RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3345
(787 letters)
>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 = 154 bits (392), Expect = 1e-44
Identities = 62/79 (78%), Positives = 67/79 (84%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
SKILVRNIPF+A E+ ELF FGELK VRLPKKM G+G HRGFGFV+FITK +AKRA
Sbjct: 1 SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60
Query: 746 KALCQSTHLYGRRLVLEWA 764
KALC STHLYGRRLVLEWA
Sbjct: 61 KALCHSTHLYGRRLVLEWA 79
Score = 49.3 bits (118), Expect = 1e-07
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAFNS 502
ILV+N+P+ +L+ LF FG+L V +P G V+F+ K AK AF +
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62
Query: 503 LAY-TKFKEVPLYLEWA 518
L + T L LEWA
Sbjct: 63 LCHSTHLYGRRLVLEWA 79
Score = 40.5 bits (95), Expect = 2e-04
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID-KETDKTKGFALVTFLMPEHATQAYQ 396
+I VRN+ + T +L +LF +G L V LP T +GF V F+ + A +A++
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61
Query: 397 HL-DGTVFLGRMLHL 410
L T GR L L
Sbjct: 62 ALCHSTHLYGRRLVL 76
Score = 33.9 bits (78), Expect = 0.038
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS-MGYGFVQFYTRES 639
+ + ++N+ F +T +R F G + +V + PK S G+GFV F T++
Sbjct: 1 SKILVRNIPFEATVKELRELFSTFGELKTVRL-----PKKMTGTGSHRGFGFVDFITKQD 55
Query: 640 LNQALKVLQNSS 651
+A K L +S+
Sbjct: 56 AKRAFKALCHST 67
Score = 27.7 bits (62), Expect = 5.7
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 30 TQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYF-NNTYVFSS 86
T ++L+ F G + V+L K T G R F F+ + + A+ A ++T+++
Sbjct: 13 TVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLYGR 72
Query: 87 RIKVE 91
R+ +E
Sbjct: 73 RLVLE 77
>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 = 141 bits (356), Expect = 7e-40
Identities = 54/79 (68%), Positives = 66/79 (83%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
ESGR+F+RNL+YT TE+DL KLF KYGPL+EV LPIDK T K KGFA VT+++PEHA +A
Sbjct: 1 ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60
Query: 395 YQHLDGTVFLGRMLHLIPG 413
+ LDGTVF GR+LHL+P
Sbjct: 61 FAELDGTVFQGRLLHLLPS 79
Score = 42.4 bits (100), Expect = 3e-05
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 502
+ ++NL Y DL+ LF +G L V +P P G V ++ A AF
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF-AFVTYMIPEHAVKAFAE 63
Query: 503 LAYTKFK 509
L T F+
Sbjct: 64 LDGTVFQ 70
Score = 41.6 bits (98), Expect = 6e-05
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 11/67 (16%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP-----KKMVGSGLHRGFGFVEFITKNEA 741
++ +RN+ + + ++E+LF +G L V LP KK +GF FV ++ A
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP------KGFAFVTYMIPEHA 57
Query: 742 KRAMKAL 748
+A L
Sbjct: 58 VKAFAEL 64
Score = 36.6 bits (85), Expect = 0.004
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
L+I+NL + TE+ + + F K GP++ V + K K P G+ FV +
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP-----KGFAFVTY 51
>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 = 128 bits (323), Expect = 3e-35
Identities = 48/82 (58%), Positives = 68/82 (82%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TTL++KNLNF +TE+++++HF+KCG + SVT+A+KKDPK PG+ LSMGYGFV+F ++E+
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 641 NQALKVLQNSSLDEHQIELKRS 662
+ALK LQ + LD H +ELK S
Sbjct: 61 QKALKRLQGTVLDGHALELKLS 82
Score = 56.8 bits (138), Expect = 3e-10
Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 5/78 (6%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFITKNEAKR 743
+ V+N+ F+ + +++ F+ G ++ V + KK G L G+GFVEF +K A++
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 744 AMKALCQSTHLYGRRLVL 761
A+K L Q T L G L L
Sbjct: 63 ALKRL-QGTVLDGHALEL 79
Score = 51.8 bits (125), Expect = 2e-08
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVIL-----PIDKETDKTKGFALVTFLMPEHATQ 393
+FV+NL++ TE+ L K FEK G + V + P + G+ V F E A +
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 394 AYQHLDGTVFLGRMLHL 410
A + L GTV G L L
Sbjct: 63 ALKRLQGTVLDGHALEL 79
>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 = 126 bits (320), Expect = 7e-35
Identities = 50/79 (63%), Positives = 64/79 (81%), Gaps = 3/79 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+K++VRN+PF+A + E+ ELF FG++K VRLPKK GS HRGF FVEF+TK EA+ AM
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGS--HRGFAFVEFVTKQEAQNAM 58
Query: 746 KALCQSTHLYGRRLVLEWA 764
+AL +STHLYGR LVLE+A
Sbjct: 59 EAL-KSTHLYGRHLVLEYA 76
Score = 52.6 bits (127), Expect = 7e-09
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 5/76 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT-KGFALVTFLMPEHATQAYQ 396
++ VRN+ + T+ +L +LF +G + V LP K+ D + +GFA V F+ + A A +
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLP--KKFDGSHRGFAFVEFVTKQEAQNAME 59
Query: 397 HLDGTVFLGRMLHLIP 412
L T GR HL+
Sbjct: 60 ALKSTHLYGR--HLVL 73
Score = 47.2 bits (113), Expect = 7e-07
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNSLA 504
++V+N+P+ +L+ LF PFG + V +P G VEF+ K +A+ A +L
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62
Query: 505 YTKFKEVPLYLEWA 518
T L LE+A
Sbjct: 63 STHLYGRHLVLEYA 76
Score = 41.8 bits (99), Expect = 5e-05
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L ++N+ F +T+ +R F G + SV + +K D G G+ FV+F T++
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD----GS--HRGFAFVEFVTKQEA 54
Query: 641 NQALKVLQNSSL 652
A++ L+++ L
Sbjct: 55 QNAMEALKSTHL 66
Score = 34.9 bits (81), Expect = 0.015
Identities = 17/63 (26%), Positives = 35/63 (55%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
T+++L+ F G V V+L +G R FAF+ + + +AQ A++ +T+++ +
Sbjct: 13 TKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLV 72
Query: 90 VEK 92
+E
Sbjct: 73 LEY 75
Score = 28.3 bits (64), Expect = 3.0
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNKN 278
++V+N+P KK+L+ F P + SVR + G A++ F ++ A+
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61
Query: 279 KS 280
KS
Sbjct: 62 KS 63
>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 = 121 bits (305), Expect = 5e-33
Identities = 47/71 (66%), Positives = 56/71 (78%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
+ILVKNLP TL +L+ LF FG LGRVL+PP GIT +VEFL+ ++AK AF LAY+KF
Sbjct: 2 VILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKLAYSKF 61
Query: 509 KEVPLYLEWAP 519
K VPLYLEWAP
Sbjct: 62 KHVPLYLEWAP 72
Score = 51.6 bits (124), Expect = 2e-08
Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 12/79 (15%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
ILV+N+P +E+ ELF FG L V LP + VEF+ +EAK A +
Sbjct: 3 ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGIT-------AIVEFLEPSEAKLAFRK 55
Query: 748 L--CQSTHLYGRRLVLEWA 764
L + H+ L LEWA
Sbjct: 56 LAYSKFKHV---PLYLEWA 71
Score = 42.7 bits (101), Expect = 2e-05
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I V+NL +L +LF K+G L V+LP T A+V FL P A A++ L
Sbjct: 3 ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGIT------AIVEFLEPSEAKLAFRKL 56
Query: 399 DGTVF 403
+ F
Sbjct: 57 AYSKF 61
Score = 29.3 bits (66), Expect = 1.4
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 20/60 (33%)
Query: 227 IVVKNLPAGVKKKDLKAYFKP--------LPLASV------------RTTFLGMAYIGFK 266
I+VKNLPAG +L+ F LP A + + F +AY FK
Sbjct: 3 ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKLAYSKFK 62
>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 = 115 bits (291), Expect = 4e-31
Identities = 42/73 (57%), Positives = 60/73 (82%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FVRNL +T TE++L +LFE +G ++EV LP+DKET ++KGFA V+F+ PEHA +AY
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 398 LDGTVFLGRMLHL 410
LDG++F GR+LH+
Sbjct: 61 LDGSIFQGRLLHV 73
Score = 51.9 bits (125), Expect = 1e-08
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEAKRA 744
++ VRN+PF + E+ ELF+AFGE+ V LP K+ + +GF FV F+ A +A
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKE---TKRSKGFAFVSFMFPEHAVKA 57
Query: 745 MKAL 748
L
Sbjct: 58 YSEL 61
Score = 47.7 bits (114), Expect = 4e-07
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+++NL F +TE+ +R F+ G I+ V + K+ K S G+ FV F E +
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKR-----SKGFAFVSFMFPEHAVK 56
Query: 643 ALKVLQNSSLD 653
A L S
Sbjct: 57 AYSELDGSIFQ 67
Score = 39.2 bits (92), Expect = 5e-04
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
+ V+NLP+ T +L+ LFE FG++ V +P T V F+ A A++ L
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 504 AYTKFK 509
+ F+
Sbjct: 62 DGSIFQ 67
Score = 31.9 bits (73), Expect = 0.17
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTYVFS 85
+ T+E+L+ FE G +++V L E K + FAF+ + + A A + + +F
Sbjct: 9 FTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGS-IFQ 67
Query: 86 SRI 88
R+
Sbjct: 68 GRL 70
>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 = 115 bits (291), Expect = 5e-31
Identities = 47/79 (59%), Positives = 62/79 (78%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E+GR+FVRNL Y+ EDDL KLF K+G L+EV + IDK++ K+KGFA V FL PE A +A
Sbjct: 1 ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
Query: 395 YQHLDGTVFLGRMLHLIPG 413
Y+ LDG VF GR++H++PG
Sbjct: 61 YKELDGKVFQGRLIHILPG 79
Score = 47.8 bits (114), Expect = 4e-07
Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 7/77 (9%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNE 740
+TG ++ VRN+P+ K+ ++E+LF FGEL V + KK SG +GF +V F+ +
Sbjct: 1 ETG-RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKK---SGKSKGFAYVLFLDPED 56
Query: 741 AKRAMKALCQSTHLYGR 757
A +A K L GR
Sbjct: 57 AVKAYKEL-DGKVFQGR 72
Score = 42.4 bits (100), Expect = 4e-05
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 502
+ V+NLPY DL+ LF FG+L V V G V FL A A+
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGF-AYVLFLDPEDAVKAYKE 63
Query: 503 LAYTKFK 509
L F+
Sbjct: 64 LDGKVFQ 70
Score = 33.9 bits (78), Expect = 0.031
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+++NL ++ ED + + F K G ++ V VA K S G+ +V F E +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGK-----SKGFAYVLFLDPEDAVK 59
Query: 643 ALKVL 647
A K L
Sbjct: 60 AYKEL 64
Score = 31.6 bits (72), Expect = 0.22
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 9/72 (12%)
Query: 227 IVVKNLPAGVKKKDLKAYFKP--------LPLASVRTTFLGMAYIGFKDEKNCNKALNK- 277
+ V+NLP K+ DL+ F + + G AY+ F D ++ KA +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 278 NKSFWKGKQLNI 289
+ ++G+ ++I
Sbjct: 65 DGKVFQGRLIHI 76
>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 = 111 bits (281), Expect = 1e-29
Identities = 43/72 (59%), Positives = 53/72 (73%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 507
+ILVKNLP+ T +L+ LFE FG LGR+L+PP LVEFL+ + A+ AF SLAY +
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKR 60
Query: 508 FKEVPLYLEWAP 519
FK VPLYLEWAP
Sbjct: 61 FKHVPLYLEWAP 72
Score = 58.4 bits (142), Expect = 6e-11
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 6/60 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I V+NL + TE++L +LFEK+G L ++LP ++ ALV FL P A +A++ L
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLGRLLLP------PSRTIALVEFLEPSDARKAFKSL 56
Score = 51.1 bits (123), Expect = 3e-08
Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
ILV+N+PF + E+ ELF+ FG L + LP R VEF+ ++A++A K+
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLGRLLLPPS-------RTIALVEFLEPSDARKAFKS 55
Query: 748 LCQSTHLYGRRLVLEWA 764
L L LEWA
Sbjct: 56 LAYK-RFKHVPLYLEWA 71
Score = 32.2 bits (74), Expect = 0.13
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKP------LPLASVRTTFLGMAYIGFKDEKNCNKALNKN 278
I+VKNLP G +++L+ F+ L L RT +A + F + + KA
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRT----IALVEFLEPSDARKAFKSL 56
Score = 29.1 bits (66), Expect = 1.6
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV 610
T + +KNL F +TE+ +R F+K G + +
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRL 30
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 98.1 bits (245), Expect = 9e-25
Identities = 35/66 (53%), Positives = 51/66 (77%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
I +++L+ FE GT+TDVQLKYT +GKFR+F F+GY E++AQ AL +FNN+++ +S+
Sbjct: 11 GIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSK 70
Query: 88 IKVEKC 93
I VE C
Sbjct: 71 ITVEIC 76
Score = 47.3 bits (113), Expect = 6e-07
Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S+++V+N+P K+ ++ +LF+AFG + V+L K G R FGFV + T+ EA++A+
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQL--KYTKDGKFRKFGFVGYKTEEEAQKAL 58
Query: 746 KALCQS 751
K S
Sbjct: 59 KHFNNS 64
Score = 46.5 bits (111), Expect = 1e-06
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V+NL + ED L KLFE +G + +V L K+ K + F V + E A +A +H
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60
Query: 398 LDGTVF 403
+ +
Sbjct: 61 FNNSFI 66
Score = 38.1 bits (89), Expect = 0.001
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 227 IVVKNLPAGVKKKDLKAYFKP---LPLASVRTT----FLGMAYIGFKDEKNCNKALNK-N 278
++VKNLP G+K+ L+ F+ + ++ T F ++G+K E+ KAL N
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62
Query: 279 KSF 281
SF
Sbjct: 63 NSF 65
Score = 35.0 bits (81), Expect = 0.013
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ L +KNL ED +R+ F+ G I V + KD G+F +GFV + T E
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD----GKF--RKFGFVGYKTEEEA 54
Query: 641 NQALKVLQNSSLDEHQIELKR 661
+ALK NS +D +I ++
Sbjct: 55 QKALKHFNNSFIDTSKITVEI 75
>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 = 96.3 bits (240), Expect = 3e-24
Identities = 38/70 (54%), Positives = 46/70 (65%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
ILVKN PY T +L+ LFEP G L RVL+PP G +VEF QA+ AF +LAY +FK
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRRFK 62
Query: 510 EVPLYLEWAP 519
+ LYLE P
Sbjct: 63 DSILYLEKGP 72
Score = 45.5 bits (108), Expect = 2e-06
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
ILV+N P+ E+ +LF+ G+L V +P +G VEF +A+ A KA
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPP----AGT---IAIVEFANPQQARLAFKA 55
Query: 748 LCQSTHLYGRRLVLEWA 764
L L LE
Sbjct: 56 LAY-RRFKDSILYLEKG 71
Score = 40.8 bits (96), Expect = 1e-04
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I V+N Y T ++L LFE +G L V++P A+V F P+ A A++ L
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTI------AIVEFANPQQARLAFKAL 56
Query: 399 DGTVFLGRMLHL 410
F +L+L
Sbjct: 57 AYRRFKDSILYL 68
Score = 28.5 bits (64), Expect = 2.2
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 20/62 (32%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKP--------LPLA------------SVRTTFLGMAYIGF 265
TI+VKN P G ++L+ F+P +P A R F +AY F
Sbjct: 2 TILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRRF 61
Query: 266 KD 267
KD
Sbjct: 62 KD 63
>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 = 91.0 bits (226), Expect = 2e-22
Identities = 44/79 (55%), Positives = 57/79 (72%), Gaps = 3/79 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+KILV+N+PF+A + +V LF ++G+LK VR+PKK S RGF FVEF T EA AM
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA--RGFAFVEFSTAKEALNAM 58
Query: 746 KALCQSTHLYGRRLVLEWA 764
AL + THL GRRLVL++A
Sbjct: 59 NAL-KDTHLLGRRLVLQYA 76
Score = 51.7 bits (124), Expect = 2e-08
Identities = 28/73 (38%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT-KGFALVTFLMPEHATQAY 395
+I V+NL + T+ D+ LF YG L V +P K+ D++ +GFA V F + A A
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVP--KKFDQSARGFAFVEFSTAKEALNAM 58
Query: 396 QHLDGTVFLGRML 408
L T LGR L
Sbjct: 59 NALKDTHLLGRRL 71
Score = 39.8 bits (93), Expect = 3e-04
Identities = 27/75 (36%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAAFNSL 503
ILVKNLP+ D++ LF +G L V VP G VEF +A A N+L
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGF-AFVEFSTAKEALNAMNAL 61
Query: 504 AYTKFKEVPLYLEWA 518
T L L++A
Sbjct: 62 KDTHLLGRRLVLQYA 76
Score = 36.7 bits (85), Expect = 0.003
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 8/73 (10%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT-RES 639
T + +KNL F +T+ +R F G + SV V +K D + G+ FV+F T +E+
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA------RGFAFVEFSTAKEA 54
Query: 640 LNQALKVLQNSSL 652
LN A+ L+++ L
Sbjct: 55 LN-AMNALKDTHL 66
>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 = 99.1 bits (247), Expect = 2e-21
Identities = 105/454 (23%), Positives = 165/454 (36%), Gaps = 115/454 (25%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V +L VTE L LF+ +GP+ V + D T ++ G+ V F P A +A + +
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 399 DGTVFLGRMLHLI-----PGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVK 453
+ G+ + ++ P + GN I VK
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSLRRSGVGN----------------------------IFVK 94
Query: 454 NLPYRTLPTDLKALFEPFGDLGRVL-----VPPYGIT---GLVEFLQKNQAKAAFNSLAY 505
NL D KALF+ F G +L G + G V F ++ AKAA +
Sbjct: 95 NLDKSV---DNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKV-- 149
Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
G+ KE G+ +K+E E ++
Sbjct: 150 --------------NGMLLNDKEVYVGRFIKKHEREAAPLKKF----------------- 178
Query: 566 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 625
T LY+KNL+ + ED +R F K G I S V KD
Sbjct: 179 ---------------TNLYVKNLDPSVNEDKLRELFAKFGEITSAAV--MKDGSG----R 217
Query: 626 SMGYGFVQFYTRESLNQALKVLQNSSLDE-----------HQIELKRSNRNLESEATTVK 674
S G+ FV F E +A++ + + Q KR+ R E +
Sbjct: 218 SRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQ---KRAEREAELRRKFEE 274
Query: 675 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 734
+ K G + V+N+ ++ ELF GE+ ++ + G+ RGFGFV
Sbjct: 275 LQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV--MLDEKGVSRGFGFVC 332
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEAD 768
F EA RA+ + L G+ L + A+ +
Sbjct: 333 FSNPEEANRAVTEM-HGRMLGGKPLYVALAQRKE 365
Score = 83.3 bits (206), Expect = 1e-16
Identities = 99/432 (22%), Positives = 153/432 (35%), Gaps = 101/432 (23%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTF-------LGMAYIGFKDEKNCNKALNK 277
++ V +L V + L FKP P+ SVR LG Y+ F++ + +AL
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 278 -NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAES 336
N GK + I +D S + SG
Sbjct: 62 MNFKRLGGKPIRIMWSQRDPSLRRSG---------------------------------V 88
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G IFV+NL +V L F K+G + + D E K++G+ V F E A A Q
Sbjct: 89 GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQ 147
Query: 397 HLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLP 456
++G + + +++ K L F + VKNL
Sbjct: 148 KVNGMLLNDKEVYVGRFIKKHEREA-----------APLKKFTNL---------YVKNLD 187
Query: 457 YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE 516
L+ LF FG IT + F + + K ++ +E
Sbjct: 188 PSVNEDKLRELFAKFG----------EITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE 237
Query: 517 WAPEGVFAEAKEKSK---GKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE 573
AKE K G+ +++ E E E + ++ + QGV
Sbjct: 238 EMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGV----------- 286
Query: 574 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQ 633
LY+KNL+ T++ +R F +CG I S V D K +S G+GFV
Sbjct: 287 --------NLYVKNLDDTVTDEKLRELFSECGEITSAKVML--DEKG----VSRGFGFVC 332
Query: 634 FYTRESLNQALK 645
F E N+A+
Sbjct: 333 FSNPEEANRAVT 344
Score = 64.4 bits (157), Expect = 1e-10
Identities = 67/310 (21%), Positives = 120/310 (38%), Gaps = 57/310 (18%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL------GMAYIGFKDEKNCNKALNKNK 279
I VKNL V K L F + S + G ++ F+ E++ A+ K
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK-- 148
Query: 280 SFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRI 339
+N G ++ + KH + +F +
Sbjct: 149 -------VN-------------GMLLNDKEVYVGRFIKKHEREAAPLKKFTN-------L 181
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
+V+NL +V ED L +LF K+G + + D + +++GFA V F E A +A + ++
Sbjct: 182 YVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMN 240
Query: 400 GTVF----LGRMLHLIPGKPK-ENEGNVDGKVHCCISERKLDAFNQVVEARSKRI-ILVK 453
G G+ L++ + + E E RK + Q + +++ + + VK
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREA---------ELRRKFEELQQERKMKAQGVNLYVK 291
Query: 454 NLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYTKF 508
NL L+ LF G++ +V++ G++ G V F +A A +
Sbjct: 292 NLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRML 351
Query: 509 KEVPLYLEWA 518
PLY+ A
Sbjct: 352 GGKPLYVALA 361
Score = 61.4 bits (149), Expect = 1e-09
Identities = 86/415 (20%), Positives = 160/415 (38%), Gaps = 72/415 (17%)
Query: 19 DLDEVEFIYKITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDY 77
DLD +T+ +L F+ G V V++ + + + + ++ + A+ AL+
Sbjct: 7 DLDP-----DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 78 FNNTYVFSSRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTKDSKP 137
N + I++ WS+ P S + NI K + + D+K
Sbjct: 62 MNFKRLGGKPIRI-------------MWSQRDP-SLRRSGVGNIFVK---NLDKSVDNKA 104
Query: 138 GKKSKNDPTFSDFLQLHGKDVS-KLLPLSNKDGEEK-----EEENEDESNNQIAHADISD 191
TFS F G +S K+ ++++G+ + E E+ A A I
Sbjct: 105 LFD-----TFSKF----GNILSCKVA--TDENGKSRGYGFVHFEKEES-----AKAAIQK 148
Query: 192 MEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PL 250
+ + L K + + +++ + VKNL V + L+ F +
Sbjct: 149 VNGMLLNDKEVYVGRF---IKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEI 205
Query: 251 ASVRTTFL------GMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAK--YSG 302
S G A++ F+ ++ KA+ + +N K K Y G
Sbjct: 206 TSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE---------MNGKKIGLAKEGKKLYVG 256
Query: 303 AADDNNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGP 362
A E + QE ++ A+ ++V+NL TVT++ L +LF + G
Sbjct: 257 RAQKRAEREAELRRKFEELQQERKMK-----AQGVNLYVKNLDDTVTDEKLRELFSECGE 311
Query: 363 LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKE 417
+ + +D E ++GF V F PE A +A + G + G+ L++ + KE
Sbjct: 312 ITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE 365
Score = 60.2 bits (146), Expect = 2e-09
Identities = 43/167 (25%), Positives = 72/167 (43%), Gaps = 19/167 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
+LY+ +L+ + TE + FK GP+ SV V R + S+GYG+V F
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRR-----SLGYGYVNFQNPADAE 56
Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE 701
+AL+ + L I + S R+ R+S I V+N+
Sbjct: 57 RALETMNFKRLGGKPIRIMWSQRD------PSLRRSGV------GNIFVKNLDKSVDNKA 104
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ + F FG + ++ +G RG+GFV F + AK A++ +
Sbjct: 105 LFDTFSKFGNILSCKV--ATDENGKSRGYGFVHFEKEESAKAAIQKV 149
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 88.4 bits (220), Expect = 2e-21
Identities = 32/73 (43%), Positives = 43/73 (58%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV NL TE++L +LF K+G + V L DKET K+KGFA V F E A +A +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 398 LDGTVFLGRMLHL 410
L+G GR L +
Sbjct: 61 LNGKELDGRPLKV 73
Score = 74.2 bits (183), Expect = 2e-16
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ NL ++TE+ +R F K G + SV + R K+ S G+ FV+F + E
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGK-----SKGFAFVEFESEEDAE 55
Query: 642 QALKVLQNSSLDEHQIEL 659
+AL+ L LD +++
Sbjct: 56 KALEALNGKELDGRPLKV 73
Score = 71.9 bits (177), Expect = 1e-15
Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V N+P + E+ ELF FG+++ VRL + +G +GF FVEF ++ +A++A++
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKE-TGKSKGFAFVEFESEEDAEKALE 59
Query: 747 ALCQSTHLYGRRLVL 761
AL L GR L +
Sbjct: 60 AL-NGKELDGRPLKV 73
Score = 53.0 bits (128), Expect = 5e-09
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
T+E+L+ F + G V V+L E GK + FAF+ + E+ A+ AL+ N +
Sbjct: 9 PDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68
Query: 86 SRIKV 90
+KV
Sbjct: 69 RPLKV 73
Score = 44.9 bits (107), Expect = 3e-06
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
+ V NLP T +L+ LF FG + V + TG VEF + A+ A +L
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 504 AYTKFKEVPLYL 515
+ PL +
Sbjct: 62 NGKELDGRPLKV 73
Score = 43.7 bits (104), Expect = 9e-06
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR-------TTFLGMAYIGFKDEKNCNKALNK 277
T+ V NLP +++L+ F + SVR G A++ F+ E++ KAL
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 278 -NKSFWKGKQLNI 289
N G+ L +
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 84.2 bits (209), Expect = 6e-20
Identities = 30/63 (47%), Positives = 46/63 (73%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
+T+++L+ FE KG VTDV++ T +GK RRF F+G+ E+ AQ A+ YFN T++ +S+I
Sbjct: 12 VTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKI 71
Query: 89 KVE 91
VE
Sbjct: 72 SVE 74
Score = 44.5 bits (106), Expect = 5e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ + +KNL TED +R HF+ G + V V R +D KS +F GFV F + E
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSR-RF-----GFVGFKSEEDA 54
Query: 641 NQALKVLQNSSLDEHQIE 658
QA+K + +D +I
Sbjct: 55 QQAVKYFNKTFIDTSKIS 72
Score = 42.6 bits (101), Expect = 3e-05
Identities = 20/66 (30%), Positives = 40/66 (60%), Gaps = 2/66 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S+I+V+N+P + + E F++ GE+ V++ + G R FGFV F ++ +A++A+
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT--RDGKSRRFGFVGFKSEEDAQQAV 58
Query: 746 KALCQS 751
K ++
Sbjct: 59 KYFNKT 64
Score = 41.0 bits (97), Expect = 9e-05
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI V+NL VTED L + FE G + +V + + K++ F V F E A QA ++
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 398 LDGT 401
+ T
Sbjct: 61 FNKT 64
Score = 34.5 bits (80), Expect = 0.021
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 227 IVVKNLPAGVKKKDLKAYFKP---LPLASVRTTFLG----MAYIGFKDEKNCNKALNK-N 278
I+VKNLP V + L+ +F+ + V T G ++GFK E++ +A+ N
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62
Query: 279 KSF 281
K+F
Sbjct: 63 KTF 65
>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 = 83.0 bits (205), Expect = 2e-19
Identities = 37/83 (44%), Positives = 48/83 (57%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++KNLNF++T + FK V K DPK PGQ LSMG+GFV F T+E
Sbjct: 2 TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61
Query: 642 QALKVLQNSSLDEHQIELKRSNR 664
ALK + LD H + +K S+R
Sbjct: 62 AALKAMDGFVLDGHTLVVKFSHR 84
Score = 39.8 bits (93), Expect = 3e-04
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRL-----PKKMVGSGLHRGFGFVEFITKNE 740
+ + V+N+ F + + FK F R+ PK+ G L GFGFV F TK +
Sbjct: 1 ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRP-GQTLSMGFGFVGFKTKEQ 59
Query: 741 AKRAMKALCQSTHLYGRRLVLEWA 764
A+ A+KA+ L G LV++++
Sbjct: 60 AQAALKAM-DGFVLDGHTLVVKFS 82
Score = 30.2 bits (68), Expect = 0.76
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTK-------GFALVTFLMPEHA 391
+FV+NL+++ T LT F+ V + + D + GF V F E A
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGF--VFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQA 60
Query: 392 TQAYQHLDGTVFLGRMLHL 410
A + +DG V G L +
Sbjct: 61 QAALKAMDGFVLDGHTLVV 79
>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 = 78.8 bits (195), Expect = 5e-18
Identities = 34/67 (50%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 28 KITQEQLKAKFEEK-GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T+ +LK F + G +TDV+L T +GK RR AFIGY E++AQ A DYFNNTY+ +S
Sbjct: 11 SLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINTS 70
Query: 87 RIKVEKC 93
+I VE
Sbjct: 71 KISVEFA 77
Score = 41.9 bits (99), Expect = 5e-05
Identities = 17/69 (24%), Positives = 33/69 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V+NL ++TE +L + F K+G + + E K++ A + + E A +A +
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61
Query: 398 LDGTVFLGR 406
+ T
Sbjct: 62 FNNTYINTS 70
Score = 41.1 bits (97), Expect = 9e-05
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 227 IVVKNLPAGVKKKDLKAYF-KPLP-------LASVRTTFLGMAYIGFKDEKNCNKALN-K 277
++VKNLPA + + +LK +F K L + +A+IG+K E+ KA +
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62
Query: 278 NKSFWKGKQLNI 289
N ++ ++++
Sbjct: 63 NNTYINTSKISV 74
Score = 39.2 bits (92), Expect = 5e-04
Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 686 SKILVRNIPFQAKQSEVEELF-KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S+++V+N+P ++E++E F K GE+ V+L + G R F+ + T+ EA++A
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE--DGKSRRIAFIGYKTEEEAQKA 58
Query: 745 MKALCQSTHLYGRRLVLEWA 764
+T++ ++ +E+A
Sbjct: 59 KDYF-NNTYINTSKISVEFA 77
Score = 36.9 bits (86), Expect = 0.003
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+ L +KNL + TE ++ HF K G I V + R +D K S F+ + T E
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK------SRRIAFIGYKTEEE 54
Query: 640 LNQALKVLQNSSLDEHQIE 658
+A N+ ++ +I
