN+ +T+DS+R +F + G + TV R
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMR 32
>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 = 31.8 bits (72), Expect = 0.061
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
D TL++ NL+ TE+ I F + GP+ V + + KD K P QF
Sbjct: 1 DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGK-PKQF 44
>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 = 31.8 bits (73), Expect = 0.062
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
+TL++ N + + IR F++ G I S+
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSI 30
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 34.1 bits (79), Expect = 0.063
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 173 AEAKEKSKGKEKEKNEEG---EGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD-- 227
E EK + +EK++ ++ ++E++E +E ++ E EE EE++E E E
Sbjct: 416 VEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKK 475
Query: 228 -TTL 230
TL
Sbjct: 476 QATL 479
>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 = 31.5 bits (72), Expect = 0.071
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
T+ +KNL ++TE+ IR+ FK CG I V + +
Sbjct: 1 LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV 40
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 33.9 bits (77), Expect = 0.072
Identities = 18/73 (24%), Positives = 34/73 (46%)
Query: 177 EKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLN 236
E + +EKE++ E E E+ E + + + + EE +E++E EPE + +L
Sbjct: 109 ETVEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLE 168
Query: 237 FNSTEDSIRRHFK 249
N+ E +
Sbjct: 169 ENNGEFMTHKLKH 181
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 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. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 31.6 bits (71), Expect = 0.073
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 46
>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 = 31.4 bits (72), Expect = 0.082
Identities = 11/42 (26%), Positives = 21/42 (50%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L++ L+ + TE + F + G ++ V + +KKD F
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGF 43
>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein.
Length = 198
Score = 33.2 bits (76), Expect = 0.086
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 175 AKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEE---REPEPDTT 229
+KSK K+KEK E E ++ + ++ E+N+ EE+ + E
Sbjct: 64 TTKKSKKKDKEKLTEEE-KKPESDDDKTEENENDPDNNEESGDSQESASANSLSDIDN 120
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 31.1 bits (71), Expect = 0.098
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIA 255
+YI L + TEDS+ F G I
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIK 26
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is 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 has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 31.0 bits (71), Expect = 0.10
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFG 121
RI+ V+NLP++ +L LF +G
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYG 27
Score = 30.3 bits (69), Expect = 0.21
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
LY++NL F + + + F K G I + + K+ +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR 41
>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 = 31.1 bits (70), Expect = 0.10
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD--PKSPG 269
D TL++ NL E+ + F + GP+ VT+ + K+ PKS G
Sbjct: 1 DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFG 45
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 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 protein
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 = 31.0 bits (70), Expect = 0.11
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAY 154
R + V N+P + L+ LFE +GD+ V GI V F AK A L
Sbjct: 2 RSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIV-TVHFYDIRDAKRAVRELCG 60
Query: 155 TKFKE 159
++
Sbjct: 61 RHMQQ 65
Score = 28.3 bits (63), Expect = 1.0
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+L++ N+ + TE ++RR F+ G + V R +
Sbjct: 3 SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISE 38
>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 = 30.8 bits (70), Expect = 0.11
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
TL+I NL +T +R F++ G I + + KK +P
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDI--KKQGGNP 41
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 31.0 bits (71), Expect = 0.12
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
LY+ NL +N TE+ ++ F + G + S V ++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRE 36
Score = 30.3 bits (69), Expect = 0.21
Identities = 22/64 (34%), Positives = 26/64 (40%), Gaps = 14/64 (21%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT----------GLVEFLQKNQAKAA 148
+ V NLPY DLK LF FG++ V IT G VE +A AA
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARV----ITDRETGRSRGFGFVEMETAEEANAA 57
Query: 149 FNSL 152
L
Sbjct: 58 IEKL 61
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
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 = 77
Score = 31.1 bits (71), Expect = 0.12
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKS 267
+ L +KNL + TE ++ HF K G I V + R +D KS
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKS 41
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal Rrp7 domain. .
Length = 102
Score = 31.5 bits (72), Expect = 0.13
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
TL++ N+ TE+S++R F +CG + SV + K P
Sbjct: 2 TLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAES 41
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 32.4 bits (74), Expect = 0.14
Identities = 15/62 (24%), Positives = 32/62 (51%)
Query: 169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 228
E V E +EK K K K+K + + +++K + ++D++ + +E ++ E+
Sbjct: 72 EKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSE 131
Query: 229 TL 230
TL
Sbjct: 132 TL 133
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of
basal transcription 1 (ABT1) and similar proteins. This
subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and ESF2
contain an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 98
Score = 31.0 bits (71), Expect = 0.14
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 18/73 (24%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRV-LVP--------------PYGIT---GLVEF 139
I+ + +P R P L+ L +G++GR+ L P G VEF
Sbjct: 2 IVYLSRIPPRMNPAKLRQLLSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEF 61
Query: 140 LQKNQAKAAFNSL 152
K AK SL
Sbjct: 62 EDKKVAKRVAESL 74
>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 = 30.5 bits (69), Expect = 0.16
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 105 PYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY 163
P T D++ LFEPFG L R + + VEF A A +L ++ L
Sbjct: 9 PGTTREEDIEKLFEPFGPLVRCDIRKTF---AFVEFEDSEDATKALEALHGSRIDGSVLT 65
Query: 164 LEWA 167
+E+
Sbjct: 66 VEFV 69
>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 = 30.6 bits (69), Expect = 0.16
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
++ V NLP + + L +G++ R + +TG VE+++K+ A A
Sbjct: 1 LLCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60
Query: 152 LAYTKFKEVPLYLEWA 167
L + E L+ +W
Sbjct: 61 LLGKQLGESTLFAQWM 76
>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 = 30.4 bits (69), Expect = 0.17
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
D TL++ NL+ TE+ + F + GP+ V + + + K
Sbjct: 1 DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP 41
>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 = 30.3 bits (69), Expect = 0.17
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFG 121
+ V NLP T +L+ALFE +G
Sbjct: 2 LFVGNLPDATTSEELRALFEKYG 24
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. 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. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 30.3 bits (69), Expect = 0.19
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
T L + NL+ + TED I F G + + R
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVR 34
>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 = 30.2 bits (69), Expect = 0.19
Identities = 17/47 (36%), Positives = 23/47 (48%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKA 147
++NLP +DL AL PFG + VL+ LVE AK+
Sbjct: 4 LRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKS 50
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 32.9 bits (75), Expect = 0.20
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 150
++ V+NLP + DL PFG + V++ P LVEF + AKA N
Sbjct: 3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVN 56
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 32.0 bits (73), Expect = 0.20
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 172 FAEAKEKSKGKEKEKNE-EGEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 221
E K EK E E E+ +E+ +E+ ++ E +E+ ++D++
Sbjct: 144 EEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDD 194
>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 = 29.9 bits (68), Expect = 0.21
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
I V+NLP+ DLK LF G++ R V
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADV 30
Score = 26.1 bits (58), Expect = 6.4
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
++++NL F+ T ++ F++CG + V D +S G
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKG 40
>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 = 30.3 bits (68), Expect = 0.22
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 218 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
ED++R + TL++ NL+ TE +RR F + G I V + R
Sbjct: 1 EDDQR---ANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKR 41
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM). This
family consists of several Plasmodium falciparum SPAM
(secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the alanine
heptad-repeat domain. Heptad repeats in which the a and
d position contain hydrophobic residues generate
amphipathic alpha-helices which give rise to helical
bundles or coiled-coil structures in proteins. SPAM is
an example of a P. falciparum antigen in which a
repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 31.8 bits (72), Expect = 0.23
Identities = 23/65 (35%), Positives = 35/65 (53%)
Query: 178 KSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNF 237
K + +E ++ EE E EEE +E ED ++ V + EE E++E+ D N F
Sbjct: 44 KDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIF 103
Query: 238 NSTED 242
NST+D
Sbjct: 104 NSTQD 108
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 29.8 bits (68), Expect = 0.24
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 228 TTLYIKNL--NFNSTEDSIRRHFKKCGPIASVTVA 260
TTL ++N+ N + HF K G I ++ V
Sbjct: 2 TTLEVRNIPPELN-NITKLNEHFSKFGTIVNIQVN 35
Score = 28.3 bits (64), Expect = 0.88
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 96 KRIILVKNLP----YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
+ V+N+P T L F FG + + V + LV+F +AK A+ S
Sbjct: 1 NTTLEVRNIPPELNNITK---LNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYRS 57
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 32.4 bits (74), Expect = 0.25
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIK 233
E K+ + E E+ ++ +NQ+ EV++ V + ++ PE DT L ++
Sbjct: 454 EFKQSIVKEAALSILEEIREKVLEQAEQGCENQE---EVKKEVPKKVKKIPEVDTYLLLE 510
Query: 234 NLNFNSTEDS 243
L N
Sbjct: 511 ELGINEETYE 520
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 29.9 bits (68), Expect = 0.25
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-PPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
++V LP DLK GD+ V G+VEF + + A L T+F
Sbjct: 3 VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTEF 62
Query: 158 K 158
+
Sbjct: 63 R 63
>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 = 29.9 bits (68), Expect = 0.25
Identities = 21/76 (27%), Positives = 29/76 (38%), Gaps = 6/76 (7%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ V NLP + L PFG + R + TG VE+ K A A N L
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 153 AYTKFKEVPLYLEWAP 168
+ L ++WA
Sbjct: 62 DGKQIGGRKLQVDWAD 77
>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional.