Sbjct: 55 AQKAKDYFNNTYINTSKIS 73
>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 = 75.4 bits (186), Expect = 7e-17
Identities = 31/72 (43%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL TE+DL +LF K+G + V + DK K+KGFA V F PE A +A + L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 399 DGTVFLGRMLHL 410
+G GR L +
Sbjct: 60 NGKELDGRKLKV 71
Score = 68.1 bits (167), Expect = 2e-14
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL ++TE+ +R F K G I SV + R KD K S G+ FV+F + E +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK------SKGFAFVEFESPEDAEK 54
Query: 643 ALKVLQNSSLDEHQIELK 660
AL+ L LD ++++
Sbjct: 55 ALEALNGKELDGRKLKVS 72
Score = 65.0 bits (159), Expect = 3e-13
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+P + ++ ELF FGE++ VR+ + G +GF FVEF + +A++A++A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK--SKGFAFVEFESPEDAEKALEA 58
Query: 748 LCQSTHLYGRRLVLE 762
L L GR+L +
Sbjct: 59 L-NGKELDGRKLKVS 72
Score = 58.9 bits (143), Expect = 4e-11
Identities = 17/65 (26%), Positives = 33/65 (50%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
T+E L+ F + G + V++ +GK + FAF+ + + A+ AL+ N +
Sbjct: 8 PDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGR 67
Query: 87 RIKVE 91
++KV
Sbjct: 68 KLKVS 72
Score = 43.8 bits (104), Expect = 1e-05
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 504
+ V NLP T DL+ LF FG++ V + VEF A+ A +L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 505 YTKFKEVPLYLE 516
+ L +
Sbjct: 61 GKELDGRKLKVS 72
Score = 39.2 bits (92), Expect = 4e-04
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNK-N 278
+ V NLP ++DL+ F + SVR G A++ F+ ++ KAL N
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 279 KSFWKGKQLNI 289
G++L +
Sbjct: 61 GKELDGRKLKV 71
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 80.4 bits (197), Expect = 2e-16
Identities = 66/267 (24%), Positives = 112/267 (41%), Gaps = 5/267 (1%)
Query: 265 FKDEKNCNKALNKNKSFWKG---KQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWK 321
E N K +S K+L + ++N + D + E +
Sbjct: 42 NSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRS 101
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
S+ + + E+ +FV NL Y VTE+DL +LF+K+GP+ V L D+ET K++GFA
Sbjct: 102 SESPKSR-QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFA 160
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQV 441
V F E A +A + L+G GR L + +P + + S K + +
Sbjct: 161 FVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ-PRSELSNNLDASFAKKLSRGKA 219
Query: 442 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
+ + V NLP +T +L LF+ GD+ R +PP + + +A+ +
Sbjct: 220 LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKD 279
Query: 502 SLAYTKFKEVPLYLEWAPEGVFAEAKE 528
+L L P F++ +
Sbjct: 280 ALESNSRGNKKKILGRGPRKAFSQPRL 306
Score = 73.4 bits (179), Expect = 4e-14
Identities = 54/235 (22%), Positives = 98/235 (41%), Gaps = 21/235 (8%)
Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE-----REPEPDT 581
E S +K E +E E + E + + EE E + E +
Sbjct: 57 SEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENN 116
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ NL ++ TE+ +R FKK GP+ V + R ++ S G+ FV+F + ES
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGK-----SRGFAFVEFESEESAE 171
Query: 642 QALKVLQNSSLDEHQIELK--------RSNRNLESEATTVKRKSSNVAKQT--GSKILVR 691
+A++ L L+ + ++ RS + +A+ K+ S A + V
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231
Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
N+P + + E+ +LFK+ G++ LP + + FV +A +
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSK-DGKIPKSRSFVGNEASKDALESNS 285
Score = 53.4 bits (127), Expect = 2e-07
Identities = 39/156 (25%), Positives = 68/156 (43%), Gaps = 7/156 (4%)
Query: 614 RKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTV 673
K + + R+ N+ QN + E + ++
Sbjct: 49 EVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFR-----SSE 103
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 733
KS +K+ + + V N+P+ + ++ ELFK FG +K VRL + +G RGF FV
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRE-TGKSRGFAFV 162
Query: 734 EFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
EF ++ A++A++ L L GR L ++ A+ A
Sbjct: 163 EFESEESAEKAIEEL-NGKELEGRPLRVQKAQPASQ 197
Score = 51.1 bits (121), Expect = 1e-06
Identities = 44/230 (19%), Positives = 86/230 (37%), Gaps = 26/230 (11%)
Query: 165 SNKDGEEKEEENEDESNNQIAHADISDMEYLKLKTKSKDTAPSDPSVPPVSKAPVHKRQY 224
+K E E+ D + + + ++ S S K +
Sbjct: 62 PSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQK------SKEEN 115
Query: 225 HTIVVKNLPAGVKKKDLKAYFKP--------LPLASVRTTFLGMAYIGFKDEKNCNKALN 276
+T+ V NLP V ++DL+ FK L G A++ F+ E++ KA+
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175
Query: 277 K-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAE 335
+ N +G+ L + K + + + + + + + + + K A + +
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGK-----------ALLLEK 224
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
S ++V NL E++L LF+ G + LP K+ K + V
Sbjct: 225 SDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN 274
Score = 47.6 bits (112), Expect = 1e-05
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYT-TEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y +T+E L+ F++ G V V+L GK R FAF+ + E+ A+ A++ N +
Sbjct: 125 YDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG 184
Query: 86 SRIKVEKCSNLGDTTKPKS 104
++V+K S
Sbjct: 185 RPLRVQKAQPASQPRSELS 203
>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 = 73.8 bits (182), Expect = 3e-16
Identities = 29/72 (40%), Positives = 42/72 (58%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
++FV LS TE +L LF K+G + EV+L D ET +++GF VTF E A A +
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 397 HLDGTVFLGRML 408
L+G GR++
Sbjct: 62 DLNGKELEGRVI 73
Score = 54.5 bits (132), Expect = 2e-09
Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G+K+ V + + + E+E LF FG ++ V L K +G RGFGFV F + +A A
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPE-TGESRGFGFVTFESVEDADAA 59
Query: 745 MKALCQSTHLYGRRLVLEWA 764
++ L L GR + +E A
Sbjct: 60 IRDL-NGKELEGRVIKVEKA 78
Score = 44.9 bits (107), Expect = 5e-06
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 28 KITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ T+++L+A F + G V +V L K G+ R F F+ + + A AA+ N +
Sbjct: 12 RTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGR 71
Query: 87 RIKVEK 92
IKVEK
Sbjct: 72 VIKVEK 77
Score = 44.1 bits (105), Expect = 7e-06
Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
L++ L+ +TE + F K G + V + KDP++ G+ S G+GFV F + E
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLM--KDPET-GE--SRGFGFVTFESVEDA 56
Query: 641 NQALKVLQNSSLDEHQIELKRSNR 664
+ A++ L L+ I+++++ R
Sbjct: 57 DAAIRDLNGKELEGRVIKVEKAKR 80
>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 = 70.7 bits (174), Expect = 2e-15
Identities = 30/71 (42%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL TE+DL LF K+GP+ + + D ET ++KGFA V F E A +A + L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 399 DGTVFLGRMLH 409
+G GR L
Sbjct: 60 NGKELGGRELR 70
Score = 61.5 bits (150), Expect = 6e-12
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL ++TE+ ++ F K GPI S+ + R + + S G+ FV+F E +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR------SKGFAFVEFEDEEDAEK 54
Query: 643 ALKVLQNSSLDEHQIE 658
AL+ L L ++
Sbjct: 55 ALEALNGKELGGRELR 70
Score = 56.8 bits (138), Expect = 2e-10
Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+P + ++++LF FG ++ +R+ + +G +GF FVEF + +A++A++A
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD--ETGRSKGFAFVEFEDEEDAEKALEA 58
Query: 748 LCQSTHLYGRRL 759
L L GR L
Sbjct: 59 L-NGKELGGREL 69
Score = 54.9 bits (133), Expect = 1e-09
Identities = 15/61 (24%), Positives = 31/61 (50%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+E LK F + G + +++ G+ + FAF+ + E+ A+ AL+ N + +
Sbjct: 10 TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
Query: 89 K 89
+
Sbjct: 70 R 70
Score = 41.8 bits (99), Expect = 4e-05
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 504
+ V NLP T DLK LF FG + + + VEF + A+ A +L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 505 YTKFK 509
+
Sbjct: 61 GKELG 65
Score = 33.0 bits (76), Expect = 0.068
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNK-N 278
+ V NLP ++DLK F P+ S+R G A++ F+DE++ KAL N
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 279 KSFWKGKQL 287
G++L
Sbjct: 61 GKELGGREL 69
>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 = 70.7 bits (174), Expect = 3e-15
Identities = 29/78 (37%), Positives = 43/78 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRNL Y T++ L + F + GP+ + DK + K +GF VTF + E A +A +
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 399 DGTVFLGRMLHLIPGKPK 416
T F GR +H+ K K
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
Score = 57.6 bits (140), Expect = 2e-10
Identities = 29/81 (35%), Positives = 47/81 (58%), Gaps = 6/81 (7%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ VRN+P+ ++EE F G +K FV K GS RGFG+V F + +AKRA+
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDK---GSKKCRGFGYVTFALEEDAKRAL 58
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
+ + T GR++ +E+A++
Sbjct: 59 EEK-KKTKFGGRKIHVEFAKK 78
Score = 41.1 bits (97), Expect = 9e-05
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL+++NL +++T++ + F + GPI V + K K G+G+V F E
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKK-----CRGFGYVTFALEEDAK 55
Query: 642 QALKVLQNSSLDEHQIELK 660
+AL+ + + +I ++
Sbjct: 56 RALEEKKKTKFGGRKIHVE 74
Score = 34.1 bits (79), Expect = 0.027
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 27 YKITQEQLKAKFEEKG------TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
Y T EQL+ F E G V D K R F ++ + E+ A+ AL+
Sbjct: 9 YDTTDEQLEEFFSEVGPIKRCFVVKD-----KGSKKCRGFGYVTFALEEDAKRALEEKKK 63
Query: 81 TYVFSSRIKVE 91
T +I VE
Sbjct: 64 TKFGGRKIHVE 74
Score = 30.3 bits (69), Expect = 0.58
Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 13/75 (17%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL----------GMAYIGFKDEKNCNKAL 275
T+ V+NLP + L+ +F + ++ F+ G Y+ F E++ +AL
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFS--EVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRAL 58
Query: 276 NK-NKSFWKGKQLNI 289
+ K+ + G+++++
Sbjct: 59 EEKKKTKFGGRKIHV 73
Score = 27.6 bits (62), Expect = 5.4
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGR-VLVPPYGIT-----GLVEFLQKNQAKAAFNSL 503
+ V+NLPY T L+ F G + R +V G G V F + AK A
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 504 AYTKFKEVPLYLEWA 518
TKF +++E+A
Sbjct: 62 KKTKFGGRKIHVEFA 76
>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 = 77.7 bits (191), Expect = 3e-15
Identities = 54/175 (30%), Positives = 81/175 (46%), Gaps = 20/175 (11%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
E T L + L T++ IR F G I S + R K GQ S+GYGFV +
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK---VTGQ--SLGYGFVNYVRP 55
Query: 638 ESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQA 697
E +A+ L L I++ + R SS+ K G+ + V +P
Sbjct: 56 EDAEKAVNSLNGLRLQNKTIKV------------SYARPSSDSIK--GANLYVSGLPKTM 101
Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST 752
Q E+E +F FG++ R+ V +GL +G GF+ F ++EA RA+K L +T
Sbjct: 102 TQHELESIFSPFGQIITSRILSDNV-TGLSKGVGFIRFDKRDEADRAIKTLNGTT 155
Score = 44.2 bits (104), Expect = 2e-04
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NLS E L +LF +G + V + D T++ KG+ V+ + A A L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 399 DGTVFLGRMLHL 410
+G R+L +
Sbjct: 332 NGYTLGNRVLQV 343
Score = 38.4 bits (89), Expect = 0.010
Identities = 40/177 (22%), Positives = 73/177 (41%), Gaps = 35/177 (19%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L T+T++++ LF G + L DK T ++ G+ V ++ PE A +A L
Sbjct: 6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSL 65
Query: 399 DGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYR 458
+G + + + +P S + N + V LP
Sbjct: 66 NGLRLQNKTIKVSYARP---------------SSDSIKGAN----------LYVSGLPKT 100
Query: 459 TLPTDLKALFEPFGDL--GRVLVPPYGITGL------VEFLQKNQAKAAFNSLAYTK 507
+L+++F PFG + R+L +TGL + F ++++A A +L T
Sbjct: 101 MTQHELESIFSPFGQIITSRILSD--NVTGLSKGVGFIRFDKRDEADRAIKTLNGTT 155
Score = 36.5 bits (84), Expect = 0.051
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 327 VQFAEDIAESGR---IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
V +A ++S + ++V L T+T+ +L +F +G + + D T +KG +
Sbjct: 77 VSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFI 136
Query: 384 TFLMPEHATQAYQHLDGTV 402
F + A +A + L+GT
Sbjct: 137 RFDKRDEADRAIKTLNGTT 155
Score = 30.7 bits (69), Expect = 3.0
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
G I V N+ ++ + +LF FG ++ V++ + + + +G+GFV +EA
Sbjct: 268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL-TTNQCKGYGFVSMTNYDEAAM 326
Query: 744 AMKALCQSTHLYGRRL 759
A+ +L L R L
Sbjct: 327 AILSL-NGYTLGNRVL 341
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 70.3 bits (173), Expect = 4e-15
Identities = 31/70 (44%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++VRNL +VTE+DL + F YG + V L +K D+ +GFA V F PE A A + L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58
Query: 399 DGTVFLGRML 408
+G V GR L
Sbjct: 59 NGLVLDGRTL 68
Score = 59.1 bits (144), Expect = 3e-11
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY++NL + TE+ +R F G + V + R KD G+ FV+F + E
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPR-------GFAFVEFASPEDAEA 53
Query: 643 ALKVLQNSSLDEHQIE 658
ALK L LD +
Sbjct: 54 ALKKLNGLVLDGRTLR 69
Score = 56.8 bits (138), Expect = 2e-10
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ VRN+P + ++ E F +G+++ VRL + RGF FVEF + +A+ A+K
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN---KDRPRGFAFVEFASPEDAEAALKK 57
Query: 748 LCQSTHLYGRRL 759
L GR L
Sbjct: 58 -LNGLVLDGRTL 68
Score = 42.2 bits (100), Expect = 3e-05
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+T+E L+ F G V V+L + + R FAF+ + + A+AAL N +
Sbjct: 8 PSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGR 66
Query: 87 RIK 89
++
Sbjct: 67 TLR 69
Score = 39.8 bits (94), Expect = 2e-04
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 4/64 (6%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI----TGLVEFLQKNQAKAAFNSLAY 505
+ V+NLP DL+ F P+G + V + VEF A+AA L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 506 TKFK 509
Sbjct: 61 LVLD 64
Score = 35.2 bits (82), Expect = 0.008
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPL-PLASVR-----TTFLGMAYIGFKDEKNCNKALNKNKS 280
+ V+NLP V ++DL+ +F P + VR G A++ F ++ AL K
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 281 FW-KGKQLN 288
G+ L
Sbjct: 61 LVLDGRTLR 69
>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 = 69.3 bits (170), Expect = 1e-14
Identities = 30/70 (42%), Positives = 43/70 (61%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++VRN++ DDL +LF KYGP+ +V +P+D T + +GFA V F A A +L
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 399 DGTVFLGRML 408
D T FLGR +
Sbjct: 63 DRTRFLGREI 72
Score = 46.2 bits (110), Expect = 2e-06
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + VRN+ + ++ LF +G + V +P + RGF +V+F +A+ A+
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFY-TRRPRGFAYVQFEDVRDAEDAL 59
Query: 746 KALCQSTHLYGRRLVLEWAE 765
L T GR + +++A+
Sbjct: 60 YYL-DRTRFLGREIEIQFAQ 78
Score = 38.9 bits (91), Expect = 7e-04
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 11/82 (13%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA---RKKDPKSPGQFLSMGYGFVQFYTR 637
T+LY++N+ + D +RR F K GPI V + + P+ G+ +VQF
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPR--------GFAYVQFEDV 52
Query: 638 ESLNQALKVLQNSSLDEHQIEL 659
AL L + +IE+
Sbjct: 53 RDAEDALYYLDRTRFLGREIEI 74
Score = 31.6 bits (72), Expect = 0.27
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 32 EQLKAKFEEKGTVTDVQLK---YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
+ L+ F + G + DV + YT R FA++ + A+ AL Y + T I
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRP--RGFAYVQFEDVRDAEDALYYLDRTRFLGREI 72
Query: 89 KVE 91
+++
Sbjct: 73 EIQ 75
Score = 31.2 bits (71), Expect = 0.35
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 480
+ V+N+ T P DL+ LF +G + V +P
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIP 33
>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 = 68.8 bits (169), Expect = 2e-14
Identities = 28/71 (39%), Positives = 41/71 (57%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++V NL Y VTE+DL LF ++G + + D+ET +++GF V E A A +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 398 LDGTVFLGRML 408
L+GT F GR L
Sbjct: 61 LNGTDFGGRTL 71
Score = 57.2 bits (139), Expect = 2e-10
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+P+ + ++++LF FGE+ R+ + +G RGFGFVE T EA A+
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRE--TGRSRGFGFVEMETAEEANAAI 58
Query: 746 KALCQSTHLYGRRLVLEWAE 765
+ L T GR L + A
Sbjct: 59 EKL-NGTDFGGRTLTVNEAR 77
Score = 47.6 bits (114), Expect = 5e-07
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
LY+ NL +N TE+ ++ F + G + S V ++ S G+GFV+ T E N
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGR-----SRGFGFVEMETAEEAN 55
Query: 642 QALKVLQNSSLDEHQI 657
A++ L + +
Sbjct: 56 AAIEKLNGTDFGGRTL 71
Score = 46.1 bits (110), Expect = 2e-06
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y +T+E LK F + G VT ++ E G+ R F F+ ++A AA++ N T
Sbjct: 9 YNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGG 68
Query: 86 SRIKV 90
+ V
Sbjct: 69 RTLTV 73
Score = 31.8 bits (73), Expect = 0.17
Identities = 22/64 (34%), Positives = 26/64 (40%), Gaps = 14/64 (21%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT----------GLVEFLQKNQAKAA 499
+ V NLPY DLK LF FG++ V IT G VE +A AA
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARV----ITDRETGRSRGFGFVEMETAEEANAA 57
Query: 500 FNSL 503
L
Sbjct: 58 IEKL 61
>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 = 68.7 bits (168), Expect = 2e-14
Identities = 26/72 (36%), Positives = 44/72 (61%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G++F+ LS+ E L ++F KYG ++EV++ D+ET +++GF VTF P+ A A
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60
Query: 397 HLDGTVFLGRML 408
++G GR +
Sbjct: 61 AMNGKSVDGRQI 72
Score = 55.2 bits (133), Expect = 1e-09
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F++ E S+ + F K G I+ V V + ++ + S G+GFV F +
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR-----SRGFGFVTFENPDDAKD 57
Query: 643 ALKVLQNSSLDEHQI 657
A+ + S+D QI
Sbjct: 58 AMMAMNGKSVDGRQI 72
Score = 37.1 bits (86), Expect = 0.003
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + + F + +E++F +G++ V + K + RGFGFV F ++AK AM
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENPDDAKDAMM 60
Query: 747 AL 748
A+
Sbjct: 61 AM 62
>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 = 68.4 bits (168), Expect = 2e-14
Identities = 26/78 (33%), Positives = 51/78 (65%), Gaps = 3/78 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+++VRN+PF+ ++++++LF FG + V +P+K G +GF FV+F +K +A++A+K
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP--DGKKKGFAFVQFTSKADAEKAIK 58
Query: 747 ALCQSTHLYGRRLVLEWA 764
+ GR + ++WA
Sbjct: 59 G-VNGKKIKGRPVAVDWA 75
Score = 61.1 bits (149), Expect = 9e-12
Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ VRNL + TE DL KLF +G + EV +P K K KGFA V F A +A +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIP-RKPDGKKKGFAFVQFTSKADAEKAIKG 59
Query: 398 LDGTVFLGR 406
++G GR
Sbjct: 60 VNGKKIKGR 68
Score = 46.9 bits (112), Expect = 8e-07
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L ++NL F TE +++ F G + VT+ RK D K G+ FVQF ++ +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGK------KKGFAFVQFTSKADAEK 55
Query: 643 ALKVLQNSSLDEHQI 657
A+K + + +
Sbjct: 56 AIKGVNGKKIKGRPV 70
Score = 39.2 bits (92), Expect = 4e-04
Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNS 502
R+I V+NLP++ DLK LF PFG + V +P P G V+F K A+ A
Sbjct: 1 RLI-VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59
Query: 503 LAYTKFKEVPLYLEWA 518
+ K K P+ ++WA
Sbjct: 60 VNGKKIKGRPVAVDWA 75
Score = 33.4 bits (77), Expect = 0.054
Identities = 17/64 (26%), Positives = 30/64 (46%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+K T+ LK F G V +V + +GK + FAF+ + + A+ A+ N +
Sbjct: 9 FKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68
Query: 87 RIKV 90
+ V
Sbjct: 69 PVAV 72
Score = 28.8 bits (65), Expect = 2.5
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---------GMAYIGFKDEKNCNKALN 276
++V+NLP + DLK F P V + G A++ F + + KA+
Sbjct: 2 LIVRNLPFKCTEADLKKLF--SPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIK 58
>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 = 67.9 bits (167), Expect = 3e-14
Identities = 30/63 (47%), Positives = 40/63 (63%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
I V NLS EDDL +LF +GP++ V L DKET +++GFA VTF E A +A +
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 398 LDG 400
L+G
Sbjct: 61 LNG 63
Score = 48.7 bits (117), Expect = 2e-07
Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 12/83 (14%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I V N+ A + ++ ELF+ FG + V L K +G RGF FV F T+ +A+RA++
Sbjct: 2 IRVTNLSEDADEDDLRELFRPFGPISRVYLAKDK-ETGQSRGFAFVTFHTREDAERAIE- 59
Query: 748 LCQSTHLYGRR---LVL--EWAE 765
L G L+L EWA+
Sbjct: 60 -----KLNGFGYDNLILSVEWAK 77
Score = 45.6 bits (109), Expect = 2e-06
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+ + NL+ ++ ED +R F+ GPI+ V +A+ K+ S G+ FV F+TRE
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETG-----QSRGFAFVTFHTREDAE 55
Query: 642 QALKVLQNSSLD 653
+A++ L D
Sbjct: 56 RAIEKLNGFGYD 67
Score = 35.6 bits (83), Expect = 0.009
Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNS 502
I V NL DL+ LF PFG + RV + TG V F + A+ A
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 503 LAYTKFKEVPLYLEWA 518
L + + L +EWA
Sbjct: 61 LNGFGYDNLILSVEWA 76
Score = 35.2 bits (82), Expect = 0.011
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFN 79
++ L+ F G ++ V L K G+ R FAF+ +H + A+ A++ N
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 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 = 65.0 bits (159), Expect = 4e-13
Identities = 28/70 (40%), Positives = 43/70 (61%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL +++T +DL K+F KYG + +V + DKET K+KG A + FL E A + + L
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 399 DGTVFLGRML 408
+ GR L
Sbjct: 64 NNKELFGRTL 73
Score = 41.9 bits (99), Expect = 5e-05
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+T+Y+ NL F+ T + + + F K G + VT+ + K+ + S G F+ F RE
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRK-----SKGVAFILFLDRED 55
Query: 640 LNQALKVLQNSSL 652
++ +K L N L
Sbjct: 56 AHKCVKALNNKEL 68
Score = 36.9 bits (86), Expect = 0.003
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S + V N+PF +++ ++F +G++ V + K + +G F+ F+ + +A + +
Sbjct: 2 STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKE-TRKSKGVAFILFLDREDAHKCV 60
Query: 746 KALCQSTHLYGRRL 759
KAL L+GR L
Sbjct: 61 KALNN-KELFGRTL 73
Score = 27.7 bits (62), Expect = 5.4
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAF 500
K + V NLP+ DL +F +G + +V + T + FL + A
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60
Query: 501 NSL 503
+L
Sbjct: 61 KAL 63
>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 = 64.2 bits (157), Expect = 6e-13
Identities = 29/68 (42%), Positives = 40/68 (58%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V NL+Y T DDL ++FEKYG + +V +P D+ T +++GFA V F A A +DG
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 401 TVFLGRML 408
GR L
Sbjct: 63 KELDGREL 70
Score = 48.4 bits (116), Expect = 2e-07
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L + NL + +T D +RR F+K G + V + P+ S G+ FV+FY +
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYI-----PRDRYTRESRGFAFVRFYDKRDAED 55
Query: 643 ALKVLQNSSLD 653
A+ + LD
Sbjct: 56 AMDAMDGKELD 66
Score = 44.2 bits (105), Expect = 6e-06
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V N+ ++ ++ +F+ +GE+ V +P+ + RGF FV F K +A+ AM A+
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDR-YTRESRGFAFVRFYDKRDAEDAMDAM- 60
Query: 750 QSTHLYGRRL 759
L GR L
Sbjct: 61 DGKELDGREL 70
Score = 40.0 bits (94), Expect = 2e-04
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 503
V NL YRT P DL+ +FE +G++G V +P Y V F K A+ A +++
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Score = 36.5 bits (85), Expect = 0.003
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 5/53 (9%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALD 76
Y+ T + L+ FE+ G V DV + +YT E R FAF+ ++ + A+ A+D
Sbjct: 8 YRTTPDDLRRVFEKYGEVGDVYIPRDRYTRES--RGFAFVRFYDKRDAEDAMD 58
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 71.1 bits (174), Expect = 8e-13
Identities = 49/215 (22%), Positives = 90/215 (41%), Gaps = 34/215 (15%)
Query: 200 KSKDTAPSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYF-KPLPLASVRTTF- 257
+ D + P+++A +R T+ V L +++DL +F K + V+
Sbjct: 68 RRDDRRSGRNTKEPLTEA---ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKD 124
Query: 258 ------LGMAYIGFKDEKNCNKALNKNKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNAS 311
G+AY+ F D ++ KAL G+ + + S A+ N A
Sbjct: 125 RNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ----------SSQAEKNRAAK 174
Query: 312 MENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID 371
+ + +++V NL + +TE +L ++FE +G + +V L D
Sbjct: 175 AATHQPGDIPNFL-------------KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRD 221
Query: 372 KETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
ET ++KGF + F E A +A + ++G GR
Sbjct: 222 PETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGR 256
Score = 63.8 bits (155), Expect = 1e-10
Identities = 48/235 (20%), Positives = 105/235 (44%), Gaps = 22/235 (9%)
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER----EPEPDT 581
++ +S+ +++ + + + + + + N+ P + + D+ R EP T
Sbjct: 24 SRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLT 83
Query: 582 -------TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
T+++ L + E + F K G + V + ++ + S G +V+F
Sbjct: 84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRR-----SKGVAYVEF 138
Query: 635 YTRESLNQALKVLQNSSLDEH-QIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNI 693
Y ES+ +AL + L ++ ++ +N ++A T K+ V N+
Sbjct: 139 YDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAAT----HQPGDIPNFLKLYVGNL 194
Query: 694 PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
F + E+ ++F+ FG+++ V+L + G +GFGF++F EAK A++ +
Sbjct: 195 HFNITEQELRQIFEPFGDIEDVQLHRDPET-GRSKGFGFIQFHDAEEAKEALEVM 248
Score = 56.1 bits (135), Expect = 4e-08
Identities = 45/171 (26%), Positives = 74/171 (43%), Gaps = 20/171 (11%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV L+ E DL + F K G + +V D+ + ++KG A V F E +A L
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-L 150
Query: 399 DGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPYR 458
G + LGR + + + + E N K A +Q + + + V NL +
Sbjct: 151 TGQMLLGRPIIV---QSSQAEKNRAAKA----------ATHQPGDIPNFLKLYVGNLHFN 197
Query: 459 TLPTDLKALFEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 503
+L+ +FEPFGD+ V + P G ++F +AK A +
Sbjct: 198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248
Score = 39.5 bits (92), Expect = 0.007
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ IT+++L+ FE G + DVQL E G+ + F FI +H ++A+ AL+ N +
Sbjct: 196 FNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAG 255
Query: 86 SRIKV 90
IKV
Sbjct: 256 RPIKV 260
>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 = 62.4 bits (152), Expect = 2e-12
Identities = 29/72 (40%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NLS+ ED + + F +YG ++ V LP D ++ + KGF V F E A A L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 399 DGTVFLGRMLHL 410
GT LGR + L
Sbjct: 61 GGTDLLGRPVRL 72
Score = 52.0 bits (125), Expect = 1e-08
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL+F++ EDSI F + G I+SV + D P G+G+V+F ++E+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRP-----KGFGYVEFSSQEAAQA 55
Query: 643 ALKVLQNSSLDEHQIEL 659
AL L + L + L
Sbjct: 56 ALDALGGTDLLGRPVRL 72
Score = 52.0 bits (125), Expect = 1e-08
Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+ F A + + E F +GE+ VRLP SG +GFG+VEF ++ A+ A+ A
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDP-DSGRPKGFGYVEFSSQEAAQAALDA 59
Query: 748 LCQSTHLYGRRLVLE 762
L T L GR + L+
Sbjct: 60 L-GGTDLLGRPVRLD 73
Score = 30.0 bits (68), Expect = 0.72
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYV 83
+ ++ + F E G ++ V+L + G+ + F ++ + ++ AQAALD T +