Length = 413
Score = 32.2 bits (73), Expect = 0.28
Identities = 14/64 (21%), Positives = 23/64 (35%)
Query: 167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 226
+P +E S + +E GE + + + QQ V +E E + E P P
Sbjct: 189 SPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPPFP 248
Query: 227 DTTL 230
Sbjct: 249 GHRS 252
Score = 30.3 bits (68), Expect = 1.2
Identities = 11/67 (16%), Positives = 15/67 (22%)
Query: 164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
L + S E + Q + ED E
Sbjct: 118 LSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEE 177
Query: 224 PEPDTTL 230
PEP T+
Sbjct: 178 PEPPTSE 184
Score = 28.4 bits (63), Expect = 4.7
Identities = 6/53 (11%), Positives = 13/53 (24%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 226
+ ++ + + ++ E E E E P P
Sbjct: 140 PPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGP 192
>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 = 29.9 bits (68), Expect = 0.28
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
T L + NL+F ++D I+ F + G + V
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAV 32
>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 = 30.0 bits (67), Expect = 0.29
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
P+P+ L + L+ +TE +R F K GPIA V++
Sbjct: 6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 41
>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 = 29.9 bits (68), Expect = 0.30
Identities = 9/38 (23%), Positives = 21/38 (55%)
Query: 231 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
++ N+ +++TE+ + F + GP+ S + +D P
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKP 39
>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 = 29.9 bits (68), Expect = 0.30
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
P+ L++ LN +T++ + F + G I S V R K
Sbjct: 2 PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDK 39
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 29.7 bits (67), Expect = 0.31
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
R + V +P ++LK +FE GD+ + V
Sbjct: 2 RYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFV 33
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 32.2 bits (73), Expect = 0.33
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVE----ENVEEDEEREPEPD 227
E + + E E+ E+GEGE E +E +A ++++ E E E V+ D++ P+
Sbjct: 213 EDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDES 270
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which 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 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. Moreover, the
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 = 81
Score = 29.7 bits (66), Expect = 0.34
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
L+I L+F +TE+S+R ++++ G + V R DP S
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMR--DPAS 40
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 31.7 bits (72), Expect = 0.34
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 230
+K K K+K + E ++ E +E +++ E E+ +DEE E
Sbjct: 149 GKAKKKTKKSKKKEAK-ESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDY 204
>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 = 29.7 bits (67), Expect = 0.34
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV-ARKKDP 265
T+Y + ++R F+ CGP+ VT+ +R P
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP 38
Score = 25.9 bits (57), Expect = 6.0
Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 2/56 (3%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--VEFLQKNQAKAAFNSL 152
+ P +D+K LFE G + +V + + + F A+ A +L
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETL 57
>gnl|CDD|241158 cd12714, RRM1_MATR3, RNA recognition motif 1 in vertebrate
matrin-3. This subgroup corresponds to the RRM1 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 = 76
Score = 29.7 bits (67), Expect = 0.34
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 112 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN----SLAYTKFKEVPLYL 164
L L +PFG + L+ +E +A A N A K V +YL
Sbjct: 17 QLLQLAKPFGTIVNHLILNKINEAFLEMSTHEEAVAMVNYYQTKPALVFGKPVRVYL 73
>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional.
Length = 196
Score = 31.4 bits (71), Expect = 0.35
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYI 232
+E+ NE+ EG E ++ + QQ V E+EE ++ +++E E L I
Sbjct: 9 NKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVEAQEYLDI 67
>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 = 29.5 bits (66), Expect = 0.37
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
++ + NLP + L PFG+L R + TG VE+++K+ A A +
Sbjct: 1 LLCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSD 60
Query: 152 LAYTKFKEVPLYLEWA 167
L + LY+ W
Sbjct: 61 LLGKQLGSRTLYVHWT 76
>gnl|CDD|241045 cd12601, RRM2_SRSF1_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF9 and
similar proteins. This subfamily corresponds to the
RRM2 of serine/arginine-rich splicing factor SRSF1,
SRSF9 and similar proteins. SRSF1, also termed ASF-1, 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, also termed SRp30C, 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. 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. .
Length = 74
Score = 29.4 bits (66), Expect = 0.39
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
++V LP DLK GD+ V G TG+VEFL+ K A L +KF+
Sbjct: 3 VIVSGLPPTGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFLRYEDMKYAVKKLDDSKFR 61
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 31.6 bits (72), Expect = 0.40
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
PE V + ++ + EK + EE E + + E+ EED + EE ++DE +
Sbjct: 268 EPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDE-----DEEEEEDDDEGDK 319
>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and
CTD-associated factor 4 (SCAF4) and similar proteins.
The CD corresponds to the RRM of SCAF4 (also termed
splicing factor, arginine/serine-rich 15 or SFR15, or
CTD-binding SR-like protein RA4) that belongs to a new
class of SCAFs (SR-like CTD-associated factors).
Although its biological function remains unclear, SCAF4
shows high sequence similarity to SCAF8 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) and may play a direct role
in coupling with both, transcription and pre-mRNA
processing, processes. SCAF4 and SCAF8 both 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 = 81
Score = 29.6 bits (66), Expect = 0.40
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK- 158
V L RT D+ +L E FG + + ++PP G + + + A A L+ K
Sbjct: 9 VGQLDKRTTQQDVTSLLEEFGPIESINMIPPRG-CAYIVMVHRQDAYRALQKLSRGNVKV 67
Query: 159 -EVPLYLEWA 167
+ + + WA
Sbjct: 68 NQKSIKIAWA 77
>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 = 29.3 bits (66), Expect = 0.40
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+YI NL + +E+ +R +K GPI + + ++K+
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKN 40
>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 = 29.4 bits (66), Expect = 0.41
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
I+++NLP ++ L + + V T V L +QA A L + +K
Sbjct: 2 IVIRNLPADVTKQEVHDLLSDY-QVKYCDVDKSKRTAQVTLLNGDQASRAIAKLHQSSYK 60
Query: 159 EVPLYLEWAP 168
E + ++ P
Sbjct: 61 ERKISVQLQP 70
>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 = 29.5 bits (67), Expect = 0.41
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
+ V NL Y DL+ LF G++ +V + Y +G V F ++ A+ A
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKI-NYDRSGRSEGTADVVFEKREDAERA 57
Score = 27.2 bits (61), Expect = 2.1
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T L + NL+++ TE+ + F + G + V + + +S G
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEG 42
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.9 bits (72), Expect = 0.41
Identities = 12/65 (18%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVP-EVEENVEEDEEREPEPDTTLYI-KNLNFNS 239
KE + + + ++KE+ E + G+ E++ +++E+ + P + L + ++L +
Sbjct: 3938 KEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDE 3997
Query: 240 TEDSI 244
E +
Sbjct: 3998 KEGDV 4002
Score = 31.9 bits (72), Expect = 0.47
Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 23/98 (23%)
Query: 136 LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGE---- 191
L+E QK+ ++A N+ + KE + K +EK +E E
Sbjct: 3916 LLETEQKSNEQSAANNESDLVSKE-------------DDNKALEDKDRQEKEDEEEMSDD 3962
Query: 192 -GEEEKKENTAEEDNQQGVPEVE-----ENVEEDEERE 223
G +++ + +E+N Q PE E E+++ DE+
Sbjct: 3963 VGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEG 4000
Score = 28.0 bits (62), Expect = 6.9
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 175 AKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
+E E++ NE+ E + E+DN+ E ++ E+++E E D
Sbjct: 3912 NEEDLLETEQKSNEQSAANNESDLVSKEDDNK--ALEDKDRQEKEDEEEMSDD 3962
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 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 = 75
Score = 29.3 bits (66), Expect = 0.41
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
L++ NL N E+ I HFK+ G + SV + K+
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGG 40
>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 = 29.4 bits (66), Expect = 0.43
Identities = 19/69 (27%), Positives = 24/69 (34%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
V N+P T DL LF+ FG + P V+ QA A L
Sbjct: 5 VGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPVHGR 64
Query: 161 PLYLEWAPE 169
PL W +
Sbjct: 65 PLRCGWGKD 73
>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 = 29.2 bits (65), Expect = 0.44
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPF-GDLGRVL-VPPYGITGLVEFLQKNQAKAAFNSLAY 154
R + V LP P +L LF PF G G ++ + G V F +++A+AA N+L
Sbjct: 2 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 61
Query: 155 TKFK-EVPLYL 164
+F E+P L
Sbjct: 62 IRFDPEIPQTL 72
>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 = 29.4 bits (67), Expect = 0.45
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 229 TLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQ 270
TLYI NLN +D ++R F + GP+ + VA K K GQ
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDI-VASKT-LKMRGQ 44
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 29.1 bits (66), Expect = 0.51
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
TT+++ N+ ++D IR+ +KCG + S R KDP +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWK--RVKDPST 38
>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 = 29.3 bits (66), Expect = 0.52
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L++ NL + TED ++ FK+ G + V + K F
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNF 47
>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 = 28.8 bits (65), Expect = 0.54
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFN 150
V NLP + K LF +G++ V + +G L +AKA +
Sbjct: 6 VGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELD 58
>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 = 28.9 bits (65), Expect = 0.54
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
TL++ NL+++ ++ ++ F+K G + V
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARV 31
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 29.0 bits (65), Expect = 0.56
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
++Y+ N+++ +T + + HF CG + VT+
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTI 31
>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 30.7 bits (70), Expect = 0.57
Identities = 13/57 (22%), Positives = 28/57 (49%)
Query: 169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
E V + +++++ + E E + E E+ AE D ++ + + E E + E+ E
Sbjct: 4 ETVVEDIRDEARARASEIRAEADEEAEEIIAEAEADAEEILEDREAEAEREIEQLRE 60
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 28.9 bits (65), Expect = 0.58
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
L++ L F+ T++ + + FKK G + SV + + K G
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKG 44
Score = 27.4 bits (61), Expect = 2.4
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVP-----PYGITGLVEFLQKNQAKAAF 149
K + V LP+ +L+ LF+ G + V LV P G+ VE+ ++ A A
Sbjct: 2 KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGL-AYVEYENESSASQAV 60
Query: 150 NSLAYTKFKE 159
+ T+ KE
Sbjct: 61 LKMDGTEIKE 70
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 31.3 bits (70), Expect = 0.61
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 165 EWAPEGVFAEAKEKSKGKEKEKNEE-GEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
E A E V +E + ++E EE E EE E EE+ ++ V E+EENVEE+ E
Sbjct: 1047 ENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEEN 1106
Query: 224 PE 225
E
Sbjct: 1107 AE 1108
Score = 30.5 bits (68), Expect = 1.1
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIK 233
E ++ +E E+N E E EE E EE +++ V E+EEN+EE+ E E + ++
Sbjct: 1035 EEYDEENVEEIEENAE-ENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVE 1093
Query: 234 NLNFNSTED 242
+ N E+
Sbjct: 1094 EIEENVEEN 1102
Score = 29.0 bits (64), Expect = 3.1
Identities = 18/60 (30%), Positives = 28/60 (46%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTED 242
E+ E E E+ E EE +++ V E+EEN EE+ E E + Y + E+
Sbjct: 1016 EENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEEN 1075
Score = 28.6 bits (63), Expect = 4.1
Identities = 23/68 (33%), Positives = 34/68 (50%)
Query: 158 KEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVE 217
+ VP +L+ E E E++ ++ E+N E EE +EN E + VEENVE
Sbjct: 933 ENVPEHLKEHAEANIEEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVE 992
Query: 218 EDEEREPE 225
E+ E E
Sbjct: 993 ENVEENVE 1000
Score = 28.6 bits (63), Expect = 4.8
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 158 KEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGE-EEKKENTAEEDNQQGVPE-VEEN 215
+ + Y E E + +E + +E EE E EE E EE+ ++ E EEN
Sbjct: 1059 ENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEENAEEN 1118
Query: 216 VEEDEEREPEPDTTLY 231
EE ++ PE Y
Sbjct: 1119 AEEYDDENPEEHNEEY 1134
Score = 28.6 bits (63), Expect = 4.9
Identities = 24/84 (28%), Positives = 34/84 (40%)
Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
KNQ + L + E E E E++ + E+N E EE +EN
Sbjct: 929 KNQNENVPEHLKEHAEANIEEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVE 988
Query: 202 EEDNQQGVPEVEENVEEDEEREPE 225
E + VEEN+EE+ E E
Sbjct: 989 ENVEENVEENVEENIEENVEENVE 1012
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It is an essential yeast protein involved in pre-rRNA
processing and ribosome assembly, and is speculated to
be required for correct assembly of rpS27 into the
pre-ribosomal particle. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 29.3 bits (66), Expect = 0.66
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKK-CGPIASVT 258
TL++ NL ++TE +R+ F G I SV
Sbjct: 2 TLFLVNLPVDTTERHLRKLFGSGGGIIESVV 32
>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 = 29.0 bits (65), Expect = 0.66