Sbjct: 8 FDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDL 65
>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 = 62.6 bits (153), Expect = 3e-12
Identities = 23/71 (32%), Positives = 36/71 (50%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+F+RNL + TE++L +LF ++G + + DK T +KG A V F E A + +
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62
Query: 399 DGTVFLGRMLH 409
D G L
Sbjct: 63 DNAEDSGLSLD 73
Score = 55.3 bits (134), Expect = 1e-09
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T++I+NL F++TE+ ++ F + G + + + K S G FV+F T+ES
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTG-----HSKGTAFVKFKTKES-- 54
Query: 642 QALKVLQNSSLDEHQIELKRSNRNLE 667
A K L+ + E L R L
Sbjct: 55 -AQKCLEAADNAE-DSGLSLDGRRLI 78
Score = 54.5 bits (132), Expect = 2e-09
Identities = 24/60 (40%), Positives = 41/60 (68%), Gaps = 1/60 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ +RN+PF A + E++ELF FGE+K+ R+ K + +G +G FV+F TK A++ ++A
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKL-TGHSKGTAFVKFKTKESAQKCLEA 61
Score = 32.6 bits (75), Expect = 0.12
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL---VEFLQKNQAKAAFNSL- 503
R + ++NLP+ +LK LF FG++ + +TG F++ ++A L
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 504 AYTKFKEVPLYLE 516
A ++ L L+
Sbjct: 61 AADNAEDSGLSLD 73
>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 = 62.3 bits (152), Expect = 3e-12
Identities = 26/70 (37%), Positives = 39/70 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV N+ Y TE+ L ++F + GP+ L D++T K KG+ F E A A ++L
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 399 DGTVFLGRML 408
+G F GR L
Sbjct: 61 NGYEFNGRAL 70
Score = 43.4 bits (103), Expect = 1e-05
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V NIP+ A + ++ E+F G + RL +G +G+GF EF A A++
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRD-TGKPKGYGFCEFEDIETAASAIRN 59
Query: 748 LCQSTHLYGRRLVLEWA 764
L GR L +++A
Sbjct: 60 L-NGYEFNGRALRVDFA 75
Score = 42.2 bits (100), Expect = 4e-05
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQA 643
++ N+ +++TE+ + F + GP+ S + +D P GYGF +F E+ A
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKP-----KGYGFCEFEDIETAASA 56
Query: 644 LKVLQNSSL 652
++ L
Sbjct: 57 IRNLNGYEF 65
Score = 33.8 bits (78), Expect = 0.033
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T+EQL F E G V +L + GK + + F + + A +A+ N Y F+
Sbjct: 8 YDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG-YEFN 66
Query: 86 SR-IKVE 91
R ++V+
Sbjct: 67 GRALRVD 73
>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 = 61.9 bits (151), Expect = 4e-12
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IFV L Y T+D L K F ++G + E ++ D++T K++G+ VTF E A +A +
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61
Query: 398 LDGTVFLGRMLHL 410
+ + GR ++
Sbjct: 62 PN-PIIDGRKANV 73
Score = 47.6 bits (114), Expect = 5e-07
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+KI V +P+ + + F FGE++ V ++ +G RG+GFV F K A+R
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQ---TGKSRGYGFVTFKDKESAER 57
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
A K + + GR+ + A
Sbjct: 58 ACKDP--NPIIDGRKANVNLA 76
Score = 44.5 bits (106), Expect = 6e-06
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T +++ L +++T+DS+R++F + G I V D + G+ S GYGFV F +ES
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVV--ITD-RQTGK--SRGYGFVTFKDKESA 55
Query: 641 NQALK 645
+A K
Sbjct: 56 ERACK 60
Score = 33.4 bits (77), Expect = 0.055
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAF 500
I V LPY T L+ F FG++ +V TG V F K A+ A
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59
>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 = 61.5 bits (150), Expect = 5e-12
Identities = 26/70 (37%), Positives = 41/70 (58%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL + +TEDDL +FE +G + V L D ET ++KG+ + F E A +A + L
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 399 DGTVFLGRML 408
+G GR +
Sbjct: 61 NGFELAGRPI 70
Score = 53.0 bits (128), Expect = 5e-09
Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ NL+FN TED +R F+ G I V + + P S GYGF+QF E +
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQL-----QRDPETGRSKGYGFIQFADAEDAKK 55
Query: 643 ALKVL 647
AL+ L
Sbjct: 56 ALEQL 60
Score = 46.9 bits (112), Expect = 7e-07
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ IT++ L+ FE G + VQL+ E G+ + + FI + + A+ AL+ N +
Sbjct: 8 FNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAG 67
Query: 86 SRIKV 90
IKV
Sbjct: 68 RPIKV 72
Score = 44.2 bits (105), Expect = 7e-06
Identities = 19/59 (32%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
V N+ F + ++ +F+ FGE++FV+L + +G +G+GF++F +AK+A++ L
Sbjct: 3 VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDP-ETGRSKGYGFIQFADAEDAKKALEQL 60
Score = 28.4 bits (64), Expect = 2.8
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
V NL + DL+ +FEPFG++ V + TG ++F AK A L
Sbjct: 3 VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
>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 = 61.0 bits (149), Expect = 8e-12
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ NL+F +TE+ I F +CG I + + + K+P G+ FV++YTRE
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTP-----CGFCFVEYYTREDAEN 55
Query: 643 ALKVLQNSSLDEHQI 657
A+K L + LD+ I
Sbjct: 56 AVKYLNGTKLDDRII 70
Score = 51.4 bits (124), Expect = 2e-08
Identities = 22/70 (31%), Positives = 40/70 (57%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NLS+ TE+ + +LF + G + +I+ +D+ T GF V + E A A ++L
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 399 DGTVFLGRML 408
+GT R++
Sbjct: 61 NGTKLDDRII 70
Score = 41.0 bits (97), Expect = 1e-04
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 14/82 (17%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR------GFGFVEFITKNEA 741
+ V N+ F + ++ ELF G++K + + GL R GF FVE+ T+ +A
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIM-------GLDRFTKTPCGFCFVEYYTREDA 53
Query: 742 KRAMKALCQSTHLYGRRLVLEW 763
+ A+K L T L R + ++W
Sbjct: 54 ENAVKYL-NGTKLDDRIIRVDW 74
Score = 28.7 bits (65), Expect = 2.3
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 27 YKITQEQLKAKFEEKGTVTDV-----QLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
+ T+EQ+ F G + + + T G F F+ Y+ + A+ A+ Y N T
Sbjct: 8 FYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCG----FCFVEYYTREDAENAVKYLNGT 63
Query: 82 YVFSSRIKVEK 92
+ I+V+
Sbjct: 64 KLDDRIIRVDW 74
Score = 27.9 bits (63), Expect = 5.0
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 18/80 (22%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------------VEFLQKNQAK 497
+ V NL + T + LF GD+ R+ I GL VE+ + A+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRI------IMGLDRFTKTPCGFCFVEYYTREDAE 54
Query: 498 AAFNSLAYTKFKEVPLYLEW 517
A L TK + + ++W
Sbjct: 55 NAVKYLNGTKLDDRIIRVDW 74
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 60.9 bits (148), Expect = 9e-12
Identities = 26/73 (35%), Positives = 44/73 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV NLS++V ++ L FEK+G + + D+ET +++GF V F PE A +A +
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 398 LDGTVFLGRMLHL 410
+DG GR +++
Sbjct: 61 MDGKELDGRPINV 73
Score = 43.1 bits (102), Expect = 2e-05
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ + E LKA+FE+ GTV ++ E G+ R F ++ + + A+ A++ + +
Sbjct: 9 WSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDG 68
Query: 86 SRIKVEK 92
I V+
Sbjct: 69 RPINVDF 75
Score = 42.8 bits (101), Expect = 3e-05
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ NL+++ ++ ++ F+K G + V ++ S G+G+V F + E
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGR-----SRGFGYVDFESPEDAK 55
Query: 642 QALKVLQNSSLDEHQIELKRS 662
+A++ + LD I + S
Sbjct: 56 KAIEAMDGKELDGRPINVDFS 76
Score = 38.5 bits (90), Expect = 7e-04
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V N+ + ++ F+ FG + R+ +G RGFG+V+F + +AK+A++
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDR-ETGRSRGFGYVDFESPEDAKKAIE 59
Query: 747 ALCQSTHLYGRRLVLEWA 764
A+ L GR + ++++
Sbjct: 60 AM-DGKELDGRPINVDFS 76
>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 = 60.0 bits (146), Expect = 2e-11
Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTK---GFALVTFLMPEHATQAY 395
I+VRNL + + EDDL +F K+G + + +P ++ + + GFA VTF A A
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 396 QHLDGTVFLGRMLH 409
Q L+GT GR +
Sbjct: 63 Q-LNGTELGGRKIS 75
Score = 60.0 bits (146), Expect = 2e-11
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK--MVGSGLHRGFGFVEFITKNEAKRA 744
+I VRN+ F+ + ++ +F FGE++ +R+PKK L+ GF FV F + A+ A
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 745 MKALCQSTHLYGRRL 759
++ T L GR++
Sbjct: 62 LQL--NGTELGGRKI 74
Score = 52.6 bits (127), Expect = 9e-09
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 12/85 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y++NL+F ED +R F K G + S+ + +K+D K L+ G+ FV F S
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQ--GRLNNGFAFVTFKDASSAEN 60
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLE 667
AL+ L+ ++ R +
Sbjct: 61 ALQ------LNGTELG----GRKIS 75
Score = 37.2 bits (87), Expect = 0.002
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTY 82
+K+ ++ L+ F + G V +++ + +G+ FAF+ + A+ AL N T
Sbjct: 10 FKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ-LNGTE 68
Query: 83 VFSSRIKVEK 92
+ +I V
Sbjct: 69 LGGRKISVSL 78
Score = 33.4 bits (77), Expect = 0.049
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP 481
R I V+NL ++ DL+ +F FG++ + +P
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPK 34
Score = 28.0 bits (63), Expect = 3.8
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 11/78 (14%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKP--------LPLASVRTTFL---GMAYIGFKDEKNCNK 273
I V+NL + + DL+ F +P G A++ FKD +
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 274 ALNKNKSFWKGKQLNIYK 291
AL N + G+++++
Sbjct: 61 ALQLNGTELGGRKISVSL 78
>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 = 59.1 bits (143), Expect = 5e-11
Identities = 28/78 (35%), Positives = 45/78 (57%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRNL+++VT++DLT F P+ ++ D ET +++G+ VTF M E A +A L
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 399 DGTVFLGRMLHLIPGKPK 416
GR+L L + +
Sbjct: 62 KNKKLHGRILRLDIAERR 79
Score = 55.6 bits (134), Expect = 9e-10
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ VRN+ F Q ++ + F +K V + +G RG+GFV F +A+ A+
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPE---TGESRGYGFVTFAMLEDAQEAL 58
Query: 746 KALCQSTHLYGRRLVLEWAE 765
L ++ L+GR L L+ AE
Sbjct: 59 AKL-KNKKLHGRILRLDIAE 77
Score = 46.0 bits (109), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL+++NL F+ T++ + F PI V DP++ G+ S GYGFV F E
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVV--TDPET-GE--SRGYGFVTFAMLEDAQ 55
Query: 642 QALKVLQNSSLDEHQIEL 659
+AL L+N L + L
Sbjct: 56 EALAKLKNKKLHGRILRL 73
>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 = 58.8 bits (143), Expect = 5e-11
Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L+ V E L F +G + ++ +P+D ET K +GFA V F PE A A ++
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 399 DGTVFLGRMLH 409
+ + GR +
Sbjct: 61 NESELFGRTIR 71
Score = 52.6 bits (127), Expect = 8e-09
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V + + + + F FG++K +++P + HRGF FVEF +A A+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYE-TQKHRGFAFVEFEEPEDAAAAIDN 59
Query: 748 LCQSTHLYGRRL 759
+ +S L+GR +
Sbjct: 60 MNES-ELFGRTI 70
Score = 42.6 bits (101), Expect = 3e-05
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL--KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ ++ L A F G + D+Q+ Y T+ K R FAF+ + + A AA+D N + +F
Sbjct: 10 VDEKVLHAAFIPFGDIKDIQIPLDYETQ-KHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68
Query: 87 RIKV 90
I+V
Sbjct: 69 TIRV 72
Score = 31.8 bits (73), Expect = 0.15
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 5/70 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ L E + F G I + + P G+ FV+F E
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQI-----PLDYETQKHRGFAFVEFEEPEDAAA 55
Query: 643 ALKVLQNSSL 652
A+ + S L
Sbjct: 56 AIDNMNESEL 65
Score = 28.3 bits (64), Expect = 2.7
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 464 LKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 499
L A F PFGD+ + +P T VEF + A AA
Sbjct: 15 LHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56
>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 = 58.5 bits (142), Expect = 7e-11
Identities = 30/72 (41%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL VTE+ L +LF + GPL V +P D K K FA VTF A Q L
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQLL 62
Query: 399 DGTVFLGRMLHL 410
+G GR L +
Sbjct: 63 NGIRLFGRELRI 74
Score = 42.7 bits (101), Expect = 2e-05
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D TL++ NL+ TE+ + F + GP+ V + + + K + FV F S
Sbjct: 1 DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPK------SFAFVTFKHEVS 54
Query: 640 LNQALKVLQNSSLDEHQIELK 660
+ A+++L L ++ +K
Sbjct: 55 VPYAIQLLNGIRLFGRELRIK 75
Score = 42.7 bits (101), Expect = 3e-05
Identities = 15/64 (23%), Positives = 31/64 (48%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++T+E L F + G + V++ GK + FAF+ + E A+ N +F
Sbjct: 12 RVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRE 71
Query: 88 IKVE 91
++++
Sbjct: 72 LRIK 75
Score = 36.9 bits (86), Expect = 0.003
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
ELF G L+ V++PK +G + F FV F + A++ L L+GR L ++
Sbjct: 20 ELFLQAGPLEGVKIPKD--PNGKPKSFAFVTFKHEVSVPYAIQLL-NGIRLFGRELRIK 75
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 57.6 bits (140), Expect = 1e-10
Identities = 25/62 (40%), Positives = 39/62 (62%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L+ V +D L ++F YG + +V LPID+E + +G+A V F PE A +A +H+
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 399 DG 400
DG
Sbjct: 61 DG 62
Score = 44.5 bits (106), Expect = 6e-06
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 7/61 (11%)
Query: 689 LVRNIPFQAKQSEVEELFKAFGELKFVRLP-KKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
L RN+ + ++E+F +G +K V LP + V L RG+ +VEF + +A++A+K
Sbjct: 6 LTRNV----NKDHLKEIFSNYGTVKDVDLPIDREVN--LPRGYAYVEFESPEDAEKAIKH 59
Query: 748 L 748
+
Sbjct: 60 M 60
Score = 38.3 bits (90), Expect = 0.001
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L N +D ++ F G + V + ++ L GY +V+F + E +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREV-----NLPRGYAYVEFESPEDAEK 55
Query: 643 ALKVLQNSSLD 653
A+K + +D
Sbjct: 56 AIKHMDGGQID 66
Score = 32.5 bits (75), Expect = 0.10
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLK-YTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+ ++ LK F GTV DV L R +A++ + + A+ A+ + + +
Sbjct: 10 VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQE 69
Query: 88 IKVE 91
+ VE
Sbjct: 70 VTVE 73
>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 = 56.4 bits (137), Expect = 4e-10
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 6/79 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++++ NL F+ E+ +R+HF+ CG + +V + R D K+ + G+G+V F T++S+
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVR--DRKTG---IGKGFGYVLFKTKDSVA 55
Query: 642 QALKVLQNSSLDEHQIELK 660
ALK L L +I +K
Sbjct: 56 LALK-LNGIKLKGRKIRVK 73
Score = 44.1 bits (105), Expect = 7e-06
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL + + E++L K FE G + V + D++T KGF V F + A + L
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-L 60
Query: 399 DGTVFLGR 406
+G GR
Sbjct: 61 NGIKLKGR 68
Score = 42.1 bits (100), Expect = 3e-05
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 9/75 (12%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRL---PKKMVGSGLHRGFGFVEFITKNEAKRA 744
+ V N+PF ++ E+ + F+ G+++ VR+ K +G+ +GFG+V F TK+ A
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRK----TGIGKGFGYVLFKTKDSVALA 57
Query: 745 MKALCQSTHLYGRRL 759
+K L GR++
Sbjct: 58 LKL--NGIKLKGRKI 70
Score = 29.8 bits (68), Expect = 0.88
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAAL 75
+ I +E+L+ FE+ G V V++ + T GK F ++ + +D AL
Sbjct: 9 FDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGK--GFGYVLFKTKDSVALAL 58
>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 = 55.8 bits (135), Expect = 5e-10
Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+ + A+Q ++EE FK GE+ VR+ + G +GFG VEF T+ A++A++
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRS--KGFGHVEFATEEGAQKALEK 59
Query: 748 LCQSTHLYGRRLVLEWAEE 766
L GR + ++ A E
Sbjct: 60 --SGEELLGREIRVDLATE 76
Score = 55.8 bits (135), Expect = 6e-10
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ NL++++ +D + FK+CG + V +A+ D +S G+G V+F T E
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSK------GFGHVEFATEEGAQ 54
Query: 642 QALKVLQNSSLDEHQI 657
+AL+ L +I
Sbjct: 55 KALE-KSGEELLGREI 69
Score = 51.5 bits (124), Expect = 2e-08
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV NLS++ +DDL + F++ G + +V + D + ++KGF V F E A +A +
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALE- 58
Query: 398 LDGTVFLGR 406
G LGR
Sbjct: 59 KSGEELLGR 67
Score = 42.7 bits (101), Expect = 3e-05
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ Q+ L+ F+E G V DV++ +G+ + F + + E+ AQ AL+ + +
Sbjct: 9 WSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KSGEELLGR 67
Query: 87 RIKVE 91
I+V+
Sbjct: 68 EIRVD 72
Score = 35.0 bits (81), Expect = 0.012
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT------FLGMAYIGFKDEKNCNKALNKN 278
T+ V NL ++ DL+ +FK + VR G ++ F E+ KAL K+
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60
Query: 279 KSFWKGKQLNI 289
G+++ +
Sbjct: 61 GEELLGREIRV 71
>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 = 56.1 bits (136), Expect = 6e-10
Identities = 26/68 (38%), Positives = 38/68 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV L+Y TE L + FE+YGP+ + L DK+T K +G+A + F AY++
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 399 DGTVFLGR 406
DG GR
Sbjct: 64 DGKKIDGR 71
Score = 48.4 bits (116), Expect = 4e-07
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ LN+++TE +RR F++ GPI + + R K P GY F++F +
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKP-----RGYAFIEFEHERDMK 57
Query: 642 QALK 645
A K
Sbjct: 58 AAYK 61
Score = 38.4 bits (90), Expect = 0.001
Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 11/94 (11%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V + + +S++ F+ +G +K +RL + +G RG+ F+EF + + K A K
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKK-TGKPRGYAFIEFEHERDMKAAYKY 62
Query: 748 LCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYF 781
+ GRR++++ VE R RT + +
Sbjct: 63 -ADGKKIDGRRVLVD-------VE--RGRTVKGW 86
Score = 36.8 bits (86), Expect = 0.004
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T+ +L+ +FEE G + ++L GK R +AFI + E +AA Y + +
Sbjct: 11 YDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDG 70
Query: 86 SRIKVE 91
R+ V+
Sbjct: 71 RRVLVD 76
>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 = 56.5 bits (136), Expect = 9e-10
Identities = 27/92 (29%), Positives = 38/92 (41%), Gaps = 4/92 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL----MPEHATQA 394
+FVRNL Y TE+ L F K+G + + IDK T + KG V F A
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGKV 426
++ G L G E ++G+V
Sbjct: 64 PAAGSTSLLSGSSLTADIGDDVMPEYVLEGRV 95
Score = 47.6 bits (113), Expect = 1e-06
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPI--ASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
D TL+++NL +++TE+S+ HF K G + A + + + G GFV F +
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTG-------RAKGTGFVCFKDQ 53
Query: 638 ESLNQALK 645
+ N LK
Sbjct: 54 YTYNACLK 61
Score = 43.4 bits (102), Expect = 3e-05
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
+ VRN+P+ A + + F FG +++ P +G +G GFV F +
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYAL-PVIDKSTGRAKGTGFVCFKDQYTYNAC 59
Query: 745 MK 746
+K
Sbjct: 60 LK 61
Score = 31.8 bits (72), Expect = 0.32
Identities = 16/57 (28%), Positives = 20/57 (35%), Gaps = 8/57 (14%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAA 499
+ V+NLPY L F FG + L G TG V F + A
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKG-TGFVCFKDQYTYNAC 59
>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 = 54.5 bits (131), Expect = 2e-09
Identities = 26/68 (38%), Positives = 37/68 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL +TED+L K+FE YG + + L DK T +G A V + E A A L
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 399 DGTVFLGR 406
+GT+ G
Sbjct: 63 NGTIPPGS 70
Score = 37.2 bits (86), Expect = 0.002
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V N+P Q + E+ ++F+A+G + L + +GL RG FV + + EA+ A+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKS-TGLPRGVAFVRYDKREEAQAAI 59
Query: 746 KAL 748
+L
Sbjct: 60 SSL 62
Score = 34.5 bits (79), Expect = 0.025
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T LY+ NL TED +R+ F+ G I + R K P G FV++ RE
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLP-----RGVAFVRYDKREEA 55
Query: 641 NQALKVLQNS 650
A+ L +
Sbjct: 56 QAAISSLNGT 65
Score = 33.3 bits (76), Expect = 0.065
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
+T+++L+ FE G + L+ + G R AF+ Y + ++AQAA+ N T
Sbjct: 12 LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTI 66
>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 = 54.1 bits (131), Expect = 2e-09
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V+NL + ++ L +LF KYG + + D + K+KGF V F E A +A + L
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62
Query: 399 DGTVFLGRML 408
+G G+ L
Sbjct: 63 NGKEVNGKKL 72
Score = 47.2 bits (113), Expect = 8e-07
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T +Y+KNL + ++ ++ F K G I S V + + K S G+GFV F E+
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK------SKGFGFVNFENHEAA 55
Query: 641 NQALKVLQNSSLDEHQI 657
+A++ L ++ ++
Sbjct: 56 QKAVEELNGKEVNGKKL 72
Score = 39.1 bits (92), Expect = 6e-04
Identities = 15/52 (28%), Positives = 27/52 (51%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
+ E+LK F + G +T ++ EGK + F F+ + + AQ A++ N
Sbjct: 13 MDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNG 64
Score = 36.0 bits (84), Expect = 0.007
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
V+N+ +++ELF +G++ ++ K G +GFGFV F A++A++ L
Sbjct: 6 VKNLGEDMDDEKLKELFGKYGKITSAKVMKD--DEGKSKGFGFVNFENHEAAQKAVEEL 62
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 54.2 bits (131), Expect = 2e-09
Identities = 23/60 (38%), Positives = 37/60 (61%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F +YGP+ +V + D++T +++GF V F E A +A + L+G
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63
Score = 38.0 bits (89), Expect = 0.001
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 6/61 (9%)
Query: 701 EVEELFKAFGELKFVRL--PKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
++ E+F +G ++ V++ +K +G RGFGFV F + +AK A + + GRR
Sbjct: 15 DLREVFSRYGPIEKVQVVYDQK---TGRSRGFGFVYFESVEDAKEAKER-LNGMEIDGRR 70
Query: 759 L 759
+
Sbjct: 71 I 71
Score = 33.4 bits (77), Expect = 0.050
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
T+ L+ F G + VQ+ + T G+ R F F+ + + A+ A + N +
Sbjct: 11 TTERDLREVFSRYGPIEKVQVVYDQKT--GRSRGFGFVYFESVEDAKEAKERLNGMEIDG 68
Query: 86 SRIKVE 91
RI+V+
Sbjct: 69 RRIRVD 74
Score = 33.0 bits (76), Expect = 0.075
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 587 NLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKV 646
L+ +TE +R F + GPI V V D K+ S G+GFV F + E +A +
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVV--YDQKTG---RSRGFGFVYFESVEDAKEAKER 60
Query: 647 LQNSSLDEHQI 657
L +D +I
Sbjct: 61 LNGMEIDGRRI 71
>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 = 53.8 bits (130), Expect = 3e-09
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 338 RI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
RI +VRNL + ++ ++L LF KYG + ++ + KE T+G A V + A A
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE---TRGTAFVVYEDIYDAKNACD 59
Query: 397 HLDGTVFLGRML 408
HL G R L
Sbjct: 60 HLSGFNVANRYL 71
Score = 31.8 bits (73), Expect = 0.15
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH---RGFGFVEFITKNEA 741
++IL VRN+PF+ E+ +LF +G ++ +R+ G RG FV + +A
Sbjct: 2 NRILYVRNLPFKISSEELYDLFGKYGAIRQIRI-------GNTKETRGTAFVVYEDIYDA 54
Query: 742 KRAMKAL 748
K A L
Sbjct: 55 KNACDHL 61
Score = 30.7 bits (70), Expect = 0.45
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFG 472
RI+ V+NLP++ +L LF +G
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYG 27
Score = 29.9 bits (68), Expect = 0.94
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 619
LY++NL F + + + F K G I + + K+ +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR 41
>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 = 53.4 bits (129), Expect = 3e-09
Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV NL +TE++ +LF KYG ++EV L K KGF + +A +A
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLDTRTNAEKAKAE 56
Query: 398 LDGTVFLGRML 408
LDG + GR L
Sbjct: 57 LDGIMRKGRQL 67
Score = 38.8 bits (91), Expect = 4e-04
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ V N+P + E +ELF +GE+ V L K+ +GFGF+ T+ A++A
Sbjct: 2 CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-------KGFGFIRLDTRTNAEKAK 54
Query: 746 KAL 748
L
Sbjct: 55 AEL 57
Score = 32.6 bits (75), Expect = 0.082
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL + TE+ + F K G ++ V + ++K G+GF++ TR + +
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK-----------GFGFIRLDTRTNAEK 52
Query: 643 ALKVLQNSSLDEHQIELK 660
A L Q+ ++
Sbjct: 53 AKAELDGIMRKGRQLRVR 70
Score = 29.2 bits (66), Expect = 1.2
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFN 501
V NLP + K LF +G++ V + +G L +AKA +
Sbjct: 6 VGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELD 58
>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 = 53.4 bits (129), Expect = 3e-09
Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+++ NL+++ ED +R+ F KCG I V + + K S GY +V+F ES+
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK------SKGYAYVEFENEESVQ 54
Query: 642 QALK 645
+ALK
Sbjct: 55 EALK 58
Score = 47.6 bits (114), Expect = 4e-07
Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 2/68 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL Y+V ED+L KLF K G + +V L + + K+KG+A V F E +A + L
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKG-KSKGYAYVEFENEESVQEALK-L 59
Query: 399 DGTVFLGR 406
D + GR
Sbjct: 60 DRELIKGR 67
Score = 45.3 bits (108), Expect = 2e-06
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V N+ + + E+ +LF GE+ VRL K G +G+ +VEF + + A+K
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK--SKGYAYVEFENEESVQEALK 58
Score = 41.1 bits (97), Expect = 9e-05
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
Y + +++L+ F + G +TDV+L +GK + +A++ + E+ Q AL
Sbjct: 9 YSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL 57
Score = 28.0 bits (63), Expect = 4.1
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNK 277
T+ V NL V + +L+ F + VR G AY+ F++E++ +AL
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59
>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 = 53.4 bits (129), Expect = 4e-09
Identities = 23/48 (47%), Positives = 31/48 (64%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++FV L VTE+DL + F +YG + V + DKET K +GFA VTF
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48
Score = 30.7 bits (70), Expect = 0.46
Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L + TE+ +R +F + G + SV + K+ G+ FV F + +++
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKK-----RGFAFVTFDDYDPVDK 56
Query: 643 ALKVLQNSSLDEHQIELK 660
+ + + +++ H++E+K
Sbjct: 57 IV-LQKYHTINGHRVEVK 73
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 53.8 bits (130), Expect = 5e-09
Identities = 20/71 (28%), Positives = 37/71 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV + E+D+ F ++G + + L +D+ T KG+AL+ + + A A + L
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 399 DGTVFLGRMLH 409
+G LG+ +
Sbjct: 69 NGKELLGQTIS 79
Score = 38.7 bits (91), Expect = 8e-04
Identities = 23/79 (29%), Positives = 45/79 (56%), Gaps = 6/79 (7%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
I V + +A++ +V + F FGE+K + L ++ +G +G+ +E+ TK EA+ A+
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRR---TGFVKGYALIEYETKKEAQAAI 65
Query: 746 KALCQSTHLYGRRLVLEWA 764
+ L L G+ + ++WA
Sbjct: 66 EGL-NGKELLGQTISVDWA 83
Score = 31.4 bits (72), Expect = 0.28
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR------FAFIGYHREDQAQAALDYFNNTY 82