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
L++ LN +++ +RRHF + G + V + K
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTK 41
>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 = 28.9 bits (64), Expect = 0.69
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
D +Y+ NL N + + R F GP+ SV VAR
Sbjct: 4 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR 38
>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 = 28.8 bits (65), Expect = 0.69
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 12/75 (16%)
Query: 98 IILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGI------TGLVEFLQKNQAKAAFN 150
++LV NL P L LF +GD+ RV I T L++ QA+ A
Sbjct: 1 VLLVSNLNEEMVTPDALFTLFGVYGDVVRV-----KILFNKKDTALIQMADPQQAQTALT 55
Query: 151 SLAYTKFKEVPLYLE 165
L + L +
Sbjct: 56 HLNGIRLHGKKLRVT 70
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 77
Score = 28.9 bits (65), Expect = 0.74
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
++V LP++T DLK F FG+L V V
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQV 31
>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 = 28.7 bits (64), Expect = 0.74
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
LY+ NL+ TED +++ F+ GP+ +V + K+ K
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNK 37
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 30.7 bits (69), Expect = 0.78
Identities = 8/55 (14%), Positives = 16/55 (29%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 228
E E +E+ + G+ + + P + DE P+
Sbjct: 365 ETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEK 419
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 28.8 bits (64), Expect = 0.78
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
++L+++N+ ++ + +RR F + GPI V V
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYV 32
>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 = 28.2 bits (63), Expect = 0.82
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFG 121
I V N+ T +L+ALFE +G
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYG 25
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 30.3 bits (68), Expect = 0.84
Identities = 15/64 (23%), Positives = 24/64 (37%)
Query: 164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
+ W + EA + E+ E E + ++E EE E + E+EE E
Sbjct: 156 IVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEE 215
Query: 224 PEPD 227
E
Sbjct: 216 AEGS 219
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is 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 = 77
Score = 28.4 bits (64), Expect = 0.84
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
P +++ L+ + TE + RHF + GP+ V + R++
Sbjct: 6 PTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQR 43
>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 = 28.5 bits (64), Expect = 0.89
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
TL++ NL TE+ +RR F++ G + V + R
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKR 36
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 28.5 bits (63), Expect = 0.93
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
LY++NL ++TE++I+ F K P V + +D
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD 38
>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 = 28.5 bits (64), Expect = 0.94
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+++ NL++ ++ FK G + + K+ KS G
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRG 40
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 30.5 bits (69), Expect = 0.95
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 228
KE EK E + EEE+++ +E+ ++ + EE EE+E+ E + T
Sbjct: 29 KEVEK-EVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKT 74
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 28.3 bits (63), Expect = 0.98
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFE 118
R R + VKNLPY +LK +FE
Sbjct: 1 RDARTLFVKNLPYNITVDELKEVFE 25
Score = 27.1 bits (60), Expect = 2.6
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
TL++KNL +N T D ++ F+ + + KD S G
Sbjct: 5 TLFVKNLPYNITVDELKEVFEDA---VDIRLPSGKDGSSKG 42
>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 = 28.1 bits (63), Expect = 1.1
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 101 VKNLPYRTLPTDLKALFEPFG 121
V N+P+R DL+ +F FG
Sbjct: 5 VSNIPFRFRDPDLRQMFGQFG 25
>gnl|CDD|235285 PRK04335, PRK04335, cell division protein ZipA; Provisional.
Length = 313
Score = 30.1 bits (68), Expect = 1.1
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 165 EWAPEGVFAEAKEKSKGKEKEKNEE--GEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 222
E AP V A+++ + + E + E E EE + A+ + PE E +E DE
Sbjct: 108 EEAPIPVQAQSQPQPEKVEPQVEEPRDEEVLEEPEPVAAKVPMAEVQPEEETEIEVDEPE 167
Query: 223 EPEPDTTLYIKNLN 236
EP+P+ L + LN
Sbjct: 168 EPKPEPELDVIVLN 181
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 28.2 bits (63), Expect = 1.1
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
+Y+ +++F ED+IR+ F GPI S+
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSID 31
>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 = 28.0 bits (63), Expect = 1.2
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGI----TGLVEFLQKNQAKAAFNSL 152
V LP +L+ALF P+G + R+L G + F ++ +A+ A +L
Sbjct: 5 VSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 30.2 bits (68), Expect = 1.2
Identities = 13/51 (25%), Positives = 22/51 (43%)
Query: 175 AKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
A E ++ E E E++ +E +ED + + + E E D E E
Sbjct: 634 ADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEE 684
>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 = 28.2 bits (63), Expect = 1.2
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 226 PDTTLYIKNLNFNSTED----SIRRHFKKCGPIASVTVAR 261
P +++ +L + ++D ++ HF K G + V V R
Sbjct: 1 PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLR 40
>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 = 27.9 bits (63), Expect = 1.3
Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 18/63 (28%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI----------TG--LVEFLQKNQA 145
++ ++ LP+ D++ F +PP GI TG VEF A
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLD------IPPDGIHIVYDDDGRPTGEAYVEFASPEDA 54
Query: 146 KAA 148
+ A
Sbjct: 55 RRA 57
Score = 27.5 bits (62), Expect = 1.5
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
+ ++ L F++TE+ IR F + + D + G
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTG 42
>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 = 28.0 bits (63), Expect = 1.4
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 113 LKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 148
L A F PFGD+ + +P T VEF + A AA
Sbjct: 15 LHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56
>gnl|CDD|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subfamily corresponds to the RRM2 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 = 76
Score = 27.9 bits (62), Expect = 1.4
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
+LV LP DLK GD+ +V G TG+V+F + K A L T+
Sbjct: 3 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTTGIVDFTNYDDMKYAIRKLDDTE 62
Query: 157 FK 158
F+
Sbjct: 63 FR 64
>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 = 27.9 bits (62), Expect = 1.4
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
TL+++NL F+ T++ + F PI V DP++
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVV--TDPET 37
>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 = 28.0 bits (63), Expect = 1.4
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
I V ++ D+K++FE FG + + P T G +E+ A+ A S+
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62
Score = 26.8 bits (60), Expect = 3.3
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+Y+ +++ + +ED I+ F+ G I S ++A
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAP 34
>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 = 27.6 bits (62), Expect = 1.5
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASV 257
LY++NL ++TE+ +R F + G + V
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERV 31
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 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 show 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 = 93
Score = 28.1 bits (62), Expect = 1.5
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 98 IILVKNL-PYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
++LV NL P R P L LF +GD+ RV ++ LV+ NQA+ A + L
Sbjct: 1 VLLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQ 60
Query: 156 KFKEVPL 162
K PL
Sbjct: 61 KLHGKPL 67
>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT. This family
consists of several bacterial cobalamin biosynthesis
(CobT) proteins. CobT is involved in the transformation
of precorrin-3 into cobyrinic acid.
Length = 282
Score = 29.8 bits (67), Expect = 1.5
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEE----DEEREPEPD 227
KE E +++GE EE ++ ED+ E+E E + P+ D
Sbjct: 231 KEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSD 280
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
subunit. The alpha-subunit of the TRAP complex (TRAP
alpha) is a single-spanning membrane protein of the
endoplasmic reticulum (ER) which is found in proximity
of nascent polypeptide chains translocating across the
membrane.
Length = 281
Score = 29.7 bits (67), Expect = 1.6
Identities = 16/56 (28%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT-LYIKNLNF 237
E E+ E+ +E++++ E+++ + E EE+ E + + P+ DTT L++K +F
Sbjct: 36 EDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEVKASPDADTTILFVKPEDF 91
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 29.7 bits (66), Expect = 1.6
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAE-EDNQQGVPEVEENVEE 218
A K KE E +E+ E EEE++E AE E+N+QG N E
Sbjct: 122 AGNAGKKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNGTSTNSTE 168
>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 = 28.0 bits (63), Expect = 1.6
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 260
T+Y+ NL+ +T D + F + G + V +A
Sbjct: 6 TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMA 37
>gnl|CDD|227219 COG4882, COG4882, Predicted aminopeptidase, Iap family [General
function prediction only].
Length = 486
Score = 29.9 bits (67), Expect = 1.7
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 25/104 (24%)
Query: 40 AMAETYNATKA---EVLTGSGAATRLAMGETEIVEKTRAFLEENGV-------QLDAFNQ 89
A+ Y+ K ++ G+G GE VE RAFLEE+ V + A+
Sbjct: 1 ALRL-YSKLKGAYGWLIVGAG-------GERGAVEVVRAFLEESLVSSRLHPFWVLAWEL 52
Query: 90 V---VEARSKRIILVKNLPYRTLPTDLKA-LFEPFGDL-GRVLV 128
+E + I + PY +L D++ GD GRV+V
Sbjct: 53 RESGLEPAASWISAI-VGPY-SLSGDIEGRPVVLEGDAGGRVVV 94
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 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 = 79
Score = 27.7 bits (62), Expect = 1.9
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 229 TLYIKNLNFNSTEDSIRR----HFKKCGPIASVTV 259
T+++K + + ED IRR HF CG I V++
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSI 35
>gnl|CDD|181386 PRK08321, PRK08321, naphthoate synthase; Validated.
Length = 302
Score = 29.2 bits (66), Expect = 1.9
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 56 SGAATRLAMGETEIVEKTRAFLE 78
+G ATRLA E E AFLE
Sbjct: 267 AGEATRLAYMTDEAQEGRDAFLE 289
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 29.8 bits (67), Expect = 2.0
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEEN----VEEDEEREPE 225
E +E G E E + + E++ + E EE E E+ E +
Sbjct: 243 NNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESD 289
>gnl|CDD|130366 TIGR01299, synapt_SV2, synaptic vesicle protein SV2. This model
describes a tightly conserved subfamily of the larger
family of sugar (and other) transporters described by
PFAM model pfam00083. Members of this subfamily include
closely related forms SV2A and SV2B of synaptic vesicle
protein from vertebrates and a more distantly related
homolog (below trusted cutoff) from Drosophila
melanogaster. Members are predicted to have two sets of
six transmembrane helices.
Length = 742
Score = 29.6 bits (66), Expect = 2.0
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 10/76 (13%)
Query: 143 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAE 202
++A+ ++ +Y++F++ E + A A S+G+ + EEGE + E E
Sbjct: 35 DRAQDEYSQRSYSRFED-----EDDDDDFPAPADGYSRGEAADDEEEGEASSDATEGHDE 89
Query: 203 ED-----NQQGVPEVE 213
+D QG+P E
Sbjct: 90 DDEIYEGEYQGIPRAE 105
>gnl|CDD|220785 pfam10498, IFT57, Intra-flagellar transport protein 57. Eukaryotic
cilia and flagella are specialised organelles found at
the periphery of cells of diverse organisms.
Intra-flagellar transport (IFT) is required for the
assembly and maintenance of eukaryotic cilia and
flagella, and consists of the bidirectional movement of
large protein particles between the base and the distal
tip of the organelle. IFT particles contain multiple
copies of two distinct protein complexes, A and B, which
contain at least 6 and 11 protein subunits. IFT57 is
part of complex B but is not, however, required for the
core subunits to stay associated. This protein is known
as Huntington-interacting protein-1 in humans.
Length = 355
Score = 29.3 bits (66), Expect = 2.0
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 189 EGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS 243
+ EE+++EN E+D + + EVEE VE +E + E K + + T +
Sbjct: 125 KYPNEEDEEENVDEDDAEIILEEVEEEVEIEEVDDDEGTQETKYKRGDTSLTPQA 179
>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 = 27.3 bits (61), Expect = 2.1
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
++V LP +L++LFE G + + IT G V+++ +N A+ A N+L
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62
Score = 26.2 bits (58), Expect = 6.5
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
T L + L + T++ +R F+ GPI S + R +
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDR 36
>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 = 27.6 bits (62), Expect = 2.1
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGR-VLVPPYGIT-----GLVEFLQKNQAKAAFNSL 152
+ V+NLPY T L+ F G + R +V G G V F + AK A
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 153 AYTKFKEVPLYLEWA 167
TKF +++E+A
Sbjct: 62 KKTKFGGRKIHVEFA 76
Score = 27.2 bits (61), Expect = 3.0
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
TL+++NL +++T++ + F + GPI V + K K
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKK 39
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 29.3 bits (65), Expect = 2.1
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 230
E KE S+G ++++ EE E E KE + + EE E+DE E E T L
Sbjct: 282 AEIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDE---IGEEKEEDDENEENERHTEL 338
Query: 231 YIKNLNFNSTEDSIRRH 247
LN +R
Sbjct: 339 LADELNELEKGIEEKRR 355
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 27.6 bits (62), Expect = 2.2
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 113 LKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL----AYTKFKEVPLYL 164
L +FE +G + +++PP V + A AA+++L + PLYL
Sbjct: 20 LLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNKPLYL 75
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 29.6 bits (66), Expect = 2.2
Identities = 12/58 (20%), Positives = 27/58 (46%)
Query: 172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
AE + +++ + +E+ + +E+ ++ E++ +EDEE E D T
Sbjct: 140 LAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFT 197
>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional.
Length = 193
Score = 28.9 bits (64), Expect = 2.2
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 178 KSKGKEKEKNEEGE-GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
K+K KE ++ + E E EK + EE +Q ++ E +E+ E PE
Sbjct: 7 KNKAKEPKRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPE 55
>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 = 27.3 bits (61), Expect = 2.3
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
LY+ NL+ TED + F + GPI S + R+
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH 34
>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 = 27.7 bits (62), Expect = 2.3
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRV 126
+R+I V +P T ++L+ F+PFG++ +
Sbjct: 2 RRVIYVGKIPIDTTRSELRQRFQPFGEIEEI 32
>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 = 27.3 bits (61), Expect = 2.4
Identities = 7/32 (21%), Positives = 18/32 (56%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 260
T+++ ++ + +ED ++ F CG + V +
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLC 33
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 29.6 bits (66), Expect = 2.5
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEE 218
EG FAE + +K G+ + ++ NT +E+ + P V +V E
Sbjct: 820 EGTFAELSKSGSLFKKLMENAGKMDATQEVNTNDENILKLGPTVTIDVSE 869
>gnl|CDD|185490 PTZ00163, PTZ00163, hypothetical protein; Provisional.