+E + KF E G + ++ L RR +A I Y + +AQAA++ N
Sbjct: 18 AQEEDVHDKFAEFGEIKNLHLNLD-----RRTGFVKGYALIEYETKKEAQAAIEGLNGKE 72
Query: 83 VFSSRIKV 90
+ I V
Sbjct: 73 LLGQTISV 80
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 52.8 bits (127), Expect = 6e-09
Identities = 21/48 (43%), Positives = 32/48 (66%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV LS TEDD+ K F ++G + + +L DK+T++ +GF VTF
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48
Score = 29.7 bits (67), Expect = 0.83
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQA 71
T++ +K F + G V D L + + R F F+ + ED
Sbjct: 12 TEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54
Score = 27.0 bits (60), Expect = 7.7
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRA 744
KI V + + +V++ F FG+++ L M + HRGFGFV F +++ +
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAML---MFDKQTNRHRGFGFVTFESEDVVDKV 57
>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 = 52.8 bits (127), Expect = 7e-09
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
R++V ++S+ + ED + + F +GP+ + + D T K KGFA V + +PE A A +
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60
Query: 397 HLDGTVFLGRML 408
++G + GR +
Sbjct: 61 QMNGVMLGGRNI 72
Score = 37.8 bits (88), Expect = 0.001
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ V +I F+ + + + F FG +K + + V + H+GF FVE+ A+ A+
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPV-TMKHKGFAFVEYEVPEAAQLAL 59
Query: 746 KALCQSTHLYGRRL 759
+ + L GR +
Sbjct: 60 EQM-NGVMLGGRNI 72
Score = 31.6 bits (72), Expect = 0.18
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ +++F ED+IR+ F GPI S+ ++ P G+ FV++ E+
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSIDMSW-----DPVTMKHKGFAFVEYEVPEAAQL 57
Query: 643 ALKVLQNSSLDEHQIELKR 661
AL+ + L I++ R
Sbjct: 58 ALEQMNGVMLGGRNIKVGR 76
Score = 30.5 bits (69), Expect = 0.52
Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+++ ++ ++ F G + + + + K + FAF+ Y + AQ AL+ N +
Sbjct: 10 FELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGG 69
Query: 86 SRIKV 90
IKV
Sbjct: 70 RNIKV 74
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 53.0 bits (128), Expect = 8e-09
Identities = 25/78 (32%), Positives = 43/78 (55%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
+ +S I++ L Y +TE D+ +F +YG + ++ L DK+T K+KGFA + +
Sbjct: 4 DQYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63
Query: 391 ATQAYQHLDGTVFLGRML 408
A +L+G LGR +
Sbjct: 64 TILAVDNLNGIKLLGRTI 81
>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 = 52.3 bits (126), Expect = 8e-09
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 584 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQA 643
++ N+++ +T + ++ HFK CG I +T+ K P G+ +++F + S+ A
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQP-----KGFAYIEFLDKSSVENA 57
Query: 644 LKVLQNSSLDEHQI 657
L +L S QI
Sbjct: 58 L-LLNESEFRGRQI 70
Score = 51.1 bits (123), Expect = 2e-08
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV N+ Y T ++L + F+ G + + + DK T + KGFA + FL A L
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60
Query: 399 DGTVFLGRML 408
+ + F GR +
Sbjct: 61 NESEFRGRQI 70
Score = 32.3 bits (74), Expect = 0.13
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---------GMAYIGFKDEKNCNKALNK 277
I V N+ G ++L+ +FK R T L G AYI F D+ + AL
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTI-NRITILCDKFTGQPKGFAYIEFLDKSSVENALLL 60
Query: 278 NKSFWKGKQLNI 289
N+S ++G+Q+ +
Sbjct: 61 NESEFRGRQIKV 72
Score = 30.7 bits (70), Expect = 0.40
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAM 745
I V N+ + E++E FK+ G + + + K G +GF ++EF+ K+ + A+
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQP--KGFAYIEFLDKSSVENAL 58
Score = 28.4 bits (64), Expect = 2.3
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYT-TEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T E+L+ F+ GT+ + + G+ + FA+I + + + AL N +
Sbjct: 9 YGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESEFRG 67
Query: 86 SRIKV 90
+IKV
Sbjct: 68 RQIKV 72
>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 = 52.2 bits (126), Expect = 9e-09
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V NL Y VTE+DL +LF + G + +V + D+ + +++G A V F E A +A +
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60
Query: 398 LDGTVFLGRMLHL 410
+G + G+ + +
Sbjct: 61 FNGVLLDGQPMQV 73
Score = 38.3 bits (90), Expect = 0.001
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y +T+E L+ F G V V++ Y G+ A + + + + A+ A+ FN +
Sbjct: 10 YDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQ 69
Query: 87 RIKVEK 92
++VE
Sbjct: 70 PMQVEL 75
Score = 37.6 bits (88), Expect = 0.002
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+++ V N+ + + ++EELF GE+K V++ SG G V F + +A+RA+
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKI--NYDRSGRSEGTADVVFEKREDAERAI 58
Query: 746 KAL 748
K
Sbjct: 59 KQF 61
Score = 31.0 bits (71), Expect = 0.34
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + NL+++ TE+ + F + G + V + + + S G V F RE
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGR------SEGTADVVFEKREDA 54
Query: 641 NQALKVLQNSSLD 653
+A+K LD
Sbjct: 55 ERAIKQFNGVLLD 67
Score = 29.1 bits (66), Expect = 1.5
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 499
+ V NL Y DL+ LF G++ +V + Y +G V F ++ A+ A
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKI-NYDRSGRSEGTADVVFEKREDAERA 57
>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 = 57.8 bits (139), Expect = 1e-08
Identities = 41/153 (26%), Positives = 79/153 (51%), Gaps = 14/153 (9%)
Query: 322 SQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFA 381
+Q+ Q + +A R++V ++S+ + ED + + F+ +GP+ + + D T K KGFA
Sbjct: 93 NQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFA 152
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQV 441
V + +PE A A + ++G + GR + + G+P N ++ +D +
Sbjct: 153 FVEYEVPEAAQLALEQMNGQMLGGRNIKV--GRP-SNMPQ---------AQPIIDMVQE- 199
Query: 442 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 474
EA+ I V ++ TD+K++FE FG++
Sbjct: 200 -EAKKFNRIYVASVHPDLSETDIKSVFEAFGEI 231
Score = 51.6 bits (123), Expect = 1e-06
Identities = 40/168 (23%), Positives = 81/168 (48%), Gaps = 13/168 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ +++F ED+IRR F GPI S+ ++ DP + G+ FV++ E+
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSW--DPATGKH---KGFAFVEYEVPEAAQL 164
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGS--KILVRNIPFQAKQS 700
AL+ + L I++ S + V ++ +I V ++ ++
Sbjct: 165 ALEQMNGQMLGGRNIKV-----GRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSET 219
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F+AFGE+ +L + G G H+G+GF+E+ A+ ++
Sbjct: 220 DIKSVFEAFGEIVKCQLARAPTGRG-HKGYGFIEYNNLQSQSEAIASM 266
Score = 35.4 bits (81), Expect = 0.13
Identities = 12/58 (20%), Positives = 27/58 (46%)
Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
E+ + RI+V ++ ++E D+ +FE +G + + L KG+ + +
Sbjct: 196 MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEY 253
Score = 32.7 bits (74), Expect = 0.87
Identities = 21/108 (19%), Positives = 47/108 (43%), Gaps = 3/108 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+++ ++ ++ F+ G + + + + GK + FAF+ Y + AQ AL+ N +
Sbjct: 117 FELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG 176
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTK 133
IKV + SN+ ++ + +++ + DL K
Sbjct: 177 RNIKVGRPSNMPQAQ--PIIDMVQEEAKKFNRIYVASVHPDLSETDIK 222
Score = 32.0 bits (72), Expect = 1.5
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ V +I F+ ++ + F FG +K + + +G H+GF FVE+ A+ A+
Sbjct: 108 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPA-TGKHKGFAFVEYEVPEAAQLAL 166
Query: 746 KALCQSTHLYGRRL 759
+ + L GR +
Sbjct: 167 EQM-NGQMLGGRNI 179
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 51.9 bits (124), Expect = 2e-08
Identities = 26/70 (37%), Positives = 41/70 (58%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F +YGPLA V + D+ T +++GFA V F + + +A +H +G
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63
Query: 401 TVFLGRMLHL 410
GR + +
Sbjct: 64 MELDGRRIRV 73
Score = 31.9 bits (72), Expect = 0.19
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+ L+ F G + V + Y G+ R FAF+ + R D ++ A+++ N + RI
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71
Query: 89 KVE 91
+V+
Sbjct: 72 RVD 74
Score = 29.9 bits (67), Expect = 0.78
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
L+ +TE +R F + GP+A V V + S G+ FV F + +A++
Sbjct: 7 LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGR-----SRGFAFVYFERIDDSKEAMEHA 61
Query: 648 QNSSLDEHQIELKRS 662
LD +I + S
Sbjct: 62 NGMELDGRRIRVDYS 76
Score = 28.8 bits (64), Expect = 2.1
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
+ ++ E+F +G L V + +G RGF FV F +++K AM+ L GRR
Sbjct: 13 ERDLREVFSRYGPLAGVNVVYDQ-RTGRSRGFAFVYFERIDDSKEAMEH-ANGMELDGRR 70
Query: 759 LVLEWA 764
+ ++++
Sbjct: 71 IRVDYS 76
>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 = 51.7 bits (124), Expect = 2e-08
Identities = 17/57 (29%), Positives = 33/57 (57%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++FV L+ ++ L + F +YG L E ++ +D T +++GF +TF + A +A
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60
Score = 47.5 bits (113), Expect = 5e-07
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ LN +++ +RRHF + G + V + K S G+GF+ F + + ++
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTK-----RSRGFGFITFSSADEADE 59
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A++ Q S+D +QIELKR+
Sbjct: 60 AMEA-QPHSIDGNQIELKRA 78
Score = 35.2 bits (81), Expect = 0.011
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
K+ V + + S + F +G+L V + S RGFGF+ F + +EA
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRS---RGFGFITFSSADEAD 58
Query: 743 RAMKA 747
AM+A
Sbjct: 59 EAMEA 63
Score = 29.0 bits (65), Expect = 1.7
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAAL 75
K + L+ F G +T+ + K R F FI + D+A A+
Sbjct: 13 KTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
>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 = 51.6 bits (124), Expect = 2e-08
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP------IDKETDKTKGFALVTFLMPEHA 391
R+++ NLSY+ +E+DL + + + P+ V++P + G A F PE A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 392 TQAYQHLDGTVFLGRMLHL 410
+ + L+G VF R L +
Sbjct: 60 EKVVKDLNGKVFKNRKLFV 78
Score = 35.8 bits (83), Expect = 0.008
Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 10/84 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGP----IASVTVAR-KKDPKSPGQFLSMGYGFVQFYT 636
+YI NL+++S+E+ + K P I S TV + P +G + +F +
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRP-----LGIAYAEFSS 55
Query: 637 RESLNQALKVLQNSSLDEHQIELK 660
E + +K L ++ +K
Sbjct: 56 PEQAEKVVKDLNGKVFKNRKLFVK 79
Score = 33.9 bits (78), Expect = 0.040
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV---GSGLHRGFG--FVEFITKNEA 741
++ + N+ + + + ++EE K F + V +P + V S R G + EF + +A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVS-VLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 742 KRAMKAL 748
++ +K L
Sbjct: 60 EKVVKDL 66
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 51.5 bits (124), Expect = 2e-08
Identities = 22/63 (34%), Positives = 35/63 (55%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RIFV +L VT++ L + F KY + + DK T K+KG+ V+F P +A +
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67
Query: 398 LDG 400
++G
Sbjct: 68 MNG 70
Score = 33.0 bits (76), Expect = 0.083
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 5/86 (5%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
PE D +++ +L T++ + R F K V R K S GYGFV F
Sbjct: 3 PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGK-----SKGYGFVSFSD 57
Query: 637 RESLNQALKVLQNSSLDEHQIELKRS 662
+A+K + + I+L++S
Sbjct: 58 PNDYLKAMKEMNGKYVGNRPIKLRKS 83
>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 = 51.5 bits (124), Expect = 2e-08
Identities = 19/71 (26%), Positives = 31/71 (43%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V NL T++ +L +G + L + T ++KG+ V + A +A L
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 399 DGTVFLGRMLH 409
DG GR L
Sbjct: 62 DGKQIGGRKLQ 72
Score = 41.5 bits (98), Expect = 7e-05
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK---FVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
+ V N+P + + EL FG ++ V +G +G+GFVE+ +K A +A
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSES----TGESKGYGFVEYASKASALKA 57
Query: 745 MKALCQSTHLYGRRLVLEWAE 765
L + GR+L ++WA+
Sbjct: 58 KNQL-DGKQIGGRKLQVDWAD 77
Score = 39.2 bits (92), Expect = 5e-04
Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 5/76 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L + NL T++ R G + + S S GYGFV++ ++ S
Sbjct: 1 LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVY-----SESTGESKGYGFVEYASKASAL 55
Query: 642 QALKVLQNSSLDEHQI 657
+A L + ++
Sbjct: 56 KAKNQLDGKQIGGRKL 71
Score = 30.3 bits (69), Expect = 0.70
Identities = 21/76 (27%), Positives = 29/76 (38%), Gaps = 6/76 (7%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 503
+ V NLP + L PFG + R + TG VE+ K A A N L
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 504 AYTKFKEVPLYLEWAP 519
+ L ++WA
Sbjct: 62 DGKQIGGRKLQVDWAD 77
>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 = 51.2 bits (123), Expect = 2e-08
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L++ +T+DS++ +F + G I V + DP + S G+GFV F + ++
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMK--DPNTKR---SRGFGFVTFASASEVDA 56
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A+ + +D ++E KR+
Sbjct: 57 AMNA-RPHKVDGREVEPKRA 75
Score = 45.8 bits (109), Expect = 2e-06
Identities = 16/48 (33%), Positives = 29/48 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++F+ LSY T+D L F ++G + + ++ D T +++GF VTF
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTF 48
Score = 32.0 bits (73), Expect = 0.17
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
Y+ T + LK F + G +TD V +K + R F F+ + + AA+
Sbjct: 9 YETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM 58
Score = 28.1 bits (63), Expect = 4.4
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELK---FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
K+ + + ++ ++ F +GE+ ++ P + RGFGFV F + +E
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPN----TKRSRGFGFVTFASASEVDA 56
Query: 744 AMKA 747
AM A
Sbjct: 57 AMNA 60
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 51.0 bits (123), Expect = 3e-08
Identities = 28/74 (37%), Positives = 42/74 (56%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV L T TE+D+ LFE+YG + EV + DK+T ++KG A V F E A +A +
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 398 LDGTVFLGRMLHLI 411
L G V + +
Sbjct: 61 LHGKVTMPGASRPL 74
Score = 42.5 bits (101), Expect = 3e-05
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V +P A + +V LF+ +G ++ V + + +G +G FV+F ++ EA++A++
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDK-DTGQSKGCAFVKFSSREEAQKAIE 59
Query: 747 ALCQSTHLYG 756
AL + G
Sbjct: 60 ALHGKVTMPG 69
Score = 38.3 bits (90), Expect = 0.001
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 28 KITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF 84
T+E ++A FEE G + +V ++ G+ + AF+ + ++AQ A++ +
Sbjct: 10 TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTM 67
Score = 36.4 bits (85), Expect = 0.004
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L +TE+ +R F++ G I VT+ R KD S G FV+F +RE +
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQ-----SKGCAFVKFSSREEAQK 56
Query: 643 ALKVLQNS 650
A++ L
Sbjct: 57 AIEALHGK 64
>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 = 51.3 bits (123), Expect = 3e-08
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E ++FV L ++VT+++L KLF+K+G + V L ++ + K KG A V + A+QA
Sbjct: 1 EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQA 59
Query: 395 YQHLDGTVFLGRML 408
+DGT + +
Sbjct: 60 VLKMDGTEIKEKTI 73
Score = 45.5 bits (108), Expect = 3e-06
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V +PF + E+E+LFK G +K VRL SG +G +VE+ ++ A +A+
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR--SGKPKGLAYVEYENESSASQAVL 61
Query: 747 AL 748
+
Sbjct: 62 KM 63
Score = 39.3 bits (92), Expect = 4e-04
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L++ L F+ T++ + + FKK G + SV + + K G +V++ S +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPK------GLAYVEYENESSAS 57
Query: 642 QALKVLQNSSLDEHQIELKRSN 663
QA+ + + + E I + SN
Sbjct: 58 QAVLKMDGTEIKEKTISVAISN 79
Score = 35.5 bits (82), Expect = 0.009
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +T+E+L+ F++ G V V+L GK + A++ Y E A A+ + T +
Sbjct: 12 FSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKEK 71
Query: 87 RIKV 90
I V
Sbjct: 72 TISV 75
Score = 33.5 bits (77), Expect = 0.048
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPL-PLASVR-TTFL-----GMAYIGFKDEKNCNKALNK 277
H + V LP V K++L+ FK + SVR T G+AY+ +++E + ++A+ K
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62
Score = 28.5 bits (64), Expect = 3.1
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVP-----PYGITGLVEFLQKNQAKAAF 500
K + V LP+ +L+ LF+ G + V LV P G+ VE+ ++ A A
Sbjct: 2 KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGL-AYVEYENESSASQAV 60
Query: 501 NSLAYTKFKE 510
+ T+ KE
Sbjct: 61 LKMDGTEIKE 70
>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 = 51.0 bits (123), Expect = 3e-08
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYG--PLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
+ +R L TE+D+ + P+ +V L DK T ++GFA V F E ATQ
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64
Query: 394 AYQHLDGTVFLGRMLHL 410
A +LD V GR++ +
Sbjct: 65 ALNNLDPFVIDGRVVRV 81
Score = 47.9 bits (115), Expect = 4e-07
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
P TL ++ L+ +TE+ I + PI V + R D + S G+ FV+F +
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIR--DKLTG---TSRGFAFVEFPS 55
Query: 637 RESLNQALKVLQNS 650
E Q + L N
Sbjct: 56 LEDATQWMDALNNL 69
Score = 45.6 bits (109), Expect = 3e-06
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ +++R + + ++ + A + VRL + + +G RGF FVEF + +A +
Sbjct: 3 NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKL-TGTSRGFAFVEFPSLEDATQ 61
Query: 744 AMKALCQSTHLY--GRRLVLEWA 764
M AL GR + + +A
Sbjct: 62 WMDALNNLDPFVIDGRVVRVSYA 84
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 50.6 bits (121), Expect = 3e-08
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IFV N+S T T D+L LFE++G + E DK K +A V E A A +
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVEC--------DKVKDYAFVHMEREEEALAAIEA 53
Query: 398 LDGTVFLGRML 408
L+G GR +
Sbjct: 54 LNGKEVKGRRI 64
Score = 33.7 bits (77), Expect = 0.032
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 7/62 (11%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
T ++L+ FEE G V + K + +AF+ RE++A AA++ N V RI
Sbjct: 13 TSDELRGLFEEFGRVVECD-------KVKDYAFVHMEREEEALAAIEALNGKEVKGRRIN 65
Query: 90 VE 91
VE
Sbjct: 66 VE 67
Score = 31.0 bits (70), Expect = 0.28
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 10/76 (13%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI V N+ E+ LF+ FG ++V + + FV + EA A++
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFG---------RVVECDKVKDYAFVHMEREEEALAAIE 52
Query: 747 ALCQSTHLYGRRLVLE 762
AL + GRR+ +E
Sbjct: 53 AL-NGKEVKGRRINVE 67
>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 = 50.7 bits (122), Expect = 3e-08
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S+ L VRNI + E+ LF+ FG++ + + + HRGF V + A+RA
Sbjct: 1 SRTLFVRNINSNVEDEELRALFEQFGDI------RTLYTACKHRGFIMVSYYDIRAARRA 54
Query: 745 MKALCQSTHLYGRRL 759
+AL Q T L GR+L
Sbjct: 55 KRAL-QGTELGGRKL 68
Score = 50.3 bits (121), Expect = 6e-08
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRN++ V +++L LFE++G + + K +GF +V++ A +A + L
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRAARRAKRAL 58
Query: 399 DGTVFLGRMLHLIPGKPKE 417
GT GR L + PK+
Sbjct: 59 QGTELGGRKLDIHFSIPKD 77
Score = 36.5 bits (85), Expect = 0.004
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 10/77 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL+++N+N N ++ +R F++ G I ++ A K G+ V +Y +
Sbjct: 3 TLFVRNINSNVEDEELRALFEQFGDIRTLYTACK----------HRGFIMVSYYDIRAAR 52
Query: 642 QALKVLQNSSLDEHQIE 658
+A + LQ + L +++
Sbjct: 53 RAKRALQGTELGGRKLD 69
Score = 31.5 bits (72), Expect = 0.21
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGD 473
R + V+N+ +L+ALFE FGD
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGD 27
>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 = 51.1 bits (123), Expect = 4e-08
Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 7/82 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEV-IL-PIDKETDKTK---GFALVTFLMPEHATQ 393
++V NL+ VTE+ L + F ++GPLA V I+ P +E + GF V F+ A +
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGF--VAFMNRADAER 61
Query: 394 AYQHLDGTVFLGRMLHLIPGKP 415
A LDG +G L L GK
Sbjct: 62 ALDELDGKDVMGYELKLGWGKA 83
Score = 49.6 bits (119), Expect = 1e-07
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV--ARKKDPKSPGQFLSMGYGFVQFYTRE 638
T LY+ NLN TE+ + + F + GP+ASV + R ++ + + GFV F R
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC----GFVAFMNRA 57
Query: 639 SLNQALKVLQNSSLDEHQIEL 659
+AL L + ++++L
Sbjct: 58 DAERALDELDGKDVMGYELKL 78
Score = 35.7 bits (83), Expect = 0.008
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRL--PKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+ + + + + F FG L V++ P+ +R GFV F+ + +A+RA+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 746 KALCQSTHLYGRRLVLEWA 764
L + G L L W
Sbjct: 64 DEL-DGKDVMGYELKLGWG 81
Score = 33.0 bits (76), Expect = 0.071
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKY--TTEGKFRR--FAFIGYHREDQAQAALDYFNNTYV 83
K+T+E L +F G + V++ + T E + R F+ + A+ ALD + V
Sbjct: 12 KVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERALDELDGKDV 71
Query: 84 FSSRIKV 90
+K+
Sbjct: 72 MGYELKL 78
>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 = 50.7 bits (122), Expect = 4e-08
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL + +TE++L + F +G + EV K KG+A V F E A A +
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEV------RVFKDKGYAFVRFDTHEAAATAIVAV 56
Query: 399 DGTVFLGRML 408
+GT G+ +
Sbjct: 57 NGTSINGQTV 66
Score = 49.9 bits (120), Expect = 7e-08
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TT+Y+ NL TE+ ++R F G I V V + K GY FV+F T E+
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-----------GYAFVRFDTHEAA 49
Query: 641 NQALKVLQNSSLDEHQI 657
A+ + +S++ +
Sbjct: 50 ATAIVAVNGTSINGQTV 66
Score = 34.9 bits (81), Expect = 0.012
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+P + E++ F FG ++ VR+ K +G+ FV F T A A+ A
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-------KGYAFVRFDTHEAAATAIVA 55
Query: 748 LCQSTHLYGRRLVLEWAEE 766
T + G+ + W +E
Sbjct: 56 -VNGTSINGQTVKCSWGKE 73
>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 = 50.5 bits (121), Expect = 4e-08
Identities = 28/69 (40%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++ NL++ +TEDD+ + F K + V L DKET + KGF V F E + A
Sbjct: 1 TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDF-ADEESLDAALK 58
Query: 398 LDGTVFLGR 406
LDGTV GR
Sbjct: 59 LDGTVLCGR 67
Score = 48.2 bits (115), Expect = 3e-07
Identities = 28/67 (41%), Positives = 38/67 (56%), Gaps = 6/67 (8%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+YI NL ++ TED +R F K I SV +A K+ G+F G+G V F ESL+
Sbjct: 1 TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKE---TGEF--KGFGHVDFADEESLD 54
Query: 642 QALKVLQ 648
ALK+
Sbjct: 55 AALKLDG 61
Score = 35.1 bits (81), Expect = 0.013
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ + N+ + + +V E FK E+ VRL +G +GFG V+F + A+K
Sbjct: 2 VYIGNLAWDITEDDVREFFKG-CEITSVRLATDK-ETGEFKGFGHVDFADEESLDAALK- 58
Query: 748 LCQSTHLYGRRL 759
T L GR +
Sbjct: 59 -LDGTVLCGRPI 69
Score = 34.7 bits (80), Expect = 0.014
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 7/71 (9%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVR-----TT--FLGMAYIGFKDEKNCNKALNKN 278
T+ + NL + + D++ +FK + SVR T F G ++ F DE++ + AL +
Sbjct: 1 TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60
Query: 279 KSFWKGKQLNI 289
+ G+ + I
Sbjct: 61 GTVLCGRPIRI 71
>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 = 50.4 bits (121), Expect = 5e-08
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V L +T+++L LFE GP+ + D+ T ++ G+ V ++ A +A L+G
Sbjct: 5 VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64
Score = 43.1 bits (102), Expect = 2e-05
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L + T++ +R F+ GPI S + R + GQ S+GYGFV +
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDR---ITGQ--SLGYGFVDYVDENDA 55
Query: 641 NQALKVLQNSSLDEHQIELKR 661
+A+ L+ +I KR
Sbjct: 56 QKAINT-----LNGFEIRNKR 71
Score = 41.9 bits (99), Expect = 4e-05
Identities = 17/63 (26%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E+ LF+A G ++ ++ + + +G G+GFV+++ +N+A++A+
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRI-TGQSLGYGFVDYVDENDAQKAI 59
Query: 746 KAL 748
L
Sbjct: 60 NTL 62
Score = 34.2 bits (79), Expect = 0.029
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+TQE+L++ FE G + ++ G+ + F+ Y E+ AQ A++ N + + R
Sbjct: 12 MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKR 71
Query: 88 IKV 90
+KV
Sbjct: 72 LKV 74
>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 = 50.0 bits (120), Expect = 7e-08
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE---HATQA 394
++FV NL +TV +L + F ++G + +P DKET +KG+ V+F + +A Q
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 395 YQH-LDGTV 402
+H L+G
Sbjct: 61 QKHILEGNK 69
Score = 43.1 bits (102), Expect = 2e-05
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 8/70 (11%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEAKRA 744
K+ V N+P+ E++E F FG++K +P K+ +GL +G+GFV F +++
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKE---TGLSKGYGFVSFSSRDG---L 54
Query: 745 MKALCQSTHL 754
AL + H+
Sbjct: 55 ENALQKQKHI 64
Score = 34.6 bits (80), Expect = 0.015
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L++ NL + ++ +F + G + S V K+ LS GYGFV F +R+ L
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETG-----LSKGYGFVSFSSRDGLE 55
Query: 642 QALK 645
AL+
Sbjct: 56 NALQ 59
Score = 30.3 bits (69), Expect = 0.54
Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 12/74 (16%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL----------GMAYIGFKDEKNCNKAL 275
+ V NLP V K+LK YF V++ + G ++ F AL
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQF--GKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL 58
Query: 276 NKNKSFWKGKQLNI 289
K K +G +L +
Sbjct: 59 QKQKHILEGNKLQV 72
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 49.7 bits (119), Expect = 7e-08
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NL Y V L ++F+ G + + DKE K++G +V F P A QA
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59
Query: 399 DGTVFLGRMLHL 410
+G + R + +
Sbjct: 60 NGQMLFDRPMRV 71
Score = 36.6 bits (85), Expect = 0.004
Identities = 18/64 (28%), Positives = 30/64 (46%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
YK+ ++LK F+ G V +K EGK R + + +A A+ FN +F
Sbjct: 8 YKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDR 67
Query: 87 RIKV 90
++V
Sbjct: 68 PMRV 71
Score = 30.4 bits (69), Expect = 0.59
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ NL++ ++ FK G + + K+ K S G G VQF Q
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGK------SRGMGVVQFEHPIEAVQ 54
Query: 643 ALKVLQNSSL 652
A+ + L
Sbjct: 55 AISMFNGQML 64
Score = 28.1 bits (63), Expect = 3.3
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I V N+ ++ +++E+FK G K VR K G RG G V+F EA +A+
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAG--KVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISM 58
Query: 748 LCQSTHLYGRRLVL 761
L+ R + +
Sbjct: 59 F-NGQMLFDRPMRV 71
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 50.0 bits (120), Expect = 8e-08
Identities = 26/70 (37%), Positives = 34/70 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NL E L +LF +G + V + D T+K KG+ VT E A A L
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 399 DGTVFLGRML 408
+G GR+L
Sbjct: 64 NGYRLGGRVL 73
Score = 33.4 bits (77), Expect = 0.056
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I V N+P A +S + +LF FG + V++ + + + +G+GFV EA A+ +
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKV-IRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62
Query: 748 L 748
L
Sbjct: 63 L 63
Score = 28.8 bits (65), Expect = 1.8
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 15/80 (18%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE-- 638