Length = 230
Score = 28.9 bits (64), Expect = 2.6
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 179 SKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN 238
S K +K E EE +K+NT +++ E+E ++ D+ + D + K + N
Sbjct: 66 SGNKNPQKRERKNEEENQKDNTKVDNDNNMENEMENHI--DDSIDDPMDDLMNDKWEHHN 123
Query: 239 STEDSIRRHFKKCGP 253
S ED I+ ++ P
Sbjct: 124 SLEDRIKEYYTLTDP 138
>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 = 27.2 bits (61), Expect = 2.7
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 229 TLYIK----NLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TLY+ E+ +RRHF + G I + V K
Sbjct: 3 TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSK 41
>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 = 27.3 bits (61), Expect = 2.8
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGR--VLVPPYGIT---GLVEFLQKNQAKAAFN 150
+ VKNL L+ F FG++ R V+V G + G+VEF +K A+AA
Sbjct: 1 ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIK 58
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 28.4 bits (64), Expect = 2.8
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
E V E +E + E E E EE+ E ++ Q + E+E ++E EER
Sbjct: 6 EQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEERY 60
Score = 27.3 bits (61), Expect = 7.4
Identities = 13/42 (30%), Positives = 20/42 (47%)
Query: 185 EKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 226
EKNE+ E E E+ E +++ VEE E + E +
Sbjct: 3 EKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQA 44
>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 = 27.3 bits (61), Expect = 2.8
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPI 254
+YI NL+++S+E+ + K P+
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPV 26
Score = 26.2 bits (58), Expect = 7.3
Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 15/79 (18%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------------PYGITGLVEFLQKNQA 145
+ + NL Y + DL+ + F + VL+P P GI EF QA
Sbjct: 2 VYISNLSYSSSEEDLEEFLKDFEPVS-VLIPSQTVRGFRSRRVRPLGI-AYAEFSSPEQA 59
Query: 146 KAAFNSLAYTKFKEVPLYL 164
+ L FK L++
Sbjct: 60 EKVVKDLNGKVFKNRKLFV 78
>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 = 27.0 bits (60), Expect = 2.9
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+YI N++ + TE+ +R F + G I SV R+K
Sbjct: 5 NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREK 39
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.3 bits (65), Expect = 3.0
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
A E + EA+E K +E +K E E ++ ++ AEE+N+ E ++ EED+++ E
Sbjct: 1690 AAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEE 1748
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 29.0 bits (65), Expect = 3.2
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEE 203
E KEK + K++EK+EE + EE +E EE
Sbjct: 278 ELKEKKEEKDEEKSEEVKTEEVDEEFEEEE 307
>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740). This
family consists of several uncharacterized plant
proteins of unknown function.
Length = 565
Score = 28.8 bits (64), Expect = 3.2
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 193 EEEKKENTAEEDNQQGVPE----VEENVEEDEEREPEP 226
EE++E EED + E V+E EE+EE E +
Sbjct: 140 LEEEEEVEMEEDEEYYEKEPGKVVDEKSEEEEEEELKT 177
>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 = 3.3
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
T Y+ NL ++ TE+ I+ F+ ++SV + R +P PG+
Sbjct: 3 TAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPR--EPGDPGRL 42
>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 = 26.8 bits (60), Expect = 3.3
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKC 251
P TL++ NL N+TE+ +R+ F +
Sbjct: 1 PCNTLFVANLGPNTTEEELRQLFSRQ 26
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 26.8 bits (60), Expect = 3.5
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP-KSPG 269
TL++ +L E I F +CG + SV + R K KS G
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAG 42
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 28.6 bits (64), Expect = 3.6
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 226
F + K K K ++KE +E EE ++E+ + + ++ED E E EP
Sbjct: 221 FFKKKTKEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDED-EDEDEP 274
>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 = 26.6 bits (59), Expect = 3.7
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCG-PIASVTVAR 261
LYI NL+ + E +R+ F++ P++SV V +
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK 33
>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 = 28.8 bits (64), Expect = 3.8
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 219 DEEREPEPDT-----TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ E E + D LY++NL +TE+ I + F + P V + +D
Sbjct: 220 EPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD 270
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 27.1 bits (61), Expect = 3.8
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIA 255
T +Y+ L + T + F KCG I
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIK 29
>gnl|CDD|165442 PHA03171, PHA03171, UL37 tegument protein; Provisional.
Length = 499
Score = 28.5 bits (63), Expect = 4.0
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 165 EWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEV 212
E + A E + E+E N+ + E +E EE+ + PEV
Sbjct: 69 ERPRDLTAALFAEAGEEAEEEDNDRECPDTEAEEEDEEEEIEAPDPEV 116
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 26.5 bits (59), Expect = 4.0
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 229 TLYIKNLNFNSTEDSIR----RHFKKCGPIASVTV 259
+ +KNL S++ S++ FKK G + SV V
Sbjct: 1 GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKV 35
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 27.7 bits (62), Expect = 4.2
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 221
E KE K E+E ++E + E E E+ E+D +G PE E+E
Sbjct: 70 KERKEALKLLEEENDDEEDAETEDTEDV-EDDEWEGFPEPTVTDYEEEY 117
>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 = 28.4 bits (63), Expect = 4.5
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
DT LY+ NL T+D + F K G I + R K +P
Sbjct: 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTP 234
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 26.5 bits (58), Expect = 4.6
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
T+L+++N+ + + +RR F + GPI V V
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYV 32
>gnl|CDD|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM2 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C, 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 = 76
Score = 26.5 bits (58), Expect = 4.6
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
++V LP DLK GD+ V G+ G+VEFL+K + A L TKF+
Sbjct: 3 VIVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM-GVVEFLRKEDMEYALRKLDDTKFR 61
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 26.6 bits (59), Expect = 4.7
Identities = 12/34 (35%), Positives = 24/34 (70%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
T+++ L N+TE+ IR F++CG I ++ +++K
Sbjct: 8 TVFVGGLPENATEEIIREVFEQCGEIIAIRMSKK 41
>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 = 26.7 bits (59), Expect = 4.7
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
L++ L+ E+ +R F G I TV R ++ +S G
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRG 43
>gnl|CDD|177802 PLN00221, PLN00221, tubulin alpha chain; Provisional.
Length = 450
Score = 28.2 bits (63), Expect = 4.7
Identities = 29/89 (32%), Positives = 39/89 (43%), Gaps = 7/89 (7%)
Query: 119 PFGDLGRVLVPPYGI---TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL-EWAPEGVFAE 174
P GDL +V I T + E + K F+ L Y K V Y+ E EG F+E
Sbjct: 364 PGGDLAKVQRAVCMISNSTAVAEVFSRIDHK--FD-LMYAKRAFVHWYVGEGMEEGEFSE 420
Query: 175 AKEKSKGKEKEKNEEGEGEEEKKENTAEE 203
A+E EK+ E G E + + EE
Sbjct: 421 AREDLAALEKDYEEVGAESAEGEGDEGEE 449
>gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional.