+++ NL ++ E + + F G + +V V R D + GYGFV E
Sbjct: 2 WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIR--DLTTN---KCKGYGFVTMTNYEEA 56
Query: 639 -----SLN---QALKVLQNS 650
SLN +VLQ S
Sbjct: 57 YSAIASLNGYRLGGRVLQVS 76
>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 = 50.0 bits (119), Expect = 8e-08
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A + +G
Sbjct: 14 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73
Query: 401 TVFLGRMLHL 410
GR + +
Sbjct: 74 MELDGRRIRV 83
Score = 40.0 bits (93), Expect = 3e-04
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 5/86 (5%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
P+P+ L + L+ +TE +R F K GPIA V++ + + S G+ FV F
Sbjct: 6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-----SRGFAFVYFEN 60
Query: 637 RESLNQALKVLQNSSLDEHQIELKRS 662
+ +A + LD +I + S
Sbjct: 61 VDDAKEAKERANGMELDGRRIRVDFS 86
Score = 29.6 bits (66), Expect = 1.6
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+ L+ F + G + DV + Y + + R FAF+ + D A+ A + N + RI
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81
Query: 89 KVE 91
+V+
Sbjct: 82 RVD 84
>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 = 50.0 bits (119), Expect = 9e-08
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRN++ +DL + F +YGP+ +V +P+D T + +GFA V F A A +L
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 399 DGTVFLGRMLHL 410
D GR + +
Sbjct: 63 DRKWICGRQIEI 74
Score = 34.9 bits (80), Expect = 0.020
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
++L+++N+ ++ + +RR F + GPI V V + P G+ +VQF
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRP-----RGFAYVQFEDVRDA 55
Query: 641 NQALKVLQNSSLDEHQIELK 660
AL L + QIE++
Sbjct: 56 EDALHNLDRKWICGRQIEIQ 75
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 49.9 bits (119), Expect = 1e-07
Identities = 20/83 (24%), Positives = 46/83 (55%), Gaps = 4/83 (4%)
Query: 687 KILVRNIPFQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+++RN+P+ K+ ++++F +G+++ +P+K G GF FV + A+ A+
Sbjct: 2 KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRK--RGGKLCGFAFVTMKKRKNAEIAL 59
Query: 746 KALCQSTHLYGRRLVLEWAEEAD 768
+ + GR + ++WA + +
Sbjct: 60 ENT-NGLEIDGRPVAVDWAVQKN 81
Score = 36.8 bits (85), Expect = 0.004
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 338 RIFVRNLSYTVTE-DDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
++ +RNL +++ + L K+F +YG + E +P + K GFA VT ++A A +
Sbjct: 2 KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALE 60
Query: 397 HLDGTVFLGRML 408
+ +G GR +
Sbjct: 61 NTNGLEIDGRPV 72
Score = 28.3 bits (63), Expect = 4.2
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 12/63 (19%)
Query: 227 IVVKNLPAGVKK-KDLKAYFKPLPLASVRTTFL---------GMAYIGFKDEKNCNKALN 276
++++NLP +KK LK F VR + G A++ K KN AL
Sbjct: 3 LIIRNLPWSIKKPVKLKKIFGRY--GKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALE 60
Query: 277 KNK 279
Sbjct: 61 NTN 63
Score = 27.5 bits (61), Expect = 6.8
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 583 LYIKNLNFNSTE-DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L I+NL ++ + +++ F + G + T+ RK+ K G+ FV R++
Sbjct: 3 LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGK------LCGFAFVTMKKRKNAE 56
Query: 642 QALKVLQNSSLD 653
AL+ +D
Sbjct: 57 IALENTNGLEID 68
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 49.0 bits (117), Expect = 1e-07
Identities = 25/70 (35%), Positives = 37/70 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV N+ Y TE+ L +F + GP+ L D+ET K KG+ + E A A ++L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 399 DGTVFLGRML 408
+G GR L
Sbjct: 61 NGYELNGRQL 70
Score = 35.9 bits (83), Expect = 0.005
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V NIP++A + +++++F G + RL +G +G+GF E+ + A AM+
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYKDQETALSAMRN 59
Query: 748 LCQSTHLYGRRLVLEWA 764
L L GR+L ++ A
Sbjct: 60 L-NGYELNGRQLRVDNA 75
Score = 35.2 bits (81), Expect = 0.012
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y+ T+EQLK F E G V +L Y E GK + + F Y ++ A +A+ N +
Sbjct: 8 YEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNG 67
Query: 86 SRIKVE 91
+++V+
Sbjct: 68 RQLRVD 73
Score = 30.5 bits (69), Expect = 0.56
Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ N+ + +TE+ ++ F + GP+ S + ++ P GYGF ++ +E+
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP-----KGYGFCEYKDQETALS 55
Query: 643 ALKVLQNSSLDEHQI 657
A++ L L+ Q+
Sbjct: 56 AMRNLNGYELNGRQL 70
>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 = 48.9 bits (117), Expect = 2e-07
Identities = 24/60 (40%), Positives = 32/60 (53%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T + L +F KYG + V LP K T KGFA + F PE A +A +HL
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Score = 48.1 bits (115), Expect = 4e-07
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V +P A ++ +F +G + +V LP+ +G +GF F+EF T EA++A K
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPR-YKHTGDIKGFAFIEFETPEEAQKACKH 60
Query: 748 LCQS 751
L
Sbjct: 61 LNNP 64
Score = 47.7 bits (114), Expect = 5e-07
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 5/84 (5%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+Y++ L N+T + ++ F K G + V++ R K G+ F++F T E
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDI-----KGFAFIEFETPEEAQ 55
Query: 642 QALKVLQNSSLDEHQIELKRSNRN 665
+A K L N K
Sbjct: 56 KACKHLNNPPETATDKPGKFPKTV 79
Score = 33.1 bits (76), Expect = 0.074
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
T E LKA F + GTV V L +Y G + FAFI + ++AQ A + NN
Sbjct: 11 ATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNN 63
>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 = 49.2 bits (118), Expect = 2e-07
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
+P TL++ L+ +TE+++R F + G I + + R G S GY FV++
Sbjct: 1 DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRD---IVTGF--SKGYAFVEYEHE 55
Query: 638 ESLNQALKVLQNSSLDEHQI 657
+A + +D +I
Sbjct: 56 RDALRAYRDAHKLVIDGSEI 75
Score = 44.2 bits (105), Expect = 1e-05
Identities = 21/64 (32%), Positives = 33/64 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV LS TE+ L ++F +YG + + L D T +KG+A V + A +AY+
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 399 DGTV 402
V
Sbjct: 66 HKLV 69
Score = 40.7 bits (96), Expect = 2e-04
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V + Q + + E+F +G+++ +RL + +V +G +G+ FVE+ + +A RA +
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIV-TGFSKGYAFVEYEHERDALRAYRD 64
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
P+ L++ LN +T++ + F + G I S V R D K+ G S+ Y F++F T+E
Sbjct: 2 PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIR--DKKT-GD--SLQYAFIEFETKE 56
Query: 639 SLNQALKVLQNSSLDEHQI 657
+A + N +D+ +I
Sbjct: 57 DCEEAYFKMDNVLIDDRRI 75
Score = 41.1 bits (97), Expect = 1e-04
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
+FV L+ T++DL +F ++G + EVI DK+T + +A + F E +AY
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIR--DKKTGDSLQYAFIEFETKEDCEEAYF 63
Query: 397 HLDGTVFLGRMLH 409
+D + R +H
Sbjct: 64 KMDNVLIDDRRIH 76
Score = 27.2 bits (61), Expect = 9.1
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 21 DEVEFIYKI----TQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAAL 75
+ V F+ K+ T E L+ F G + + ++ G ++AFI + ++ + A
Sbjct: 3 ENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA- 61
Query: 76 DYF--NNTYVFSSRIKVEKC 93
YF +N + RI V+
Sbjct: 62 -YFKMDNVLIDDRRIHVDFS 80
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGP---LAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
R+++ NL +TE L KLF KYG + + +G+ VTF E A +A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 395 YQHLDGTVFLGRML 408
+ L+G LG+ L
Sbjct: 61 LKSLNGKTALGKKL 74
Score = 43.4 bits (103), Expect = 2e-05
Identities = 24/66 (36%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L+I NL+ TE + + F K G I K GQ GY FV F T+E
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQ--PRGYCFVTFETKEEAE 58
Query: 642 QALKVL 647
+ALK L
Sbjct: 59 KALKSL 64
Score = 43.0 bits (102), Expect = 2e-05
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
++ + N+ + + + +LF +G++K K G RG+ FV F TK EA++A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 745 MKALCQSTHLYGRRLVLEWA 764
+K+L T G++LV+ WA
Sbjct: 61 LKSLNGKT-ALGKKLVVRWA 79
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 48.1 bits (115), Expect = 3e-07
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IFV L VTE DL K F ++G + EV++ D E + +GF +TF + Q
Sbjct: 4 KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63
Score = 34.6 bits (80), Expect = 0.017
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 12/75 (16%)
Query: 591 NSTEDSIRRHFKKCGPIASVTV---ARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
N TE +R++F + G + V V KK P+ G+GF+ F + +S++Q +
Sbjct: 13 NVTETDLRKYFSQFGTVTEVVVMYDHEKKRPR--------GFGFITFESEDSVDQVVN-E 63
Query: 648 QNSSLDEHQIELKRS 662
++ ++E+KR+
Sbjct: 64 HFHDINGKKVEVKRA 78
Score = 32.0 bits (73), Expect = 0.19
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAAL 75
+T+ L+ F + GTVT+V + Y E K R F FI + ED +
Sbjct: 14 VTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
>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 = 48.1 bits (115), Expect = 3e-07
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L++ NL +++T + + HFK G SV + K G FV+F T E++
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKS-----KGCAFVEFDTAEAMT 56
Query: 642 QALKVLQNSSLDEHQI 657
+ALK L ++ L +I
Sbjct: 57 KALK-LHHTLLKGRKI 71
Score = 47.3 bits (113), Expect = 5e-07
Identities = 28/68 (41%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL Y T +DL F+ G V L DK+T K+KG A V F E T+A + L
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-L 61
Query: 399 DGTVFLGR 406
T+ GR
Sbjct: 62 HHTLLKGR 69
Score = 34.2 bits (79), Expect = 0.025
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKP-LPLASVR-------TTFLGMAYIGFKDEKNCNKALNK 277
+ V NLP +DL A+FK SVR G A++ F + KAL
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61
Query: 278 NKSFWKGKQLNI 289
+ + KG+++N+
Sbjct: 62 HHTLLKGRKINV 73
Score = 33.9 bits (78), Expect = 0.035
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+P+ ++ FK G VRL +G +G FVEF T A+ KA
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDK-KTGKSKGCAFVEFDT---AEAMTKA 58
Query: 748 LCQ-STHLYGRRLVLE 762
L T L GR++ +E
Sbjct: 59 LKLHHTLLKGRKINVE 74
Score = 31.6 bits (72), Expect = 0.18
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 2/66 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDV-QLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T E L A F+ G V L GK + AF+ + + AL +T +
Sbjct: 10 YDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH-HTLLKG 68
Query: 86 SRIKVE 91
+I VE
Sbjct: 69 RKINVE 74
>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 = 47.6 bits (114), Expect = 4e-07
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH- 397
+F+ LS+ TE+ L + F KYG + + ++ D T +++GF VTF P +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 398 ---LDG 400
LDG
Sbjct: 61 PHVLDG 66
Score = 45.7 bits (109), Expect = 2e-06
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L++++TE+S+R +F K G + + KDP + G+ S G+GFV F S+++
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVI--MKDPIT-GR--SRGFGFVTFADPSSVDK 55
Query: 643 ALKVLQNSSLDEHQIELK 660
L + LD +I+ K
Sbjct: 56 VLA-AKPHVLDGREIDPK 72
Score = 29.5 bits (67), Expect = 1.1
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 30 TQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
T+E L+ F + G V D V +K G+ R F F+ + L
Sbjct: 11 TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58
Score = 27.9 bits (63), Expect = 4.0
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
E F +GE+ + K +G RGFGFV F + + + A
Sbjct: 17 EYFSKYGEVVDCVI-MKDPITGRSRGFGFVTFADPSSVDKVLAA 59
>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 = 47.6 bits (114), Expect = 5e-07
Identities = 21/72 (29%), Positives = 37/72 (51%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI+V ++ ++EDD+ +FE +G + L D ET K KG+ + + P+ A A
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61
Query: 398 LDGTVFLGRMLH 409
++ G+ L
Sbjct: 62 MNLFDLGGQQLR 73
Score = 44.6 bits (106), Expect = 6e-06
Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+I V ++ + +++ +F+AFG++K L +G H+G+GF+E+ A+ A+
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPE-TGKHKGYGFIEYENPQSAQDAIA 60
Query: 747 AL 748
++
Sbjct: 61 SM 62
Score = 39.2 bits (92), Expect = 4e-04
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ +++ + +ED I+ F+ G I S ++A G+ GYGF+++ +S
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAP---DPETGKHK--GYGFIEYENPQSAQD 57
Query: 643 ALK 645
A+
Sbjct: 58 AIA 60
Score = 29.9 bits (68), Expect = 0.76
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
++++ +K+ FE G + L GK + + FI Y AQ A+ N
Sbjct: 12 LSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64
>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 = 47.7 bits (114), Expect = 5e-07
Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
V +P Q E+E LF +G + R+ V GL RG GF+ F + EA+RA+KAL
Sbjct: 5 VSGLPKTMTQQELEALFSPYGRIITSRILCDNVT-GLSRGVGFIRFDKRIEAERAIKAL 62
Score = 32.7 bits (75), Expect = 0.091
Identities = 19/67 (28%), Positives = 33/67 (49%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+T+ +L LF YG + + D T ++G + F A +A + L
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 399 DGTVFLG 405
+GT+ G
Sbjct: 63 NGTIPPG 69
Score = 28.8 bits (65), Expect = 2.4
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGI----TGLVEFLQKNQAKAAFNSL 503
V LP +L+ALF P+G + R+L G + F ++ +A+ A +L
Sbjct: 5 VSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
>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 = 47.6 bits (114), Expect = 5e-07
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V+NL ++ ++ L + F +G + + D E ++KGF V F PE AT+A +
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTEM 62
Query: 399 DGTVFLGRMLHLIPGKP 415
+G +I GKP
Sbjct: 63 NG--------RIIGGKP 71
Score = 45.3 bits (108), Expect = 3e-06
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+KNL+ + ++ +R F G I S V D K G+ S G+GFV F + E +
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMT--DEK--GR--SKGFGFVCFSSPEEATK 57
Query: 643 ALK 645
A+
Sbjct: 58 AVT 60
Score = 35.7 bits (83), Expect = 0.008
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V+N+ + E F FG + ++ G +GFGFV F + EA +A
Sbjct: 1 GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD--EKGRSKGFGFVCFSSPEEATKA 58
Query: 745 MK 746
+
Sbjct: 59 VT 60
Score = 31.1 bits (71), Expect = 0.32
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
I E+L+ +F GT+T ++ +G+ + F F+ + ++A A+ N +
Sbjct: 13 IDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGRII 67
>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 = 47.4 bits (113), Expect = 6e-07
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V N+ + + DL ++F ++GP+ +V I +KGF VTF A +A +
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDV--EIIFNERGSKGFGFVTFANSADADRAREK 59
Query: 398 LDGTVFLGRML 408
L GTV GR +
Sbjct: 60 LHGTVVEGRKI 70
Score = 46.6 bits (111), Expect = 1e-06
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ V NIPF+ + ++ ++F FG + V + GS +GFGFV F +A RA +
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS---KGFGFVTFANSADADRARE 58
Query: 747 ALCQSTHLYGRRL 759
L T + GR++
Sbjct: 59 KL-HGTVVEGRKI 70
Score = 31.6 bits (72), Expect = 0.23
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ N+ F + +R+ F + GPI V + + S G+GFV F ++
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-------SKGFGFVTFANSADADR 55
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A + L + ++ +IE+ +
Sbjct: 56 AREKLHGTVVEGRKIEVNNA 75
Score = 28.5 bits (64), Expect = 2.8
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 452 VKNLPYRTLPTDLKALFEPFG 472
V N+P+R DL+ +F FG
Sbjct: 5 VSNIPFRFRDPDLRQMFGQFG 25
Score = 27.8 bits (62), Expect = 4.4
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
++ L+ F + G + DV++ + G + F F+ + A A + + T V
Sbjct: 10 FRFRDPDLRQMFGQFGPILDVEIIFNERGS-KGFGFVTFANSADADRAREKLHGTVVEGR 68
Query: 87 RIKV 90
+I+V
Sbjct: 69 KIEV 72
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 47.4 bits (113), Expect = 7e-07
Identities = 26/80 (32%), Positives = 39/80 (48%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV + + E DL LFE++G + E+ + DK T KG A +T+ E A +A
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66
Query: 398 LDGTVFLGRMLHLIPGKPKE 417
L L M I KP +
Sbjct: 67 LHEQKTLPGMNRPIQVKPAD 86
Score = 34.3 bits (79), Expect = 0.026
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V IP ++ ++ LF+ FG++ + + K +G+H+G F+ + + A +A
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKY-TGMHKGCAFLTYCARESALKAQS 65
Query: 747 AL 748
AL
Sbjct: 66 AL 67
>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 = 46.8 bits (111), Expect = 8e-07
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+P +S + LF+ +G+++ V+ + G V F +AKRA++
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGDVRGVQT------ERISEGIVTVHFYDIRDAKRAVRE 57
Query: 748 LCQSTHLYGRRL 759
LC H+ + L
Sbjct: 58 LC-GRHMQQQAL 68
Score = 36.8 bits (85), Expect = 0.003
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV N+ VTE L +LFE YG + + E ++G V F A +A + L
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGD----VRGVQTER-ISEGIVTVHFYDIRDAKRAVREL 58
Query: 399 DGTVFLGRML 408
G + L
Sbjct: 59 CGRHMQQQAL 68
Score = 32.9 bits (75), Expect = 0.062
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
+L++ N+ + TE ++RR F+ G + V R + G V FY
Sbjct: 3 SLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISE----------GIVTVHFYDIRDAK 52
Query: 642 QALKVLQNSSL 652
+A++ L +
Sbjct: 53 RAVRELCGRHM 63
Score = 29.8 bits (67), Expect = 0.70
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAY 505
R + V N+P + L+ LFE +GD+ V GI V F AK A L
Sbjct: 2 RSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIV-TVHFYDIRDAKRAVRELCG 60
Query: 506 TKFKE 510
++
Sbjct: 61 RHMQQ 65
>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 = 46.5 bits (111), Expect = 8e-07
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 11/75 (14%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHATQA 394
R+ V NL +VTEDD+ +LF G L A ++ P G A V ++ + A A
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP---------GVAEVVYVRKDDALTA 51
Query: 395 YQHLDGTVFLGRMLH 409
+ G+ +
Sbjct: 52 IDKYNNRELDGQPMK 66
Score = 32.6 bits (75), Expect = 0.085
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+++V N+ + ++ ELF A G LK RL + G V ++ K++A A+
Sbjct: 2 RLVVSNLHPSVTEDDIVELFSAIGALKRARL--------VRPGVAEVVYVRKDDALTAID 53
Score = 31.9 bits (73), Expect = 0.15
Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 12/73 (16%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + NL+ + TED I F G + + R PG V + ++
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVR------PGV------AEVVYVRKDDA 48
Query: 641 NQALKVLQNSSLD 653
A+ N LD
Sbjct: 49 LTAIDKYNNRELD 61
>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 = 46.4 bits (111), Expect = 8e-07
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 353 LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL 410
L KLF +G + ++ L K GFA V F E A +A Q+L+G +F GR L +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53
Score = 42.1 bits (100), Expect = 2e-05
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW 763
+LF FG ++ ++L KK GF FVEF T+ A++A++ L GR L +++
Sbjct: 3 KLFSPFGNVEKIKLLKK------KPGFAFVEFSTEEAAEKAVQYL-NGVLFGGRPLRVDY 55
Query: 764 A 764
+
Sbjct: 56 S 56
Score = 39.0 bits (92), Expect = 3e-04
Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 10/66 (15%)
Query: 597 IRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSLDEHQ 656
+ + F G + + + +KK G+ FV+F T E+ +A++ L
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKP----------GFAFVEFSTEEAAEKAVQYLNGVLFGGRP 50
Query: 657 IELKRS 662
+ + S
Sbjct: 51 LRVDYS 56
Score = 36.7 bits (86), Expect = 0.002
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 34 LKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE 91
L F G V ++L FAF+ + E+ A+ A+ Y N ++V+
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
Score = 35.6 bits (83), Expect = 0.006
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 464 LKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 518
L LF PFG++ ++ + VEF + A+ A L F PL ++++
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 46.8 bits (112), Expect = 9e-07
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + + ED+L LFEK GP+ E+ L +D +G+A VT+ E A +A + L
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSG-LNRGYAFVTYTNKEAAQRAVKQL 62
Query: 399 DG 400
Sbjct: 63 HN 64
Score = 46.4 bits (111), Expect = 1e-06
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G ++ V IP + E+ LF+ G + +RL M SGL+RG+ FV + K A+RA
Sbjct: 1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRL--MMDFSGLNRGYAFVTYTNKEAAQRA 58
Query: 745 MKAL 748
+K L
Sbjct: 59 VKQL 62
Score = 31.4 bits (72), Expect = 0.27
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 7/64 (10%)
Query: 22 EVEFIYKITQ----EQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGY-HREDQAQAALD 76
EV F+ KI + ++L FE+ G + +++L G R +AF+ Y ++E AQ A+
Sbjct: 3 EV-FVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEA-AQRAVK 60
Query: 77 YFNN 80
+N
Sbjct: 61 QLHN 64
Score = 31.4 bits (72), Expect = 0.27
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 11/82 (13%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+++ + + ED + F+K GPI + + D L+ GY FV + +E+
Sbjct: 1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRL--MMDFSG----LNRGYAFVTYTNKEA 54
Query: 640 LNQALKVLQNSSLDEHQIELKR 661
+A+K L ++I +
Sbjct: 55 AQRAVK-----QLHNYEIRPGK 71
>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 = 46.6 bits (111), Expect = 1e-06
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV LS VT+++L + F ++G + EV L K + T FA + F + A +A +
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63
Query: 399 DGTVFLGRMLH 409
+ ++ + +H
Sbjct: 64 NHSMLKNKTMH 74
Score = 39.2 bits (92), Expect = 5e-04
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+T+E+L +F G + +V L FAFI + RE A A++ N++ + +
Sbjct: 14 DVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESENHSMLKNKT 72
Query: 88 IKVEK 92
+ V+
Sbjct: 73 MHVQY 77
Score = 28.1 bits (63), Expect = 3.8
Identities = 11/76 (14%), Positives = 38/76 (50%), Gaps = 12/76 (15%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++++ L+ + T++ + F + G I V + ++ + + + F++F ++
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-------AFAFIKFEREQAAA 57
Query: 642 QALK-----VLQNSSL 652
+A++ +L+N ++
Sbjct: 58 RAVESENHSMLKNKTM 73
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 46.5 bits (111), Expect = 1e-06
Identities = 22/71 (30%), Positives = 34/71 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IF+ L ++ED + +L E +G L L D T +KG+A +L P QA
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 398 LDGTVFLGRML 408
L+G + L
Sbjct: 62 LNGMQLGDKKL 72
Score = 39.9 bits (94), Expect = 3e-04
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI + +P + +V+EL ++FG+LK L K +GL +G+ F E++ + +A+
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKD-SATGLSKGYAFCEYLDPSVTDQAIA 60
Query: 747 AL 748
L
Sbjct: 61 GL 62
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 46.2 bits (110), Expect = 1e-06
Identities = 22/70 (31%), Positives = 33/70 (47%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V LS T DL +LF KYG + + + + + F VT E A + QHL
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 399 DGTVFLGRML 408
T GR++
Sbjct: 62 HRTELHGRVI 71
Score = 30.0 bits (68), Expect = 0.78
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L+ + +++ F K G + + +SPG + +GFV + E +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNA--RSPG---ARCFGFVTMASVEEAAK 56
Query: 643 ALKVLQNSSLDEHQI 657
++ L + L I
Sbjct: 57 CIQHLHRTELHGRVI 71
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 46.0 bits (110), Expect = 1e-06
Identities = 23/70 (32%), Positives = 38/70 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL VTE+ L +LF + GP+ V +P D+ T +G+ V FL E A A + +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 399 DGTVFLGRML 408
+ G+ +
Sbjct: 61 NMIKLYGKPI 70
Score = 44.9 bits (107), Expect = 4e-06
Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+ + + + ELF G + V +PK V + H+G+GFVEF+++ +A A+K
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRV-TQAHQGYGFVEFLSEEDADYAIKI 59
Query: 748 LCQSTHLYGR 757
+ LYG+
Sbjct: 60 M-NMIKLYGK 68
Score = 38.7 bits (91), Expect = 7e-04
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ NL+ TE+ + F + GP+ +V + + + ++ GYGFV+F + E +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAH-----QGYGFVEFLSEEDADY 55
Query: 643 ALKVLQNSSL 652
A+K++ L
Sbjct: 56 AIKIMNMIKL 65
Score = 29.5 bits (67), Expect = 0.96
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 19 DLDEVEFIYKITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDY 77
+LDE K+T+E L F + G V +V + K + + F+ + E+ A A+
Sbjct: 5 NLDE-----KVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59
Query: 78 FNNTYVFSSRIKVEK 92
N ++ I+V K
Sbjct: 60 MNMIKLYGKPIRVNK 74
>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 = 45.7 bits (109), Expect = 2e-06
Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD---KTKGFALVTFLMPEHATQAY 395
IFVRNL ++VT DL LF + G +L D +TD ++KGF V F PE A +A
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGN----VLRADVKTDNDGRSKGFGTVLFESPEDAQRAI 56
Query: 396 QHLDGTVFLGRML 408
+ +G GR L
Sbjct: 57 EMFNGYDLEGREL 69
Score = 38.4 bits (90), Expect = 7e-04
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
I VRN+PF ++++LF+ G + +R K G +GFG V F + +A+RA
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNV--LRADVKTDNDGRSKGFGTVLFESPEDAQRA 55
Score = 37.2 bits (87), Expect = 0.002
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++++NL F+ T ++ F++CG + V D + S G+G V F + E +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGR------SKGFGTVLFESPEDAQR 54
Query: 643 ALKVLQNSSLDEHQIELK 660
A+++ L+ ++E++
Sbjct: 55 AIEMFNGYDLEGRELEVR 72
Score = 33.0 bits (76), Expect = 0.068
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ +T + LK F E G V +K +G+ + F + + + AQ A++ FN Y
Sbjct: 8 FSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNG-YDLEG 66
Query: 87 RI 88
R
Sbjct: 67 RE 68
Score = 29.9 bits (68), Expect = 0.64
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 479
I V+NLP+ DLK LF G++ R V
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADV 30
Score = 28.4 bits (64), Expect = 3.0
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 227 IVVKNLPAGVKKKDLKAYFKP---LPLASVRTTF----LGMAYIGFKDEKNCNKALNK-N 278
I V+NLP V +DLK F+ + A V+T G + F+ ++ +A+ N
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 279 KSFWKGKQLNI 289
+G++L +
Sbjct: 61 GYDLEGRELEV 71
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 45.8 bits (109), Expect = 2e-06
Identities = 22/68 (32%), Positives = 37/68 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV +LS + + L F +G +++ + D +T K+KG+ V+F+ E A A Q +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 399 DGTVFLGR 406
+G GR
Sbjct: 62 NGQWLGGR 69
Score = 39.7 bits (93), Expect = 2e-04
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW 763
F FGE+ R+ K M +G +G+GFV F+ K +A+ A++++ L GR + W
Sbjct: 20 FAPFGEISDARVVKDM-QTGKSKGYGFVSFVKKEDAENAIQSM-NGQWLGGRAIRTNW 75
Score = 35.4 bits (82), Expect = 0.009
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ +L+ +++R F G I+ V KD ++ S GYGFV F +E
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVV--KDMQTGK---SKGYGFVSFVKKEDAEN 56
Query: 643 ALKVLQNSSLDEHQIELKRSN 663
A++ + L I R+N
Sbjct: 57 AIQSMNGQWLGGRAI---RTN 74
Score = 32.0 bits (73), Expect = 0.17
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 14 HISLLDLDEVEFIYKITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQ 72
HI + DL +I E L+A F G ++D + +K GK + + F+ + +++ A+
Sbjct: 1 HIFVGDLSP-----EIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAE 55
Query: 73 AALDYFNNTYVFSSRIK 89
A+ N ++ I+
Sbjct: 56 NAIQSMNGQWLGGRAIR 72
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions as
a translational regulator that activates translation in
an mRNA-specific manner. DAZAP1 was initially identified
as a binding partner of Deleted in Azoospermia (DAZ). It
also interacts with numerous hnRNPs, including hnRNP U,
hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D,
suggesting DAZAP1 might associate and cooperate with
hnRNP particles to regulate adenylate-uridylate-rich
elements (AU-rich element or ARE)-containing mRNAs.