Length = 815
Score = 28.2 bits (63), Expect = 5.0
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
EG + K K KEK++++ G G + E+ +E ++ +EE++ ++ RE
Sbjct: 30 EHEGEQSPKKAK---KEKKQDDSGNGNGKSAEDAVKE-FEEFCKAIEEHLSIEQMRE 82
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 26.0 bits (58), Expect = 5.2
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
T+Y+K ++T D I+ F+K G + ++ + R D
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLD 36
>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 = 28.0 bits (62), Expect = 5.4
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 272
E T L + L T++ IR F G I S + R K GQ L
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRD---KVTGQSL 45
>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 = 26.1 bits (58), Expect = 5.4
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L++ L + TE+ +R +F + G + SV + K+
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKE 36
>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 = 26.0 bits (57), Expect = 5.4
Identities = 19/68 (27%), Positives = 28/68 (41%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
+ V NLP D K LFE +G+ V + G + + A+ A L T K
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 63
Query: 159 EVPLYLEW 166
PL + +
Sbjct: 64 NRPLRIRF 71
>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 = 26.0 bits (57), Expect = 5.4
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
+ V NLP ++++LFE +G + ++ Y G V K A A +L + K
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNY---GFVHMDDKTAADEAIRNLHHYKL 59
Query: 158 KEVPLYLE 165
V + +E
Sbjct: 60 HGVAINVE 67
>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 = 26.1 bits (58), Expect = 5.6
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAK 146
+ V L DL+ F FG++ V +P P+ V F A+
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQ 51
>gnl|CDD|218253 pfam04765, DUF616, Protein of unknown function (DUF616). Family of
uncharacterized proteins.
Length = 306
Score = 28.1 bits (63), Expect = 5.6
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 71 EKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPY 106
E+T + L+ G D N V RI++VKNLPY
Sbjct: 101 EETLSTLKSEGHVPDD-NGRVGLW--RIVVVKNLPY 133
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 26.8 bits (59), Expect = 5.6
Identities = 16/56 (28%), Positives = 25/56 (44%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
E KE K NE E ++ ++ EE+ + + EE E +EE E + T
Sbjct: 24 EEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEET 79
>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 = 26.2 bits (58), Expect = 5.9
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 240 TEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
TE+ +R FK+ G I V++ + K+ F
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGF 44
>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing 2 (RBP-MS2).
This subfamily corresponds to the RRM of RBP-MS2,
encoded by RBPMS2 gene, a paralog of RNA-binding protein
with multiple splicing (RBP-MS). The biological function
of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 76
Score = 26.2 bits (57), Expect = 5.9
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPF-GDLGRVL-VPPYGITGLVEFLQKNQAKAAFNSLAY 154
R + V LP P +L LF PF G G ++ + G V F + A+AA N+L
Sbjct: 2 RTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVTFDSRAGAEAAKNALNG 61
Query: 155 TKF 157
+F
Sbjct: 62 IRF 64
>gnl|CDD|225743 COG3202, COG3202, ATP/ADP translocase [Energy production and
conversion].
Length = 509
Score = 28.0 bits (63), Expect = 5.9
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 126 VLVPPYGIT-GLVEFLQKNQAKAAF-NSLAYTKF 157
+LV YG++ LVE + K+ K + + YT F
Sbjct: 289 LLVLAYGVSINLVEGVWKSGIKELYPTTNEYTAF 322
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and 2
(NRF-1 and NRF-2), CREB (cAMP-response element-binding
protein), and estrogen-related receptor alpha
(ERRalpha). It interacts indirectly with the NRF-2beta
subunit through host cell factor (HCF), a cellular
protein involved in herpes simplex virus (HSV) infection
and cell cycle regulation. Furthermore, like PGC-1alpha
and PGC-1beta, PRC can transactivate a number of
NRF-dependent nuclear genes required for mitochondrial
respiratory function, including those encoding
cytochrome c, 5-aminolevulinate synthase, Tfam, and
TFB1M, and TFB2M. Further research indicates that PRC
may also act as a sensor of metabolic stress that
orchestrates a redox-sensitive program of inflammatory
gene expression. PRC is a multi-domain protein
containing an N-terminal activation domain, an LXXLL
coactivator signature, a central proline-rich region, a
tetrapeptide motif (DHDY) responsible for HCF binding, a
C-terminal arginine/serine-rich (SR) domain, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 91
Score = 26.4 bits (58), Expect = 6.0
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 96 KRIILVKNLPYRTLPTDLKALFEPFGDL 123
+R++ + +P R ++LK F FG++
Sbjct: 2 RRVVYIGKIPSRMTRSELKDRFSVFGEI 29
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 26.1 bits (58), Expect = 6.2
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 1/63 (1%)
Query: 97 RIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
R++ + NLP +L L EPFG + + P +E A+A +
Sbjct: 1 RVVRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLPNRNKAFIEMESPEDAQALVSFYKTY 60
Query: 156 KFK 158
Sbjct: 61 PLT 63
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 26.0 bits (57), Expect = 6.4
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+Y+ N++ +TE I F CG I+++ + D +S
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKISNLDL--TNDGES 36
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 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 = 74
Score = 26.1 bits (57), Expect = 6.5
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
LY++NL ++ED+I++ F + P V + +D
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD 38
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by YNL110C
from Saccharomyces cerevisiae, and localizes to the
nucleoplasm and nucleolus. Nop15p has been identified as
a component of a pre-60S particle. It interacts with RNA
components of the early pre-60S particles. Furthermore,
Nop15p binds directly to a pre-rRNA transcript in vitro
and is required for pre-rRNA processing. It functions as
a ribosome synthesis factor required for the 5' to 3'
exonuclease digestion that generates the 5' end of the
major, short form of the 5.8S rRNA as well as for
processing of 27SB to 7S pre-rRNA. Nop15p also play a
specific role in cell cycle progression. Nop15p contains
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 25.9 bits (57), Expect = 6.7
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNS 151
+I + +LP+ L +LK F FG + V V T G ++FL A A S
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60
Query: 152 L 152
+
Sbjct: 61 M 61
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 25.8 bits (57), Expect = 6.9
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 232 IKNLNFNSTEDSIRRHFKK-CGPIASVTVARKKDPKSPG 269
+ NL + TE IR +F GPI V ++ + KS G
Sbjct: 4 VSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTG 42
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 25.7 bits (57), Expect = 7.3
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 129
+ V NLP+ +LK F FG + VP
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVP 32
>gnl|CDD|150392 pfam09710, Trep_dent_lipo, Treponema clustered lipoprotein
(Trep_dent_lipo). This entry represents a family of six
predicted lipoproteins from a region of about 20
tandemly arranged genes in the Treponema denticola
genome. Two other neighboring genes share the
lipoprotein signal peptide region but do not show more
extensive homology. The function of this locus is
unknown.
Length = 394
Score = 27.6 bits (61), Expect = 7.4
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENT----AEEDNQQGVPEVEENVEEDEERE 223
+F+ +KE + +E E + E KEN E D PE + +EE + E
Sbjct: 15 LFSCSKEVKEQREMRIKVESSMKIEPKENEFLSKPEYDEHVKTPEQIKELEEKKAYE 71
>gnl|CDD|177798 PLN00208, PLN00208, translation initiation factor (eIF);
Provisional.
Length = 145
Score = 27.1 bits (60), Expect = 7.5
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 176 KEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQ 207
K K KG + K + E ++EK+E +ED Q+
Sbjct: 3 KNKGKGGKNRKRGKNEADDEKRELIFKEDGQE 34
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 27.7 bits (62), Expect = 7.5
Identities = 6/54 (11%), Positives = 21/54 (38%)
Query: 172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
+ + E + +++ + E+E+K+ E + + + ++ E
Sbjct: 147 IDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQA 200
>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 = 26.1 bits (58), Expect = 7.5
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGP 253
T+Y L T++ +R FK P
Sbjct: 2 KDTVYCGKLPKKVTDEDLREFFKDYNP 28
>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP).
This family consists of several Trypanosoma brucei
procyclic acidic repetitive protein (PARP) like
sequences. The procyclic acidic repetitive protein
(parp) genes of Trypanosoma brucei encode a small family
of abundant surface proteins whose expression is
restricted to the procyclic form of the parasite. They
are found at two unlinked loci, parpA and parpB;
transcription of both loci is developmentally regulated.
Length = 145
Score = 26.8 bits (58), Expect = 7.5
Identities = 21/45 (46%), Positives = 27/45 (60%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
E E+ EE E EEE +E E+ + PE EE EE+ E EPEP+
Sbjct: 63 EPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPE 107
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subgroup corresponds
to the RRM2 in 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 = 70
Score = 25.6 bits (56), Expect = 7.5
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 105 PYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL 164
P T DL+ FEP+G L V + V++ + A A S +K + + +
Sbjct: 9 PINTRTRDLERHFEPYGKLVNVRIRRN--FAFVQYETQEDATKALESTNMSKVLDRVISV 66
Query: 165 EWA 167
E+A
Sbjct: 67 EYA 69
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 25.6 bits (57), Expect = 7.8
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAK 146
++ + +LP+ +L+ F FG + R+ + TG VEF AK
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAK 55
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 27.5 bits (61), Expect = 7.8
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 176 KEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPE---VEENVEEDEEREPEPDTT 229
KEK K KEK+ E + EEEKK ++ P +E E E +
Sbjct: 144 KEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAA 200
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 26.0 bits (57), Expect = 8.2
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
T LY+ NL TED +R+ F+ G I + R K P
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLP 41
>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413). This is
a family of proteins conserved in fungi. The function is
not known.
Length = 436
Score = 27.4 bits (61), Expect = 8.2
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 165 EWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENV-EEDEERE 223
E + G K+ SK E E + +++ + + EE+EE E
Sbjct: 55 EASRPGTPRNPKKSSKPTESSAASSEEKPAKPRKSAESTRSSHPKSKAPSTESEEEEEPE 114
Query: 224 PEPD 227
PD
Sbjct: 115 ETPD 118
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 26.0 bits (57), Expect = 8.4
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPI 254
+T+Y++ LN N T + + FK CG +
Sbjct: 1 STIYVQGLNDNVTLEELADFFKHCGVV 27
>gnl|CDD|226839 COG4408, COG4408, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 431
Score = 27.4 bits (61), Expect = 8.4
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 52 VLTGSGAATRLAMGETEI----VEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYR 107
LT R+ +G E A L ++G+ ++ + A ++ I L + P
Sbjct: 163 ALT-KAVKKRIYLGSQHGNSGSAEMLTAVLAQHGIDVEPCESPLAAETRNITLYVHPPLF 221
Query: 108 TLPTDLKALFEPFG 121
L+A+F P
Sbjct: 222 LNDFSLQAIFYPEQ 235
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 27.5 bits (61), Expect = 8.5
Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEK-KENTAEEDNQQGVPEVEENVEEDEER 222
+ E + + E + +EEK K+ E+ ++ E +E ++DE +
Sbjct: 384 KLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDERK 433
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 27.7 bits (61), Expect = 8.9
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 260
+Y+ +++F ED+IRR F GPI S+ ++
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMS 140
>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 = 25.8 bits (57), Expect = 9.0
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGR---VLVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
I + N+P DL +L +G + V T V + QA+ A N L
Sbjct: 3 IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNGH 62
Query: 156 KFKEVPLYLEWAPE 169
+++ L + + P+
Sbjct: 63 EYEGSKLKVSYIPD 76
>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 = 25.8 bits (57), Expect = 9.0
Identities = 7/44 (15%), Positives = 23/44 (52%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 272
++++ L+ + T++ + F + G I V + ++ + + F+
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFI 48
>gnl|CDD|130691 TIGR01630, psiM2_ORF9, phage uncharacterized protein (putative
large terminase), C-terminal domain. This model
represents the C-terminal region of a set of phage
proteins typically about 400-500 amino acids in length,
although some members are considerably shorter. An
article on Methanobacterium phage Psi-M2 (PMID:9791169)
calls the member from that phage, ORF9, a putative large
terminase subunit, and ORF8 a candidate terminase small
subunit. Most proteins in this family have an apparent
P-loop nucleotide-binding sequence toward the N-terminus
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 142
Score = 26.7 bits (59), Expect = 9.5
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 1/78 (1%)
Query: 64 MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
E L + V L E +S LVK L + + T +A++
Sbjct: 26 EPPPETERLVIRLLNAHRVNLAIIESNQEGKSFGRSLVKILKEKGIRTPARAVYPSGDKE 85
Query: 124 GRVL-VPPYGITGLVEFL 140
R+L V P+ G V
Sbjct: 86 TRILSVAPWVEAGNVFPP 103
>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 = 25.7 bits (57), Expect = 9.5
Identities = 13/42 (30%), Positives = 17/42 (40%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 270
L+I NL+ TE + + F K G I K GQ
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQ 42
>gnl|CDD|131353 TIGR02300, FYDLN_acid, TIGR02300 family protein. Members of this
family are bacterial proteins with a conserved motif
[KR]FYDLN, sometimes flanked by a pair of CXXC motifs,
followed by a long region of low complexity sequence in
which roughly half the residues are Asp and Glu,
including multiple runs of five or more acidic residues.
The function of members of this family is unknown.
Length = 129
Score = 26.5 bits (58), Expect = 9.6
Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 2/79 (2%)
Query: 158 KEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG--VPEVEEN 215
++ P V A+ ++++ ++ E E E A+E+ G P ++
Sbjct: 34 EQFPPEEALKSRRVRADDEKEAVAVKEVDPEIDEAAELVSLEEADEEVDPGAPTPAGGDD 93
Query: 216 VEEDEEREPEPDTTLYIKN 234
+ EDE+ + D ++++
Sbjct: 94 LAEDEDIADDDDDVTFLED 112
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 27.3 bits (60), Expect = 9.9
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 176 KEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 228
+EK K KE+E+ E E E K +++ +++ P++ EP P T
Sbjct: 602 REKEKEKEREREREREAERAAKASSSSHESRMSEPQLSGPAHMRPSFEPPPTT 654
>gnl|CDD|183075 PRK11283, gltP, glutamate/aspartate:proton symporter; Provisional.
Length = 437
Score = 27.4 bits (61), Expect = 10.0
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFA 173
F S++ T FK + + +AP GVFA
Sbjct: 189 FRSVSETMFKVTHMVMRYAPVGVFA 213
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
0.309 0.129 0.357
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,069,170
Number of extensions: 1378725
Number of successful extensions: 4041
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3348
Number of HSP's successfully gapped: 621
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.0 bits)