DAZAP1 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
proline-rich domain. .
Length = 82
Score = 46.3 bits (110), Expect = 2e-06
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP---EHATQA 394
++FV LS+ T++ L + F +YG + + ++ DK T++++GF V F P
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 395 YQH-LDG 400
H LDG
Sbjct: 61 GPHTLDG 67
Score = 34.8 bits (80), Expect = 0.020
Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 10/83 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L++ +T++++RR+F + G + + KD + + S G+GFV+F ++
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIM--KDKTT-NR--SRGFGFVKF--KDPNCV 54
Query: 643 ALKVLQNS--SLDEHQIELKRSN 663
VL +LD I+ K
Sbjct: 55 GT-VLAGGPHTLDGRTIDPKPCT 76
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 45.4 bits (108), Expect = 2e-06
Identities = 21/48 (43%), Positives = 33/48 (68%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV LS TE+ + + F K+G + E+ LP+DK+T+K +GF +TF
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF 48
Score = 31.2 bits (71), Expect = 0.32
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI V + + + ++ E F FG + + LP + RGF F+ F ++ K+ ++
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKK-TNKRRGFCFITFDSEEPVKKILE 59
>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 = 45.5 bits (108), Expect = 2e-06
Identities = 23/56 (41%), Positives = 32/56 (57%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+FV NLS+ TED+L F + G + V + +++ K KGFA V F E AT A
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56
Score = 44.7 bits (106), Expect = 4e-06
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL+F +TED +R HF + G I V + +D G+ FV F E
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGK-----CKGFAFVDFEEIEFATN 55
Query: 643 ALK 645
ALK
Sbjct: 56 ALK 58
Score = 39.7 bits (93), Expect = 3e-04
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+ F+ + E+ F G ++ VR+ SG +GF FV+F A A+K
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRM-MTFEDSGKCKGFAFVDFEEIEFATNALK- 58
Query: 748 LCQSTHLYGRRLVLEWAE 765
HL GR L +E+ E
Sbjct: 59 ---GKHLNGRALRVEYGE 73
>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 = 45.3 bits (108), Expect = 3e-06
Identities = 25/69 (36%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL T+ +L FEKYGPL V + GFA V F P A A +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRA 55
Query: 398 LDGTVFLGR 406
LDG G
Sbjct: 56 LDGRRICGN 64
Score = 38.4 bits (90), Expect = 7e-04
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ NL +T+ + F+K GP+ SV VAR P P G+ FV+F
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN--P--P------GFAFVEFEDPRDAED 51
Query: 643 ALKVLQNSSL 652
A++ L +
Sbjct: 52 AVRALDGRRI 61
Score = 37.2 bits (87), Expect = 0.002
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 13/81 (16%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFV---RLPKKMVGSGLHRGFGFVEFITKNEAKR 743
K+ V N+ +A + E+E+ F+ +G L+ V R P GF FVEF +A+
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---------GFAFVEFEDPRDAED 51
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
A++AL + G R+ +E +
Sbjct: 52 AVRAL-DGRRICGNRVRVELS 71
Score = 30.3 bits (69), Expect = 0.61
Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+ T+ +L+ +FE+ G + V + G FAF+ + A+ A+ + + +R
Sbjct: 10 RATKRELEDEFEKYGPLRSVWVARNPPG----FAFVEFEDPRDAEDAVRALDGRRICGNR 65
Query: 88 IKVE 91
++VE
Sbjct: 66 VRVE 69
>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 = 45.4 bits (107), Expect = 3e-06
Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRN++ +DL + F +YGP+ +V +P+D T + +GFA + F A A +L
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 399 DGTVFLGRMLHL 410
+ GR + +
Sbjct: 63 NRKWVCGRQIEI 74
Score = 31.5 bits (71), Expect = 0.24
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T+L+++N+ + + +RR F + GPI V V + P G+ ++QF
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRP-----RGFAYIQFEDVRDA 55
Query: 641 NQALKVLQNSSLDEHQIELK 660
AL L + QIE++
Sbjct: 56 EDALYNLNRKWVCGRQIEIQ 75
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 44.9 bits (106), Expect = 3e-06
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV NL +TE+++ KLFEKYG E+ + K KGF + A A
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAKAE 56
Query: 398 LDGTVFLGRMLHL 410
LD G+ L +
Sbjct: 57 LDNMPLRGKQLRV 69
Score = 33.7 bits (77), Expect = 0.037
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S++ V N+P + E+ +LF+ +G+ + + K +GFGF+ T+ A+ A
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD-------KGFGFIRLETRTLAEIA- 53
Query: 746 KALCQSTHLYGRRL 759
KA + L G++L
Sbjct: 54 KAELDNMPLRGKQL 67
Score = 28.7 bits (64), Expect = 1.8
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL + TE+ +R+ F+K G + + + K G+GF++ TR
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDK-----------GFGFIRLETRTLAEI 52
Query: 643 ALKVLQNSSLDEHQIELK 660
A L N L Q+ ++
Sbjct: 53 AKAELDNMPLRGKQLRVR 70
>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 = 45.3 bits (108), Expect = 4e-06
Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TT+++ N+ ++D IR+ +KCG + S R KDP + G+ +GF +F E
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWK--RVKDPST-GKLK--AFGFCEFEDPEGA 55
Query: 641 NQALKVLQNSSLDEHQIELK--RSNRNL 666
+AL++L L ++ +K R L
Sbjct: 56 LRALRLLNGLELGGKKLLVKVDAKTRKL 83
Score = 35.7 bits (83), Expect = 0.008
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV N+ V++D + KL EK G + D T K K F F PE A +A +
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61
Query: 398 LDGTVFLGRMLHL 410
L+G G+ L +
Sbjct: 62 LNGLELGGKKLLV 74
Score = 28.0 bits (63), Expect = 5.4
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V NIP + +L + G++ + R+ K +G + FGF EF A RA+
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRV--KDPSTGKLKAFGFCEFEDPEGALRAL 59
Query: 746 KAL 748
+ L
Sbjct: 60 RLL 62
>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 = 45.1 bits (107), Expect = 4e-06
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 6/76 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T Y+ NL ++ TE+ I+ F+ ++SV + R +P PG+ G+G+ +F R+SL
Sbjct: 3 TAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPR--EPGDPGRL--RGFGYAEFEDRDSLL 57
Query: 642 QALKVLQNSSLDEHQI 657
QAL L + SL +I
Sbjct: 58 QALS-LNDESLKNRRI 72
Score = 39.3 bits (92), Expect = 4e-04
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
N+P+ + +++E F+ + VRLP++ G RGFG+ EF ++ +A+
Sbjct: 8 NLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL 60
Score = 33.1 bits (76), Expect = 0.066
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTF 385
++ NL Y VTE+D+ + F ++ V LP + + + +GF F
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEF 50
Score = 32.4 bits (74), Expect = 0.12
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVR--------TTFLGMAYIGFKDEKNCNKALNK 277
T + NLP V ++D+K +F+ L ++SVR G Y F+D + +AL+
Sbjct: 3 TAYLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL 62
Query: 278 NKSFWKGKQLNI 289
N K +++ +
Sbjct: 63 NDESLKNRRIRV 74
>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 = 44.8 bits (107), Expect = 4e-06
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ +L+ + TE + F GP+ S+ V R D + S+GY +V F +
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCR--DLITRR---SLGYAYVNFQNPADAER 56
Query: 643 ALKVLQNSSLDEHQIELKRSNRN 665
AL L + I + S R+
Sbjct: 57 ALDTLNFDVIKGKPIRIMWSQRD 79
Score = 41.4 bits (98), Expect = 8e-05
Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
+V +L VTE L ++F GP+ + + D T ++ G+A V F P A +A L+
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Query: 400 GTVFLGR 406
V G+
Sbjct: 63 FDVIKGK 69
Score = 33.7 bits (78), Expect = 0.043
Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
E+F G + +R+ + ++ + G+ +V F +A+RA+ L + G+ + +
Sbjct: 17 YEIFSPAGPVLSIRVCRDLI-TRRSLGYAYVNFQNPADAERALDTLNF-DVIKGKPIRIM 74
Query: 763 W 763
W
Sbjct: 75 W 75
Score = 32.5 bits (75), Expect = 0.12
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 229 VKNLPAGVKKKDLKAYFKPL-PLASVRT-------TFLGMAYIGFKDEKNCNKALNK-NK 279
V +L V + L F P P+ S+R LG AY+ F++ + +AL+ N
Sbjct: 4 VGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNF 63
Query: 280 SFWKGKQLNIYKYSKDN 296
KGK + I +D
Sbjct: 64 DVIKGKPIRIMWSQRDP 80
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 44.4 bits (105), Expect = 5e-06
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 338 RIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
R+F+ NL + V+++DL ++F YG LA+++L + V F PE A
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAIN 52
Query: 397 HLDGTVFLGRMLHLIPGKP 415
G + GR LHL KP
Sbjct: 53 CEQGKMIRGRKLHLEVSKP 71
Score = 30.1 bits (68), Expect = 0.62
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 11/77 (14%)
Query: 687 KILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ + N+P + + ++ +F +GEL + L +GFV+F + A+
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQI---------VLKNAYGFVQFDSPESCANAI 51
Query: 746 KALCQSTHLYGRRLVLE 762
Q + GR+L LE
Sbjct: 52 NCE-QGKMIRGRKLHLE 67
Score = 30.1 bits (68), Expect = 0.69
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 583 LYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L+I NL +++ + R F G +A + L YGFVQF + ES
Sbjct: 2 LFIGNLPTKRVSKEDLFRIFSTYGELAQIV-------------LKNAYGFVQFDSPESCA 48
Query: 642 QALKVLQNSSLDEHQIELKRS 662
A+ Q + ++ L+ S
Sbjct: 49 NAINCEQGKMIRGRKLHLEVS 69
>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 = 44.2 bits (105), Expect = 7e-06
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL TVTED L +LF + GP+ L + D +A V + A A Q +
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP---YAFVEYYDHRSAAAALQTM 57
Query: 399 DGTVFLGR 406
+G + LG+
Sbjct: 58 NGRLILGQ 65
Score = 38.4 bits (90), Expect = 8e-04
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ NL+ TED + F + GPI S + R+ Y FV++Y S
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--------YAFVEYYDHRSAAA 52
Query: 643 ALKVL 647
AL+ +
Sbjct: 53 ALQTM 57
Score = 29.6 bits (67), Expect = 1.1
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V N+ + + ELF G +K +L ++ + FVE+ A A++ +
Sbjct: 3 VGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP----YAFVEYYDHRSAAAALQTMN 58
Query: 750 QSTHLYGRRLVLEWA 764
+ G+ + + WA
Sbjct: 59 GR-LILGQEIKVNWA 72
Score = 29.2 bits (66), Expect = 1.3
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+T++ L F + G + +L E +AF+ Y+ A AAL N +
Sbjct: 9 TVTEDLLAELFSQIGPIKSCKL--IREHGNDPYAFVEYYDHRSAAAALQTMNGRLILGQE 66
Query: 88 IKV 90
IKV
Sbjct: 67 IKV 69
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 46.2 bits (109), Expect = 7e-06
Identities = 22/77 (28%), Positives = 39/77 (50%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S ++F+ LS+ + L F +G + + + +D+ET +++GF V F AT A
Sbjct: 34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93
Query: 396 QHLDGTVFLGRMLHLIP 412
+DG GR + + P
Sbjct: 94 SEMDGKELNGRHIRVNP 110
Score = 35.8 bits (82), Expect = 0.029
Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 10/105 (9%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L+I L++ + + S+R F G + V ++ S G+GFV F +
Sbjct: 35 TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGR-----SRGFGFVNFNDEGAA 89
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
A+ + L+ I + N ++ + R +G
Sbjct: 90 TAAISEMDGKELNGRHIRV-----NPANDRPSAPRAYGGGGGYSG 129
Score = 31.5 bits (71), Expect = 0.67
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG--SGLHRGFGFVEFITKNEAKR 743
+K+ + + + + + + F FG+ V K +V +G RGFGFV F + A
Sbjct: 35 TKLFIGGLSWGTDDASLRDAFAHFGD---VVDAKVIVDRETGRSRGFGFVNFNDEGAATA 91
Query: 744 AMKALCQSTHLYGRRLVLEWAEE 766
A+ + L GR + + A +
Sbjct: 92 AISEM-DGKELNGRHIRVNPAND 113
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 44.1 bits (105), Expect = 7e-06
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV LS V E DL + F K G + +V + D+ + ++KG A V F E A L
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-L 60
Query: 399 DGTVFLG 405
G LG
Sbjct: 61 TGQRLLG 67
Score = 32.2 bits (74), Expect = 0.11
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V + + ++ ++ E F G+++ VR+ + S +G +VEF + A+
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRN-SRRSKGVAYVEFYDEESVPLALG- 59
Query: 748 LCQSTHLYGRRL 759
L G+RL
Sbjct: 60 ------LTGQRL 65
Score = 29.1 bits (66), Expect = 1.3
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+++ L+ E + F K G + V + R ++ + S G +V+FY ES+
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRR-----SKGVAYVEFYDEESVP 55
Query: 642 QAL 644
AL
Sbjct: 56 LAL 58
Score = 28.3 bits (64), Expect = 2.6
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 226 TIVVKNLPAGVKKKDLKAYF-KPLPLASVR-------TTFLGMAYIGFKDEKNCNKAL 275
T+ V L V+++DL +F K + VR G+AY+ F DE++ AL
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58
>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 = 44.5 bits (105), Expect = 7e-06
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ NL F E+ + R F KCG I V + R DPK+ + G+ +VQF ++ +
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVR--DPKTN---VGKGFAYVQFKDENAVEK 56
Query: 643 AL 644
AL
Sbjct: 57 AL 58
Score = 34.1 bits (78), Expect = 0.033
Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+FV NL + E+ L ++F K G + V + D +T+ KGFA V F
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQF 48
>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 = 44.3 bits (104), Expect = 8e-06
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T+DS+R HF+K G + V R DP++ S G+GFV + E ++
Sbjct: 5 LFIGGLSFETTDDSLREHFEKWGTLTDCVVMR--DPQTK---RSRGFGFVTYSCVEEVDA 59
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A+ + +D +E KR+
Sbjct: 60 AM-SARPHKVDGRVVEPKRA 78
Score = 43.6 bits (102), Expect = 1e-05
Identities = 19/57 (33%), Positives = 34/57 (59%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++F+ LS+ T+D L + FEK+G L + ++ D +T +++GF VT+ E A
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60
Score = 28.5 bits (63), Expect = 3.3
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
++ T + L+ FE+ GT+TD V ++ + R F F+ Y ++ AA+
Sbjct: 12 FETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 43.9 bits (104), Expect = 9e-06
Identities = 27/69 (39%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
FV NL + + DL +F+ + V L DKETDK KGF V F E +A + D
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62
Query: 400 GTVFLGRML 408
G +F R L
Sbjct: 63 GALFDDRSL 71
Score = 35.0 bits (81), Expect = 0.012
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTT-------FLGMAYIGFKDEKNCNKALNKN 278
T V NLP + DL A FK L + SVR F G Y+ F+D ++ +AL +
Sbjct: 3 TAFVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYD 62
Query: 279 KSFWKGKQLNI 289
+ + + L +
Sbjct: 63 GALFDDRSLRV 73
Score = 32.3 bits (74), Expect = 0.10
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
V N+PF Q +++ +FK +K VRL + + +GF +VEF K A++
Sbjct: 6 VGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDK-ETDKFKGFCYVEFEDVESLKEALE 60
Score = 30.0 bits (68), Expect = 0.68
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 12/68 (17%)
Query: 582 TLYIKNLNFNSTE---DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
T ++ NL FN+ + D+I + + SV + R K+ +F G+ +V+F E
Sbjct: 3 TAFVGNLPFNTVQGDLDAIFKDLS----VKSVRLVRDKET---DKF--KGFCYVEFEDVE 53
Query: 639 SLNQALKV 646
SL +AL+
Sbjct: 54 SLKEALEY 61
>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 = 43.8 bits (104), Expect = 1e-05
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++VRNL + TE+ L +LF +YG + V D +A V F + A +A + +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 399 DGTVFLGRMLHLIPGKP 415
+G G + + KP
Sbjct: 56 NGKELEGSPIEVSLAKP 72
Score = 40.7 bits (96), Expect = 1e-04
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY++NL ++TE+ +R F + G V R K K Y FV F R+ +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGE-----VERVKKIKD--------YAFVHFEERDDAVK 50
Query: 643 ALKVLQNSSLDEHQIEL 659
A++ + L+ IE+
Sbjct: 51 AMEEMNGKELEGSPIEV 67
Score = 40.3 bits (95), Expect = 1e-04
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 11/80 (13%)
Query: 687 KIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+L VRN+P + ++ ELF +GE++ V+ K + FV F +++A +AM
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD---------YAFVHFEERDDAVKAM 52
Query: 746 KALCQSTHLYGRRLVLEWAE 765
+ + L G + + A+
Sbjct: 53 EEM-NGKELEGSPIEVSLAK 71
Score = 34.9 bits (81), Expect = 0.014
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
T+EQL+ F E G V V+ K + +AF+ + D A A++ N + S I+
Sbjct: 14 TEEQLRELFSEYGEVERVK-------KIKDYAFVHFEERDDAVKAMEEMNGKELEGSPIE 66
Query: 90 V 90
V
Sbjct: 67 V 67
>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 = 43.8 bits (104), Expect = 1e-05
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
L + E + F + G + V + +K+T K+ G+ V F E A QA Q L+G
Sbjct: 7 LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGK-- 64
Query: 404 LGRMLHLIPGKPK 416
IP +
Sbjct: 65 ------PIPNTQQ 71
Score = 41.1 bits (97), Expect = 1e-04
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ +L E I F +CG + SV + R K S GYGFV+F T E+
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTG-----KSAGYGFVEFATHEAAE 55
Query: 642 QALK 645
QAL+
Sbjct: 56 QALQ 59
Score = 36.5 bits (85), Expect = 0.005
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ F GE+ V++ + +G G+GFVEF T A++A+++L
Sbjct: 16 IYSAFAECGEVTSVKI-IRNKQTGKSAGYGFVEFATHEAAEQALQSL 61
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 43.8 bits (104), Expect = 1e-05
Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TTLY+ L TE +R HF + G I S+TV ++ FV F TRE+
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ-----------QCAFVTFTTREAA 50
Query: 641 NQALKVLQNS 650
+A + L N
Sbjct: 51 EKAAERLFNK 60
Score = 39.6 bits (93), Expect = 3e-04
Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V + + + ++ + F FGE++ + + + + FV F T+ A++A + L
Sbjct: 6 VGGLGERVTEKDLRDHFYQFGEIRSITVVPR-------QQCAFVTFTTREAAEKAAERLF 58
Query: 750 QSTHLYGRRLVLEWAE 765
+ GRRL L+W
Sbjct: 59 NKLIINGRRLKLKWGR 74
>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 = 43.4 bits (102), Expect = 1e-05
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV NL +TE+D KLFEKYG +EV + ++ +GF + A A
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56
Query: 398 LDGTVFLGRMLHL 410
LDGT+ R L +
Sbjct: 57 LDGTILKNRPLRI 69
Score = 28.7 bits (64), Expect = 1.9
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ V N+P + + ++LF+ +GE V + + RGFGF+ ++ A+ A K
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-------RGFGFIRLESRTLAEIA-K 54
Query: 747 ALCQSTHLYGRRL 759
A T L R L
Sbjct: 55 AELDGTILKNRPL 67
>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 = 43.7 bits (103), Expect = 1e-05
Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 8/83 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++Y+ N+++ ST + + HF CGPI VT+ K P GY +++F TR+S+
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHP-----KGYAYIEFATRDSVE 55
Query: 642 QALKVLQNSSLDEHQIEL--KRS 662
A+ L SS I++ KR+
Sbjct: 56 AAVA-LDESSFRGRVIKVLPKRT 77
Score = 43.7 bits (103), Expect = 1e-05
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V N+ Y T ++L F GP+ V + DK + KG+A + F + +A L
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVAL 60
Query: 399 DGTVFLGRMLHLIP 412
D + F GR++ ++P
Sbjct: 61 DESSFRGRVIKVLP 74
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 43.1 bits (102), Expect = 1e-05
Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI+V NL + E D+ LF KYGP+ + L K + FA V F P A A +
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRG 57
Query: 398 LDGTVFLGRML 408
DG F G L
Sbjct: 58 RDGYDFDGYRL 68
Score = 33.5 bits (77), Expect = 0.038
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+I V N+P ++ ++E+LF +G +K + L + G F FVEF +A+ A++
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGP----PFAFVEFEDPRDAEDAVR 56
Query: 747 A 747
Sbjct: 57 G 57
>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 = 43.5 bits (103), Expect = 1e-05
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV + + TE+DL + F+++G + V + DK T ++KGF V F P A A ++
Sbjct: 3 RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61
Query: 398 LDGT 401
D +
Sbjct: 62 CDKS 65
Score = 31.2 bits (71), Expect = 0.29
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 593 TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQN 649
TE+ +R FK+ G I V++ + K+ G+G+V+F+ +QA L+N
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGES-----KGFGYVKFH---KPSQAAVALEN 61
Score = 30.1 bits (68), Expect = 0.68
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 693 IPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
IP + ++ E FK FG++++V + K +G +GFG+V+F ++A A+
Sbjct: 8 IPKSYTEEDLREKFKEFGDIEYVSIVKDK-NTGESKGFGYVKFHKPSQAAVAL 59
Score = 29.7 bits (67), Expect = 1.1
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTY 82
T+E L+ KF+E G + V + K G+ + F ++ +H+ QA AL+ + ++
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKSF 66
>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 = 43.3 bits (103), Expect = 1e-05
Identities = 18/52 (34%), Positives = 30/52 (57%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
R+FV LS +VTE DL + F ++G +++V + K+ +GFA + E
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52
Score = 37.9 bits (89), Expect = 0.001
Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE-SLN 641
L++ L+ + TE + F + G ++ V + +KKD G+ ++ T E L
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPD-----RGFAYIDLRTSEAQLK 56
Query: 642 QALKVLQNS 650
+ L +
Sbjct: 57 KCKSTLNGT 65
Score = 34.1 bits (79), Expect = 0.027
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF-ITKNEAKRAMK 746
+ V + +S++EE F FG + V + KK +G RGF +++ ++ + K+
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKK-DAGPDRGFAYIDLRTSEAQLKKCKS 60
Query: 747 ALCQSTHLYGRRLVLEWA 764
L + G L +E A
Sbjct: 61 TLNGTKW-KGSVLKIEEA 77
Score = 28.3 bits (64), Expect = 2.7
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIG-YHREDQAQAALDYFNNTYVFSS 86
+T+ L+ +F GTV+DV++ K G R FA+I E Q + N T S
Sbjct: 11 VTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLNGTKWKGS 70
Query: 87 RIKVEK 92
+K+E+
Sbjct: 71 VLKIEE 76
Score = 28.3 bits (64), Expect = 2.9
Identities = 21/78 (26%), Positives = 24/78 (30%), Gaps = 20/78 (25%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPL-----------PLASVRTTFLGMAYIGF----KDEKNC 271
+ V L V + DL+ F A F AYI K C
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGF---AYIDLRTSEAQLKKC 58
Query: 272 NKALNKNKSFWKGKQLNI 289
LN K WKG L I
Sbjct: 59 KSTLNGTK--WKGSVLKI 74
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 43.3 bits (103), Expect = 1e-05
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL-PID----KETDKTKGFALVTFLMPEH 390
S R++V+NLS VTE+DL +F ++ + D E + KG A VTF E
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTE-GRMKGQAFVTFPSEEI 59
Query: 391 ATQAYQHLDGTVFLGR 406
AT+A ++G V G+
Sbjct: 60 ATKALNLVNGYVLKGK 75
Score = 30.6 bits (70), Expect = 0.55
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 27 YKITQEQLKA---KFEEKGTVTDVQLKYT--TEGKFRRFAFIGYHREDQAQAALDYFN 79
++T+E L +F + + TEG+ + AF+ + E+ A AL+ N
Sbjct: 11 KRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKALNLVN 68
Score = 29.8 bits (68), Expect = 0.95
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 13/73 (17%)
Query: 226 TIVVKNLPAGVKKKDLKAYF------KPLPLASVRTTFL------GMAYIGFKDEKNCNK 273
+ VKNL V ++DL F + G A++ F E+ K
Sbjct: 3 RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62
Query: 274 ALNKNKSF-WKGK 285
ALN + KGK
Sbjct: 63 ALNLVNGYVLKGK 75
>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 = 43.3 bits (103), Expect = 2e-05
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 339 IFVRNLSYTVTEDDLTK----LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+++ NL+ + +D+L + LF ++GP+ +++ +T K +G A V F E AT A
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATNA 58
Query: 395 YQHLDGTVFLGRMLHL 410
+ L G F + + +
Sbjct: 59 LRALQGFPFYDKPMRI 74
Score = 34.8 bits (81), Expect = 0.014
Identities = 27/72 (37%), Positives = 34/72 (47%), Gaps = 12/72 (16%)
Query: 582 TLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
TLYI NLN +D ++R F + GP+ + VA K K GQ FV F
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDI-VASKT-LKMRGQ------AFVVFKDV 52
Query: 638 ESLNQALKVLQN 649
ES AL+ LQ
Sbjct: 53 ESATNALRALQG 64
Score = 31.0 bits (71), Expect = 0.34
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 688 ILVRNIPFQAKQSEV----EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ + N+ + K+ E+ LF FG + + K + RG FV F A
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL----KMRGQAFVVFKDVESATN 57
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
A++AL Q Y + + +++A
Sbjct: 58 ALRAL-QGFPFYDKPMRIQYA 77
Score = 29.0 bits (66), Expect = 1.5
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 28 KITQEQLK----AKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
KI +++LK A F + G V D+ T K R AF+ + + A AL
Sbjct: 10 KIKKDELKRSLYALFSQFGPVLDIVASKTL--KMRGQAFVVFKDVESATNALRALQGFPF 67
Query: 84 FSSRIKVE 91
+ ++++
Sbjct: 68 YDKPMRIQ 75
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 11/80 (13%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+TT+++ L+ TED +R F G I V K P PG+ G GFVQF R +
Sbjct: 1 NTTVFVGGLDPAVTEDELRSLFGPFGEIVYV-----KIP--PGK----GCGFVQFVHRAA 49
Query: 640 LNQALKVLQNSSLDEHQIEL 659
A++ LQ + + +I L
Sbjct: 50 AEAAIQQLQGTIIGGSRIRL 69
Score = 40.0 bits (94), Expect = 2e-04
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 8/63 (12%)
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
E+ LF FGE+ +V++P G +G GFV+F+ + A+ A++ L Q T + G R+
Sbjct: 17 ELRSLFGPFGEIVYVKIP---PG----KGCGFVQFVHRAAAEAAIQQL-QGTIIGGSRIR 68
Query: 761 LEW 763
L W
Sbjct: 69 LSW 71
Score = 39.6 bits (93), Expect = 3e-04
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 463 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW 517
+L++LF PFG++ V +PP G V+F+ + A+AA L T + L W
Sbjct: 17 ELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLSW 71
Score = 38.8 bits (91), Expect = 5e-04
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV L VTED+L LF +G + V +P KG V F+ A A Q L
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQQL 57
Query: 399 DGTV 402
GT+
Sbjct: 58 QGTI 61
>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 = 43.6 bits (103), Expect = 2e-05
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 14/94 (14%)
Query: 579 PDTTLYIKNLNFNSTED----SIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
P +++ +L + ++D ++ HF K G + V V R + Y FVQF
Sbjct: 1 PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLR--------DWRQRPYAFVQF 52
Query: 635 YTRESLNQALKVLQNSSLDEHQI--ELKRSNRNL 666
+ AL Q + LD I E + NR L
Sbjct: 53 TNDDDAKNALAKGQGTILDGRHIRCERAKVNRTL 86
Score = 38.2 bits (89), Expect = 0.001
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRR 758
++ V E F +G L FV++ + R + FV+F ++AK A+ A Q T L GR
Sbjct: 20 EAAVTEHFSKYGTLVFVKVLRDWRQ----RPYAFVQFTNDDDAKNAL-AKGQGTILDGRH 74
Query: 759 LVLEWA 764
+ E A
Sbjct: 75 IRCERA 80
Score = 29.3 bits (66), Expect = 1.8
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 31 QEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV 90
+ + F + GT+ V++ R +AF+ + +D A+ AL T + I+
Sbjct: 20 EAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNALAKGQGTILDGRHIRC 77
Query: 91 E 91
E
Sbjct: 78 E 78
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 43.3 bits (102), Expect = 2e-05
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RIFV + + E+DL K F +YG + EV + D+ +KG+ VTF E A + Q
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62
Query: 398 LDGTVFLGRMLHLIP 412
+ F + L++
Sbjct: 63 ANRLCFRDKKLNIGQ 77
Score = 31.3 bits (71), Expect = 0.28
Identities = 16/58 (27%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
++I V I F+ ++++ + F +G +K V++ +G+ +G+GFV F T+ +A++
Sbjct: 3 NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR--AGVSKGYGFVTFETQEDAQK 58
Score = 30.5 bits (69), Expect = 0.49
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ ++F + E+ +R+ F + G + V + + +S GYGFV F T+E
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAG------VSKGYGFVTFETQED--- 55
Query: 643 ALKVLQNS 650
A K+LQ +
Sbjct: 56 AQKILQEA 63
>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 = 42.9 bits (102), Expect = 2e-05
Identities = 20/70 (28%), Positives = 38/70 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++ +L + E +L K F ++G + + L K+T K+KG+A V F PE A + +
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 399 DGTVFLGRML 408
+ + R+L
Sbjct: 62 NNYLLFERLL 71
Score = 34.5 bits (80), Expect = 0.017
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 32 EQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV 90
+L+ F + GTVT ++L + GK + +AF+ + + A+ + NN +F +K
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73
Query: 91 E 91
+
Sbjct: 74 K 74
Score = 34.1 bits (79), Expect = 0.022
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
+ + ++P + E+ + F FG + +RL + +G +G+ FVEF + AK
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSK-KTGKSKGYAFVEFESPEVAK 55
Score = 32.5 bits (75), Expect = 0.092
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
+YI +L E +R++F + G + + ++R K S GY FV+F + E
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKK-----TGKSKGYAFVEFESPE 52
>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 = 43.0 bits (101), Expect = 2e-05
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL VTE+ + +LF + GP+ +V +P DK+ K K FA V F A L
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNLL 62
Query: 399 DGTVFLGRMLHL 410
+G GR L++
Sbjct: 63 NGIKLYGRPLNI 74
Score = 38.0 bits (88), Expect = 0.001
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D TL++ NL+ TE+ I F + GP+ V + + KD K P QF FV F S
Sbjct: 1 DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGK-PKQF-----AFVNFKHEVS 54
Query: 640 LNQALKVLQNSSLDEHQIELK 660
+ A+ +L L + ++
Sbjct: 55 VPYAMNLLNGIKLYGRPLNIQ 75
Score = 34.1 bits (78), Expect = 0.025
Identities = 15/64 (23%), Positives = 33/64 (51%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
K+T+E + F + G V V++ +GK ++FAF+ + E A++ N ++
Sbjct: 12 KVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRP 71
Query: 88 IKVE 91
+ ++
Sbjct: 72 LNIQ 75
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 43.1 bits (102), Expect = 2e-05
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
I++R +P + ++ + G E K VRL ++ +G RGF FVEF++ EA R M+
Sbjct: 5 IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRK-TTGASRGFAFVEFMSLEEATRWME 63
Query: 747 A 747
Sbjct: 64 L 64
Score = 38.5 bits (90), Expect = 8e-04
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLA-EVILPIDKETDKTKGFALVTFLMPEHATQ 393
+ I +R L +VTE+D+ +G +V L K T ++GFA V F+ E AT+
Sbjct: 1 PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60
Query: 394 AYQHLDGTVFLGR 406
+ G + L
Sbjct: 61 WMELNQGKLQLQD 73
Score = 30.8 bits (70), Expect = 0.49
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
P+ T+ ++ L + TE+ IR G V + R+K G S G+ FV+F +
Sbjct: 1 PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTT---GA--SRGFAFVEFMSL 55
Query: 638 E 638
E
Sbjct: 56 E 56
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 43.0 bits (101), Expect = 2e-05
Identities = 21/61 (34%), Positives = 36/61 (59%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + + ED+L LFEK GP+ ++ L +D + + +G+A +TF E A +A +
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63
Query: 399 D 399
D
Sbjct: 64 D 64
Score = 35.7 bits (82), Expect = 0.009
Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G+++ V IP + E+ LF+ G + +RL + SG +RG+ F+ F K A+ A
Sbjct: 1 GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPL-SGQNRGYAFITFCGKEAAQEA 59
Query: 745 MKALCQS 751
+K LC +
Sbjct: 60 VK-LCDN 65
Score = 30.3 bits (68), Expect = 0.62
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T +++ + + ED + F+K GPI + + DP S GQ + GY F+ F +E+
Sbjct: 2 TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLM--MDPLS-GQ--NRGYAFITFCGKEAA 56
Query: 641 NQALKVLQN 649
+A+K+ N
Sbjct: 57 QEAVKLCDN 65
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 43.2 bits (102), Expect = 2e-05
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL--------AEVILPIDKETDKTKGFALVTFLMPEH 390
+FV NL TE DL + F G + ++ L DK+T + KG A VT+ P
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 391 ATQAYQHLDGTVFLGRML 408
A+ A + + F+G +
Sbjct: 61 ASAAIEWFNNKDFMGNTI 78
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 42.6 bits (100), Expect = 2e-05
Identities = 28/73 (38%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV NL +TED+ KLF KYG EV + +K KGF + A A
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56
Query: 398 LDGTVFLGRMLHL 410
LD T GR L +
Sbjct: 57 LDDTPMRGRQLRV 69
Score = 28.7 bits (64), Expect = 2.3
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ V N+P + E ++LF +GE V + K +GFGF++ ++ A+ A K
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINKG-------KGFGFIKLESRALAEIA-K 54
Query: 747 ALCQSTHLYGRRL 759
A T + GR+L
Sbjct: 55 AELDDTPMRGRQL 67
Score = 26.8 bits (59), Expect = 8.9
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 16/72 (22%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL + TED ++ F K G V + + K G+GF++ +R
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFINKGK-----------GFGFIKLESR----- 47
Query: 643 ALKVLQNSSLDE 654
AL + + LD+
Sbjct: 48 ALAEIAKAELDD 59
>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 = 42.8 bits (101), Expect = 2e-05
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++V +P++ + ++++ F FGEL V++ KK +G +GFGFV F + + +K
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQV-KKDPKTGQSKGFGFVRF---ADYEDQVK 56
Query: 747 ALCQSTHLYGRRL 759
L Q + GR
Sbjct: 57 VLSQRHMIDGRWC 69
Score = 41.2 bits (97), Expect = 1e-04
Identities = 18/49 (36%), Positives = 24/49 (48%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
V L + TE DL F +G L V + D +T ++KGF V F E
Sbjct: 4 VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYE 52
Score = 38.1 bits (89), Expect = 0.001
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L + L + +TE ++ +F G + V V KKDPK+ GQ S G+GFV+F E
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQV--KKDPKT-GQ--SKGFGFVRFADYED--- 53
Query: 643 ALKVLQNS-SLDEHQIELK 660
+KVL +D ++K
Sbjct: 54 QVKVLSQRHMIDGRWCDVK 72
Score = 28.1 bits (63), Expect = 3.4
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 479
++V LP++T DLK F FG+L V V
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQV 31
>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 = 42.6 bits (101), Expect = 2e-05
Identities = 27/78 (34%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 339 IFVRNLS-YTVTEDDLTKLFEKYGPLAEV-ILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
+ V NL+ VT D L LF YG + V IL K+T AL+ P+ A A
Sbjct: 2 LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDT------ALIQMADPQQAQTALT 55
Query: 397 HLDGTVFLGRMLHLIPGK 414
HL+G G+ L + K
Sbjct: 56 HLNGIRLHGKKLRVTLSK 73
Score = 27.2 bits (61), Expect = 6.7
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 12/75 (16%)
Query: 449 IILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGI------TGLVEFLQKNQAKAAFN 501
++LV NL P L LF +GD+ RV I T L++ QA+ A
Sbjct: 1 VLLVSNLNEEMVTPDALFTLFGVYGDVVRV-----KILFNKKDTALIQMADPQQAQTALT 55
Query: 502 SLAYTKFKEVPLYLE 516
L + L +
Sbjct: 56 HLNGIRLHGKKLRVT 70
>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 = 42.2 bits (100), Expect = 3e-05
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV NL T ++L LFEKYG V E D K + V E A A +
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGT---VT-----ECDVVKNYGFVHMEEEEDAEDAIKA 52
Query: 398 LDGTVFLGRMLH 409
L+G F+G+ ++
Sbjct: 53 LNGYEFMGKRIN 64
Score = 39.9 bits (94), Expect = 2e-04
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 30 TQEQLKAKFEEKGTVT--DVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
T E+L+A FE+ GTVT DV + + F+ E+ A+ A+ N R
Sbjct: 12 TSEELRALFEKYGTVTECDV---------VKNYGFVHMEEEEDAEDAIKALNGYEFMGKR 62
Query: 88 IKVE 91
I VE
Sbjct: 63 INVE 66
Score = 38.4 bits (90), Expect = 6e-04
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V N+P E+ LF+ +G + + + +GFV + +A+ A+K
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYG---------TVTECDVVKNYGFVHMEEEEDAEDAIK 51
Query: 747 ALCQSTHLYGRRLVLE 762
AL G+R+ +E
Sbjct: 52 AL-NGYEFMGKRINVE 66
Score = 30.7 bits (70), Expect = 0.40
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFG 472
+ V NLP T +L+ALFE +G
Sbjct: 2 LFVGNLPDATTSEELRALFEKYG 24
Score = 29.1 bits (66), Expect = 1.1
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 13/75 (17%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL +T + +R F+K G + V + YGFV E
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------------YGFVHMEEEEDAED 48
Query: 643 ALKVLQNSSLDEHQI 657
A+K L +I
Sbjct: 49 AIKALNGYEFMGKRI 63
>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 = 42.6 bits (100), Expect = 3e-05
Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL V E+ L +LF + GPL +V + DKE K K F V F E A L
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62
Query: 399 DGTVFLGR 406
+G GR
Sbjct: 63 NGIRLYGR 70
Score = 38.8 bits (90), Expect = 7e-04
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D TL++ NL E+ + F + GP+ VT+ + K+ K +GFV F ES
Sbjct: 1 DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPK------SFGFVCFKHSES 54
Query: 640 LNQALKVL 647
+ A+ +L
Sbjct: 55 VPYAIALL 62
Score = 27.6 bits (61), Expect = 5.3
Identities = 16/63 (25%), Positives = 29/63 (46%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++ +E L F + G +T V + EGK + F F+ + + A+ N ++
Sbjct: 12 RVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLNGIRLYGRP 71
Query: 88 IKV 90
IKV
Sbjct: 72 IKV 74
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 42.8 bits (100), Expect = 3e-05
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV +LS +T +D+ F +G +++ + D T K+KG+ V+F A A H+
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 399 DGTVFLGRML 408
G GR +
Sbjct: 64 GGQWLGGRQI 73
Score = 34.7 bits (79), Expect = 0.017
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V ++ + +++ F FG++ R+ K M +G +G+GFV F K +A+ A+
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMA-TGKSKGYGFVSFYNKLDAENAIVH 62
Query: 748 LCQSTHLYGRRLVLEWA 764
+ L GR++ WA
Sbjct: 63 M-GGQWLGGRQIRTNWA 78
Score = 32.0 bits (72), Expect = 0.15
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ +L+ T + I+ F P ++ AR + G+ S GYGFV FY +
Sbjct: 4 VFVGDLSPEITTEDIKSAF---APFGKISDARVVKDMATGK--SKGYGFVSFYNKLDAEN 58
Query: 643 ALKVLQNSSLDEHQIELKRSNR 664
A+ + L QI + R
Sbjct: 59 AIVHMGGQWLGGRQIRTNWATR 80
>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 = 42.4 bits (100), Expect = 3e-05
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 11/81 (13%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV-ARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T+Y + ++R F+ CGP+ VT+ +R P + F+ F E+
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP----------HAFITFENLEAA 50
Query: 641 NQALKVLQNSSLDEHQIELKR 661
A++ L +S+D + I+++R
Sbjct: 51 QLAIETLNGASVDGNCIKVQR 71
Score = 39.3 bits (92), Expect = 4e-04
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++ + D+ +LFE GP+ +V + + + A +TF E A A +
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56
Query: 398 LDGTVFLGRML 408
L+G G +
Sbjct: 57 LNGASVDGNCI 67
Score = 32.0 bits (73), Expect = 0.14
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ P S+V+ LF+ G ++ V + + V + F+ F A+ A++
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV-----QPHAFITFENLEAAQLAIET 56
Query: 748 LCQSTHLYGRRLVLE 762
L + G + ++
Sbjct: 57 L-NGASVDGNCIKVQ 70
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 42.3 bits (99), Expect = 3e-05
Identities = 23/56 (41%), Positives = 33/56 (58%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
IFV + + ED+L LFEK GP+ ++ L +D T +G+A VTF E A +A
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59
Score = 38.1 bits (88), Expect = 0.001
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G++I V IP + E+ LF+ G + +RL + +GL+RG+ FV F TK A+ A
Sbjct: 1 GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPL-TGLNRGYAFVTFCTKEAAQEA 59
Query: 745 MKALCQS 751
+K L +
Sbjct: 60 VK-LYNN 65
Score = 35.0 bits (80), Expect = 0.016
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T +++ + + ED + F+K GPI + + DP + L+ GY FV F T+E+
Sbjct: 2 TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLM--MDPLTG---LNRGYAFVTFCTKEAA 56
Query: 641 NQALKVLQNSSL 652
+A+K+ N +
Sbjct: 57 QEAVKLYNNHEI 68
Score = 28.0 bits (62), Expect = 3.7
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 31 QEQLKAKFEEKGTVTDVQLKYTT-EGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+++L FE+ G + D++L G R +AF+ + ++ AQ A+ +NN + +
Sbjct: 15 EDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLYNNHEIRPGK 72
>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 = 42.3 bits (100), Expect = 3e-05
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
++FV L+ +TE+DL + F ++G + +V +P + FA VTF PE A
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVA 50
Score = 35.7 bits (83), Expect = 0.007
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 11/81 (13%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V + + ++ + F FGE+ V +PK R F FV F A+
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF------RAFAFVTFADPEVAQS-- 52
Query: 746 KALCQSTH-LYGRRLVLEWAE 765
LC H + G + + AE
Sbjct: 53 --LCGEDHIIKGVSVHVSNAE 71
Score = 27.2 bits (61), Expect = 5.8
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQ 72
+T+E L+ F + G VTDV + FR FAF+ + + AQ
Sbjct: 11 DMTEEDLRQYFSQFGEVTDVYIP----KPFRAFAFVTFADPEVAQ 51
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 42.2 bits (100), Expect = 3e-05
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 689 LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
LVR++P + + + E+L K FG + M G + F F + A +A+ L
Sbjct: 3 LVRHLPPELSEDDKEDLLKHFGASSV----RVMSRRGKLKNTAFATFDNEQAASQALSRL 58
Query: 749 CQSTHLYGRRLVLEWA 764
Q L G+RLV+E+A
Sbjct: 59 HQLKIL-GKRLVVEYA 73
Score = 31.4 bits (72), Expect = 0.20
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+ VR+L ++EDD L + +G A + + K K A TF + A+QA
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFG--ASSVRVM-SRRGKLKNTAFATFDNEQAASQALSR 57
Query: 398 LDGTVFLGRML 408
L LG+ L
Sbjct: 58 LHQLKILGKRL 68
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 42.0 bits (99), Expect = 4e-05
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV L VTE++ + F ++G + + L D +T +++GF VTF
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF 48
Score = 30.4 bits (69), Expect = 0.55
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRA 744
KI V +P + E +E F FG++ +L M +G RGFGFV F +++ +R
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQL---MQDHDTGRSRGFGFVTFDSESAVERV 57
Query: 745 MKA 747
A
Sbjct: 58 FSA 60
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. 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 = 84
Score = 42.5 bits (100), Expect = 4e-05
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET--DKTKGFALVTFLMPEHATQAY 395
++FV + + +E DL +LFE+YG + ++ + D+ ++KG VTF + A +A
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62
Query: 396 QHLDGTVFLGRMLHLIPGKP 415
L L M H I KP
Sbjct: 63 NALHNMKTLPGMHHPIQMKP 82
Score = 38.6 bits (90), Expect = 9e-04
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 594 EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQN 649
E +R F++ G + + V R + S S G FV FYTR++ +A L N
Sbjct: 15 EKDLRELFEQYGAVYQINVLRDR---SQNPPQSKGCCFVTFYTRKAALEAQNALHN 67
Score = 31.7 bits (72), Expect = 0.21
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+ V IP + ++ ELF+ +G + + L + +G FV F T+ A A
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62
Query: 746 KAL 748
AL
Sbjct: 63 NAL 65
>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 = 42.4 bits (99), Expect = 4e-05
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R + K S G+GFV + + E ++
Sbjct: 5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKR-----SRGFGFVTYSSVEEVDA 59
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A+ + +D +E KR+
Sbjct: 60 AMNA-RPHKVDGRVVEPKRA 78
Score = 39.3 bits (91), Expect = 4e-04
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60
Score = 34.7 bits (79), Expect = 0.020
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 12 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62
Score = 28.1 bits (62), Expect = 3.6
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELK---FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
K+ + + F+ + F+ +G L +R P + RGFGFV + + E
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN----TKRSRGFGFVTYSSVEEVDA 59
Query: 744 AMKA 747
AM A
Sbjct: 60 AMNA 63
>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 = 42.2 bits (100), Expect = 4e-05
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
V N P QS++ +LF+ +GE+ +R P R F +V+F + A A+ L
Sbjct: 5 VTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNK--TRRFCYVQFTSPESAAAAVALL 61
Score = 37.9 bits (89), Expect = 0.001
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFN 79
Q ++ FE+ G + ++ K RRF ++ + + A AA+ N
Sbjct: 13 DQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLN 62
Score = 37.9 bits (89), Expect = 0.001
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V N + + D+ LFE+YG + + P +KT+ F V F PE A A L
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRFP-SLRFNKTRRFCYVQFTSPESAAAAVALL 61
Query: 399 DGT 401
+G
Sbjct: 62 NGK 64
Score = 34.5 bits (80), Expect = 0.019
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 18/89 (20%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG------FVQF 634
+TL++ N + + IR F++ G I S+ +F S+ + +VQF
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSI------------RFPSLRFNKTRRFCYVQF 48
Query: 635 YTRESLNQALKVLQNSSLDEHQIELKRSN 663
+ ES A+ +L + +++ +K S+
Sbjct: 49 TSPESAAAAVALLNGKLGEGYKLVVKISD 77
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 41.9 bits (99), Expect = 4e-05
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 10/78 (12%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ + +P++A++ +VE FK +G ++ + L GFGFVEF +A A+
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREIN---------LKNGFGFVEFEDPRDADDAVY 51
Query: 747 ALCQSTHLYGRRLVLEWA 764
L L G R+++E A
Sbjct: 52 EL-NGKELCGERVIVEHA 68
Score = 38.8 bits (91), Expect = 5e-04
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+++ L Y E D+ + F+ YG + E+ L GF V F P A A
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52
Query: 398 LDGTVFLG 405
L+G G
Sbjct: 53 LNGKELCG 60
Score = 31.5 bits (72), Expect = 0.21
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 13/52 (25%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+YI L + + E + R FK G I + L G+GFV+F
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREIN-------------LKNGFGFVEF 40
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 41.8 bits (99), Expect = 5e-05
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++IKNL+ + ++ F G I S VA ++ S GYGFV F T E+ +
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGS------KGYGFVHFETEEAAVR 58
Query: 643 ALKVLQNSSLDEHQI 657
A++ + L++ ++
Sbjct: 59 AIEKVNGMLLNDKKV 73
Score = 37.5 bits (88), Expect = 0.002
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVIL---PIDKETDKTKGFALVTFLMPEHATQ 393
G IF++NL ++ L F +G IL E +KG+ V F E A +
Sbjct: 3 GNIFIKNLDKSIDNKALYDTFSAFGN----ILSCKVATDENGGSKGYGFVHFETEEAAVR 58
Query: 394 AYQHLDGTVFLGR 406
A + ++G + +
Sbjct: 59 AIEKVNGMLLNDK 71
Score = 32.1 bits (74), Expect = 0.13
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRAM 745
I ++N+ + + F AFG + L K+ +G +G+GFV F T+ A RA+
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNI----LSCKVATDENGGSKGYGFVHFETEEAAVRAI 60
Query: 746 KAL 748
+ +
Sbjct: 61 EKV 63
>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 = 42.0 bits (98), Expect = 5e-05
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY++NL ++TE++I+ F K P V + +D Y FV F+ RE
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-----------YAFVHFFNREDAVA 52
Query: 643 ALKVLQNSSLDEHQIEL 659
A+ V+ +D IE+
Sbjct: 53 AMSVMNGKCIDGASIEV 69
Score = 32.3 bits (73), Expect = 0.11
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++VRNL + TE+ + F K+ P + K + +A V F E A A +
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVV------ERVKKLRDYAFVHFFNREDAVAAMSVM 57
Query: 399 DGTVFLGRMLHLIPGKP 415
+G G + + KP
Sbjct: 58 NGKCIDGASIEVTLAKP 74
Score = 29.6 bits (66), Expect = 1.0
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 30 TQEQLKAKFE--EKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
T+E +KA+F + G V V+ K R +AF+ + + A AA+ N + +
Sbjct: 14 TEETIKAEFNKFKPGVVERVK-------KLRDYAFVHFFNREDAVAAMSVMNGKCIDGAS 66
Query: 88 IKV 90
I+V
Sbjct: 67 IEV 69
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), 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-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 41.8 bits (99), Expect = 5e-05
Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 353 LTKLFEKYGPLAEVIL--PIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
L K+F K+G V + P+D ET KTKG+A V F PE A +A + L+G
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATPEEAKEAVKALNGYKL 75
Score = 30.6 bits (70), Expect = 0.60
Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 34 LKAKFEEKG--TVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
L+ F + G + + + GK + +AF+ + ++A+ A+ N
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 72
Score = 29.9 bits (68), Expect = 0.96
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 685 GSKILVRNIPFQAKQSEVEEL-------FKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 737
+ ++V +P + ++E+L F FG K V + + +G +G+ FVEF T
Sbjct: 1 DNVVVVDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFAT 59
Query: 738 KNEAKRAMKAL 748
EAK A+KAL
Sbjct: 60 PEEAKEAVKAL 70
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 41.5 bits (97), Expect = 5e-05
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++ V N+S + T +L FE+YGP+ E D K +A V E A +A +
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIEC--------DIVKDYAFVHMERAEDAVEAIRG 53
Query: 398 LDGTVFLGRMLHL 410
LD T F G+ +H+
Sbjct: 54 LDNTEFQGKRMHV 66
Score = 30.4 bits (68), Expect = 0.44
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
T ++L+AKFEE G V + + + +AF+ R + A A+ +NT R+
Sbjct: 13 TNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMH 65
Query: 90 VE 91
V+
Sbjct: 66 VQ 67
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 46.0 bits (109), Expect = 6e-05
Identities = 23/95 (24%), Positives = 34/95 (35%), Gaps = 7/95 (7%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
RI++ NL + ED + +L E +G L L D T +KG+A + P A
Sbjct: 294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVA 353
Query: 395 YQHLDGTVFLGRMLH-------LIPGKPKENEGNV 422
L+G LH + G
Sbjct: 354 IAALNGKDTGDNKLHVQRACVGANQATIDTSNGMA 388
Score = 45.7 bits (108), Expect = 8e-05
Identities = 38/192 (19%), Positives = 73/192 (38%), Gaps = 23/192 (11%)
Query: 578 EPDTT-----LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS-MGYGF 631
+ T LY+ + E+++ F A S + F
Sbjct: 168 QQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAF 227
Query: 632 VQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN-------VAKQT 684
++F T E A+ L + ++++R + + T + N V K
Sbjct: 228 LEFRTVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLV 286
Query: 685 GS--------KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
S +I + N+P + +++EL ++FG+LK L K + +GL +G+ F E+
Sbjct: 287 NSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKD-IATGLSKGYAFCEYK 345
Query: 737 TKNEAKRAMKAL 748
+ A+ AL
Sbjct: 346 DPSVTDVAIAAL 357
Score = 32.9 bits (75), Expect = 0.64
Identities = 36/162 (22%), Positives = 53/162 (32%), Gaps = 41/162 (25%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKET------------DKTKGFALVTF 385
R++V + E+ + F ++++ +K K FA + F
Sbjct: 177 RLYVGGIPPEFVEEAVVDFFN------DLMIATGYHKAEDGKHVSSVNINKEKNFAFLEF 230
Query: 386 LMPEHATQAYQHLDGTVF------LGRMLHLIP-------GKPKENEGNVDGKVHCCISE 432
E AT A LD ++ + R IP K + N S
Sbjct: 231 RTVEEATFAMA-LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNST 289
Query: 433 RKLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 474
LD SK I + NLP +K L E FGDL
Sbjct: 290 TVLD---------SKDRIYIGNLPLYLGEDQIKELLESFGDL 322
Score = 29.1 bits (65), Expect = 9.4
Identities = 33/198 (16%), Positives = 70/198 (35%), Gaps = 31/198 (15%)
Query: 577 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYT 636
+ +YI NL ED I+ + G + + + K LS GY F ++
Sbjct: 292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLI-----KDIATGLSKGYAFCEYKD 346
Query: 637 RESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQ------------- 683
+ A+ L ++++ ++R+ + V
Sbjct: 347 PSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGG 406
Query: 684 TGSKIL-VRNIPFQAK---QSEVEELFKA-------FGELKFVRLPKKMV--GSGLHRGF 730
+K++ + N+ E EE+++ +G L + +P+ S G
Sbjct: 407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGK 466
Query: 731 GFVEFITKNEAKRAMKAL 748
F+E+ A++AM+ +
Sbjct: 467 VFLEYADVRSAEKAMEGM 484
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 41.5 bits (98), Expect = 6e-05
Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+F+ +L T+ DL +LF +G + + +DK T ++K F V++ PE A A + +
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 399 DG 400
+G
Sbjct: 61 NG 62
Score = 32.2 bits (74), Expect = 0.13
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 25 FIYKITQE----QLKAKFEEKGTVTD--VQLKYTTEGKFRRFAFIGYHREDQAQAALDYF 78
FIY + E L F G V V + T G+ + F F+ Y + AQAA+
Sbjct: 2 FIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNT-GQSKCFGFVSYDNPESAQAAIKAM 60
Query: 79 NNTYVFSSRIKVE 91
N V R+KV+
Sbjct: 61 NGFQVGGKRLKVQ 73
Score = 31.5 bits (72), Expect = 0.25
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ + ++P + ++ +LF FG + ++ G + FGFV + A+ A+KA
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNT-GQSKCFGFVSYDNPESAQAAIKA 59
Query: 748 L--CQSTHLYGRRL 759
+ Q + G+RL
Sbjct: 60 MNGFQ---VGGKRL 70
Score = 27.2 bits (61), Expect = 6.1
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 10/79 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I +L T+ + + F G + S V K+ S +GFV + ES
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTG-----QSKCFGFVSYDNPESAQA 55
Query: 643 ALKVLQNSSLDEHQIELKR 661
A+K ++ Q+ KR
Sbjct: 56 AIKA-----MNGFQVGGKR 69
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 41.9 bits (99), Expect = 6e-05
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+F+ +VTEDDL + F +G + ++ + DK+T ++KG A V F A +A +
Sbjct: 5 RLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEE 63
Query: 398 LDGTV 402
++G
Sbjct: 64 MNGKC 68
Score = 31.1 bits (71), Expect = 0.39
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 593 TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL 652
TED +R F G I + V + K K S G +V+F S +A++ + L
Sbjct: 15 TEDDLREAFAPFGEIQDIWVVKDKQTKE-----SKGVAYVKFAKASSAARAMEEMNGKCL 69
Query: 653 DEHQIELK 660
LK
Sbjct: 70 GGDTKPLK 77
Score = 28.5 bits (64), Expect = 3.6
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 697 AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ ++ E F FGE++ + + K + +G +V+F + A RAM+ +
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQ-TKESKGVAYVKFAKASSAARAMEEM 64
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 41.9 bits (99), Expect = 6e-05
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RIFV + TE++L F ++G + +V + D+ +KG+ VTF E A +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKI-LA 61
Query: 398 LDGTVFLGRMLHLIP 412
+ F G+ L++ P
Sbjct: 62 MGNLNFRGKKLNIGP 76
Score = 38.4 bits (90), Expect = 0.001
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++I V IP + E+ + F FG +K V++ +G+ +G+GFV F T+ +A++ +
Sbjct: 3 NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR--AGVSKGYGFVTFETQEDAEKIL 60
Query: 746 K 746
Sbjct: 61 A 61
Score = 33.8 bits (78), Expect = 0.043
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 9/71 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
+++ + ++TE+ +R F + G + V + + G S GYGFV F T+E
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA----GV--SKGYGFVTFETQE--- 54
Query: 642 QALKVLQNSSL 652
A K+L +L
Sbjct: 55 DAEKILAMGNL 65
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 41.6 bits (98), Expect = 7e-05
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA----TQA 394
+F+ LS+ T + L + F K+G + E ++ D T +++GF VTF P Q
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 395 YQHLDG 400
LDG
Sbjct: 61 PHELDG 66
Score = 35.9 bits (83), Expect = 0.007
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++I L++ +T + +R +F K G I V R DP + S G+GFV F S++
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMR--DPTTK---RSRGFGFVTFSDPASVD- 54
Query: 643 ALKVLQNSS--LDEHQIELK 660
KVL LD +I+ K
Sbjct: 55 --KVLAQGPHELDGKKIDPK 72
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 41.6 bits (97), Expect = 7e-05
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV LS +D+ + FE++G + + +L DK T++ +GF VTF
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 42.2 bits (100), Expect = 7e-05
Identities = 27/97 (27%), Positives = 54/97 (55%), Gaps = 16/97 (16%)
Query: 686 SKILVRNIPFQAKQSEVEELF-KAFG-----------ELKFVRLPKKMVGSGLHR--GFG 731
+++ +RN+P + +++ELF KA ++K +R K++ +G + G+G
Sbjct: 1 TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60
Query: 732 FVEFITKNEAKRAMKALCQSTHLYG--RRLVLEWAEE 766
FVEF A +A++AL + ++G +R ++E+A E
Sbjct: 61 FVEFTNHEHALKALRALNNNPEIFGPDKRPIVEFAIE 97
Score = 34.5 bits (80), Expect = 0.030
Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 581 TTLYIKNLNFNSTEDSIRRHF---------KKCGPIASVTVARKKDPKSP-GQFLSMGYG 630
T L I+NL + E ++ F KK I V + R P G+ S GYG
Sbjct: 1 TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60
Query: 631 FVQFYTRESLNQALKVLQN 649
FV+F E +AL+ L N
Sbjct: 61 FVEFTNHEHALKALRALNN 79
Score = 31.0 bits (71), Expect = 0.51
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKY---------GPLAEVILPIDKE------TDKTKGFAL 382
R+ +RNL +V E L +LF K + +V + D + K+KG+
Sbjct: 2 RLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGF 61
Query: 383 VTFLMPEHATQAYQHL 398
V F EHA +A + L
Sbjct: 62 VEFTNHEHALKALRAL 77
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 41.5 bits (97), Expect = 7e-05
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL Y V L ++F G + + DK+ K++G VTF P A QA
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAISMF 61
Query: 399 DGTVFLGRMLHL 410
+G + R +H+
Sbjct: 62 NGQLLFDRPMHV 73
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has been
implied in regulating DNA replication, transcription,
apoptosis induction, and cell-cycle movement, via the
interaction with C-MYC, the product of protooncogene
c-myc. MSSP-2 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 75
Score = 41.3 bits (96), Expect = 8e-05
Identities = 22/72 (30%), Positives = 34/72 (47%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+++R L T+ DL KL + YG + +DK T+K KG+ V F P A +A
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
Query: 396 QHLDGTVFLGRM 407
L + +M
Sbjct: 61 TALKASGVQAQM 72
>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 = 41.4 bits (97), Expect = 8e-05
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ NL+ TED +++ F+ GP+ +V + K+ K + YGFV+++
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNK------GVNYGFVEYHQSHDAEI 54
Query: 643 ALKVLQNSSLDEHQIEL 659
AL+ L ++ ++I +
Sbjct: 55 ALQTLNGRQIENNEIRV 71
Score = 37.5 bits (87), Expect = 0.002
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL VTED L ++F+ GP+ V + DK +K + V + A A Q L
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 399 DG 400
+G
Sbjct: 60 NG 61
Score = 34.1 bits (78), Expect = 0.030
Identities = 17/63 (26%), Positives = 33/63 (52%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
++T++ LK F+ G V +V++ K + F+ YH+ A+ AL N + ++
Sbjct: 9 RVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLNGRQIENNE 68
Query: 88 IKV 90
I+V
Sbjct: 69 IRV 71
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1) and has been implicated in the maintenance of
the stem-cell state, differentiation, and tumorigenesis.
It translationally regulates the expression of a
mammalian numb gene by binding to the 3'-untranslated
region of mRNA of Numb, encoding a membrane-associated
inhibitor of Notch signaling, and further influences
neural development. It represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 74
Score = 41.2 bits (96), Expect = 8e-05
Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV LS T +D+ + FE++G + + +L DK T++ +GF VTF
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>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 = 40.8 bits (96), Expect = 9e-05
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ + + STED IR +F CG I + + D G+F G F+ F T E+ +
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPD---TGRF--RGIAFITFKTEEAAKR 55
Query: 643 ALK 645
AL
Sbjct: 56 ALA 58
Score = 39.6 bits (93), Expect = 2e-04
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V + Y TED++ F G + E+ L +T + +G A +TF E A +A L
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59
Query: 399 DGTVFLGRML 408
DG GR L
Sbjct: 60 DGEDMGGRFL 69
Score = 36.6 bits (85), Expect = 0.003
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V IP+ + + E+ F GE++ + L +G RG F+ F T+ AKRA+
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDL-MTFPDTGRFRGIAFITFKTEEAAKRALA- 58
Query: 748 LCQSTHLYGRRLVLE 762
+ GR L +E
Sbjct: 59 -LDGEDMGGRFLKVE 72
Score = 35.0 bits (81), Expect = 0.010
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLK-YTTEGKFRRFAFIGYHREDQAQAAL 75
Y T++++++ F G + ++ L + G+FR AFI + E+ A+ AL
Sbjct: 8 YYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL 57
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 41.2 bits (96), Expect = 1e-04
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV +LS +T DD+ F +G +++ + D T K+KG+ V+F A A Q +
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 399 DGTVFLGRML 408
G GR +
Sbjct: 64 GGQWLGGRQI 73
Score = 36.2 bits (83), Expect = 0.005
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V ++ + +++ F FG + R+ K M +G +G+GFV F K +A+ A++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAENAIQQ 62
Query: 748 LCQSTHLYGRRLVLEWA 764
+ L GR++ WA
Sbjct: 63 M-GGQWLGGRQIRTNWA 78
Score = 29.3 bits (65), Expect = 1.5
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ +L+ T D I+ F P ++ AR + G+ S GYGFV F+ +
Sbjct: 4 VFVGDLSPEITTDDIKAAF---APFGRISDARVVKDMATGK--SKGYGFVSFFNKWDAEN 58
Query: 643 ALKVLQNSSLDEHQIELKRSNR 664
A++ + L QI + R
Sbjct: 59 AIQQMGGQWLGGRQIRTNWATR 80
>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 = 41.2 bits (96), Expect = 1e-04
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +TE+S+R ++++ G + V R DP S S G+GFV F ++
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMR--DPASK---RSRGFGFVTFSCMNEVDA 59
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A+ + ++D +E KR+
Sbjct: 60 AMAA-RPHTIDGRVVEPKRA 78
Score = 39.7 bits (92), Expect = 4e-04
Identities = 15/48 (31%), Positives = 30/48 (62%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++F+ LS+ TE+ L +E++G L + ++ D + +++GF VTF
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51
Score = 29.3 bits (65), Expect = 1.6
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELK---FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
K+ + + F+ + + ++ +G+L +R P S RGFGFV F NE
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP----ASKRSRGFGFVTFSCMNEVDA 59
Query: 744 AMKA 747
AM A
Sbjct: 60 AMAA 63
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a ubiquitously
expressed Hu family member. It has a variety of
biological functions mostly related to the regulation of
cellular response to DNA damage and other types of
stress. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 41.2 bits (96), Expect = 1e-04
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++ +A+RA+
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVNAKDAERAI 60
Query: 746 KAL 748
L
Sbjct: 61 NTL 63
Score = 33.5 bits (76), Expect = 0.046
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D +R F G + S + R K S+GYGFV + +
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVNAKDA 56
Query: 641 NQALKVLQNSSLDEHQIEL 659
+A+ L L I++
Sbjct: 57 ERAINTLNGLRLQSKTIKV 75
Score = 31.6 bits (71), Expect = 0.25
Identities = 18/77 (23%), Positives = 34/77 (44%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L +T+D+L LF G + L DK + G+ V ++ + A +A L
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63
Query: 399 DGTVFLGRMLHLIPGKP 415
+G + + + +P
Sbjct: 64 NGLRLQSKTIKVSYARP 80
>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 = 41.0 bits (96), Expect = 1e-04
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 7/80 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++I LN+ +T+DS+R +F + G + TV R S G+GF+ F +S+N+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMR-----DSATGRSRGFGFLTFKKPKSVNE 55
Query: 643 ALKVLQNSSLDEHQIELKRS 662
+K + LD I+ KR+
Sbjct: 56 VMK--KEHILDGKIIDPKRA 73
Score = 40.6 bits (95), Expect = 1e-04
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY--- 395
+F+ L++ T+D L + F ++G + + + D T +++GF +TF P+ +
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 396 QHLDGTV 402
LDG +
Sbjct: 61 HILDGKI 67
>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 = 40.8 bits (96), Expect = 1e-04
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 339 IFVRNLSYTVTEDD----LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
IFV+ ++ EDD LT+ F G + V +P D+ET +KGFA + F + +A
Sbjct: 2 IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61
Query: 395 YQHLDGTVFLGRMLH 409
LDG+ G L
Sbjct: 62 L-ELDGSDLGGGNLV 75
Score = 34.3 bits (79), Expect = 0.028
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 582 TLYIKNLNFNSTEDSIRR----HFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
T+++K + + ED IRR HF CG I V++ P S G+ +++F +
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSI-----PTDRETGASKGFAYIEFKSV 55
Query: 638 ESLNQALKVLQN 649
+ + +AL++ +
Sbjct: 56 DGVEKALELDGS 67
Score = 28.9 bits (65), Expect = 2.4
Identities = 12/47 (25%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ E F + GE+ V +P +G +GF ++EF + + ++A++
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDR-ETGASKGFAYIEFKSVDGVEKALE 63
>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM3 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 81
Score = 40.8 bits (96), Expect = 1e-04
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 8/80 (10%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFLGM--------AYIGFKDEKNCNKALN 276
+ I ++NLP V+K+D++A+F L L + TFL A++ FK ++ AL
Sbjct: 1 YYIHLENLPFSVEKRDIRAFFGDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAALA 60
Query: 277 KNKSFWKGKQLNIYKYSKDN 296
+K +++ ++ S+++
Sbjct: 61 HHKRVLYNREVYVFPISRED 80
Score = 27.7 bits (62), Expect = 5.8
Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 11/79 (13%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLA----EVILPIDKETDKTK-GFALVTFLMPEHATQ 393
I + NL ++V + D+ F G L ++ DK+ +T+ F + L A
Sbjct: 3 IHLENLPFSVEKRDIRAFF---GDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAAL 59
Query: 394 AYQHLDGTVFLGRMLHLIP 412
A+ V R +++ P
Sbjct: 60 AHH---KRVLYNREVYVFP 75
>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 = 40.5 bits (95), Expect = 1e-04
Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V N+ T+ DL LF+ +G + E D +GFA V E A A L
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56
Query: 399 DGTVFLGRMLHLIPGK 414
G GR L GK
Sbjct: 57 QGFPVHGRPLRCGWGK 72
Score = 35.9 bits (83), Expect = 0.007
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V NIP Q+++ LF+ FG + R RGF FV+ T +A A+
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD-------RGFAFVKLDTHEQAAMAI 53
Query: 746 KALCQSTHLYGRRLVLEWAEE 766
L Q ++GR L W ++
Sbjct: 54 VQL-QGFPVHGRPLRCGWGKD 73
Score = 29.0 bits (65), Expect = 1.7
Identities = 19/69 (27%), Positives = 24/69 (34%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 511
V N+P T DL LF+ FG + P V+ QA A L
Sbjct: 5 VGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPVHGR 64
Query: 512 PLYLEWAPE 520
PL W +
Sbjct: 65 PLRCGWGKD 73
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 40.7 bits (95), Expect = 1e-04
Identities = 18/67 (26%), Positives = 34/67 (50%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+T+ +L +LF +YG + + D+ T ++G + F A +A + L
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 399 DGTVFLG 405
+G G
Sbjct: 63 NGQKPEG 69
Score = 37.2 bits (86), Expect = 0.003
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V +P Q E+E+LF +G + R+ + + +G+ RG GF+ F + EA+ A+
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQL-TGVSRGVGFIRFDKRIEAEEAI 59
Query: 746 KAL 748
K L
Sbjct: 60 KGL 62
Score = 30.7 bits (69), Expect = 0.48
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
LY+ L T+ + + F + G I + + R + G GF++F R
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVS-----RGVGFIRFDKRIEA 55
Query: 641 NQALKVLQN 649
+A+K L
Sbjct: 56 EEAIKGLNG 64
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 40.7 bits (95), Expect = 1e-04
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G ++ V IP + E+ +F++ G + +RL M G +RG+ FV + K+EAKRA
Sbjct: 1 GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRL--MMDFDGKNRGYAFVMYTQKHEAKRA 58
Query: 745 MKAL 748
++ L
Sbjct: 59 VREL 62
Score = 35.3 bits (81), Expect = 0.010
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + V ED+L +FE G + E+ L +D + K +G+A V + A +A + L
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVREL 62
Query: 399 DG-TVFLGRML 408
+ + GR+L
Sbjct: 63 NNYEIRPGRLL 73
Score = 32.6 bits (74), Expect = 0.089
Identities = 18/66 (27%), Positives = 36/66 (54%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
+ +++L FE G + +++L +GK R +AF+ Y ++ +A+ A+ NN + R+
Sbjct: 13 VYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELNNYEIRPGRL 72
Query: 89 KVEKCS 94
CS
Sbjct: 73 LGVCCS 78
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 40.7 bits (96), Expect = 2e-04
Identities = 19/71 (26%), Positives = 36/71 (50%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ NL+ + E L + +KYG + EV + +T+K G A V F + A + + L
Sbjct: 5 VTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKL 64
Query: 399 DGTVFLGRMLH 409
+ T +G+++
Sbjct: 65 NQTSVMGKIIK 75
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 40.3 bits (95), Expect = 2e-04
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 10/60 (16%)
Query: 686 SKILVRNIP-FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S++ V N+ + + ++EE+F +G K++G LH+G+GFV+F + +A+ A
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYG---------KILGISLHKGYGFVQFDNEEDARAA 51
Score = 39.1 bits (92), Expect = 4e-04
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 338 RIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
R+FV NL + V+++DL ++F KYG + + L KG+ V F E A A
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53
Query: 397 HLDGTVFLG 405
+G G
Sbjct: 54 GENGREIAG 62
Score = 28.0 bits (63), Expect = 3.2
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 14/58 (24%)
Query: 583 LYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+++ NLN +++ + F K G I +++ + GYGFVQF E
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK-------------GYGFVQFDNEED 47
Score = 28.0 bits (63), Expect = 3.7
Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
K+++E L+ F + G + + L + + F+ + E+ A+AA+
Sbjct: 12 KVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVA 53
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 40.3 bits (94), Expect = 2e-04
Identities = 25/79 (31%), Positives = 48/79 (60%), Gaps = 8/79 (10%)
Query: 686 SKILV-RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
SK+LV N+ + A + ++E+F+ + +R+P+ +G +G+ FVEF + +AK A
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVFE---KATSIRIPQN---NGRPKGYAFVEFESAEDAKEA 54
Query: 745 MKALCQSTHLYGRRLVLEW 763
+ + C +T + GR + LE+
Sbjct: 55 LNS-CNNTEIEGRSIRLEF 72
Score = 38.3 bits (89), Expect = 8e-04
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S + V NLSY+ +ED L ++FEK + I + + KG+A V F E A +A
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55
Query: 396 QHLDGTVFLGRMLHL 410
+ T GR + L
Sbjct: 56 NSCNNTEIEGRSIRL 70
Score = 37.2 bits (86), Expect = 0.002
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 10/79 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
L + NL+++++EDS++ F+K I + P++ G+ GY FV+F + E
Sbjct: 3 VLVVNNLSYSASEDSLQEVFEKATSI--------RIPQNNGR--PKGYAFVEFESAEDAK 52
Query: 642 QALKVLQNSSLDEHQIELK 660
+AL N+ ++ I L+
Sbjct: 53 EALNSCNNTEIEGRSIRLE 71
Score = 27.9 bits (62), Expect = 3.8
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y +++ L+ FE+ ++ Q G+ + +AF+ + + A+ AL+ NNT +
Sbjct: 11 YSASEDSLQEVFEKATSIRIPQ----NNGRPKGYAFVEFESAEDAKEALNSCNNTEIEGR 66
Query: 87 RIKVE 91
I++E
Sbjct: 67 SIRLE 71
>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 = 40.2 bits (95), Expect = 2e-04
Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ ++ L F++TE+ IR F + + D + G +V+F + E
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGR------PTGEAYVEFASPEDA 54
Query: 641 NQALKVLQNSSLDEHQIEL 659
+AL+ N+ + IE+
Sbjct: 55 RRALRKH-NNKMGGRYIEV 72
Score = 36.4 bits (85), Expect = 0.004
Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFG----ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ +R +PF A + ++ + F + V G G +VEF + +A+R
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-----GRPTGEAYVEFASPEDARR 56
Query: 744 AMK 746
A++
Sbjct: 57 ALR 59
Score = 35.6 bits (83), Expect = 0.008
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE-VILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+ +R L ++ TE+D+ F + + + D + + G A V F PE A +A +
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDG-RPTGEAYVEFASPEDARRALR- 59
Query: 398 LDGTVFLGR 406
GR
Sbjct: 60 KHNNKMGGR 68
Score = 32.9 bits (76), Expect = 0.069
Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALNK 277
+ ++ LP ++D++ +F L + + G AY+ F ++ +AL K
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60
Query: 278 NKSFWKGKQLNIY 290
+ + G+ + ++
Sbjct: 61 HNNKMGGRYIEVF 73
Score = 27.5 bits (62), Expect = 5.4
Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 18/63 (28%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI----------TG--LVEFLQKNQA 496
++ ++ LP+ D++ F +PP GI TG VEF A
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLD------IPPDGIHIVYDDDGRPTGEAYVEFASPEDA 54
Query: 497 KAA 499
+ A
Sbjct: 55 RRA 57
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 40.5 bits (95), Expect = 2e-04
Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D IR F G I S + R K GQ S+GYGFV + E
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDK---VTGQ--SLGYGFVNYVDPEDA 56
Query: 641 NQALKVLQNSSL 652
+A+ L L
Sbjct: 57 EKAINTLNGLRL 68
Score = 37.0 bits (86), Expect = 0.003
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V L +T+D++ LF G + L DK T ++ G+ V ++ PE A +A L+G
Sbjct: 6 VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65
Query: 401 T 401
Sbjct: 66 L 66
Score = 35.9 bits (83), Expect = 0.006
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++ +A++A+
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKV-TGQSLGYGFVNYVDPEDAEKAI 60
Query: 746 KAL 748
L
Sbjct: 61 NTL 63
Score = 32.0 bits (73), Expect = 0.17
Identities = 14/63 (22%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+TQ+++++ F G + +L + G+ + F+ Y + A+ A++ N + +
Sbjct: 13 MTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72
Query: 88 IKV 90
IKV
Sbjct: 73 IKV 75
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 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 = 39.9 bits (94), Expect = 2e-04
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGP-LAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
+ N+S TV E+ + FEK GP + ++ L D E ALV F P A +A L+
Sbjct: 5 LFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG------ALVEFESPSDAGKASLSLN 58
Query: 400 GTVFLGRMLHL 410
G+ F G+ + +
Sbjct: 59 GSQFGGKTIKI 69
>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 = 44.2 bits (104), Expect = 2e-04
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 327 VQFAEDIAESGR---IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
V +A ES + ++V NL T+T+D L +F KYG + + + DK T +G A V
Sbjct: 181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFV 240
Query: 384 TFLMPEHATQAYQHLDGTV 402
F E A +A L+ +
Sbjct: 241 RFNKREEAQEAISALNNVI 259
Score = 39.2 bits (91), Expect = 0.006
Identities = 42/170 (24%), Positives = 75/170 (44%), Gaps = 24/170 (14%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L + T+ + F+ GPI + + R D K+ S GY FV F +
Sbjct: 108 TNLIVNYLPQDMTDRELYALFRTIGPINTCRIMR--DYKTG---YSFGYAFVDFGSEADS 162
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+A+K L ++ ++++ + ES T + V N+P
Sbjct: 163 QRAIKNLNGITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITDD 208
Query: 701 EVEELFKAFGEL--KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F +G++ K + L K+ G+ RG FV F + EA+ A+ AL
Sbjct: 209 QLDTIFGKYGQIVQKNI-LRDKLTGTP--RGVAFVRFNKREEAQEAISAL 255
Score = 39.2 bits (91), Expect = 0.006
Identities = 24/70 (34%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
DT LY+ NL T+D + F K G I + R K +P G FV+F RE
Sbjct: 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTP-----RGVAFVRFNKREE 247
Query: 640 LNQALKVLQN 649
+A+ L N
Sbjct: 248 AQEAISALNN 257
Score = 35.8 bits (82), Expect = 0.082
Identities = 27/105 (25%), Positives = 51/105 (48%), Gaps = 5/105 (4%)
Query: 676 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
N +G+ ++V +P E+ LF+ G + R+ + +G G+ FV+F
Sbjct: 98 SDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY-KTGYSFGYAFVDF 156
Query: 736 ITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
++ +++RA+K L T + +RL + +A E I+ TN Y
Sbjct: 157 GSEADSQRAIKNLNGIT-VRNKRLKVSYARPGG--ESIKD-TNLY 197
Score = 32.3 bits (73), Expect = 0.99
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 29 ITQEQLKAKFEEKGTVTDVQ---LKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
IT +QL F + G + VQ L+ G R AF+ +++ ++AQ A+ NN
Sbjct: 205 ITDDQLDTIFGKYGQI--VQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN 257
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 81
Score = 40.4 bits (94), Expect = 2e-04
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V +P Q E+E+LF +G + R+ V +G+ RG GF+ F + EA+ A+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQV-TGISRGVGFIRFDKRIEAEEAI 60
Query: 746 KAL 748
K L
Sbjct: 61 KGL 63
Score = 31.1 bits (70), Expect = 0.35
Identities = 17/67 (25%), Positives = 36/67 (53%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+++ ++ +LF +YG + + +D+ T ++G + F A +A + L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 399 DGTVFLG 405
+G LG
Sbjct: 64 NGQKPLG 70
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains). The
RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 40.0 bits (94), Expect = 2e-04
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVIL--PIDKETDKTKGFALVTFLMPEHATQAYQHL 398
V N+S TE+ + LF G + E+ L D V + PE A HL
Sbjct: 4 VTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVA-LHL 62
Query: 399 DGTVFLGRMLHLIP 412
TVF+ R L ++P
Sbjct: 63 TNTVFIDRALIVVP 76
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 40.2 bits (93), Expect = 2e-04
Identities = 22/69 (31%), Positives = 34/69 (49%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++R L T+ DL KL + YG + +DK T+K KG+ V F P A +A L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69
Query: 399 DGTVFLGRM 407
+ +M
Sbjct: 70 KASGVQAQM 78
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 39.9 bits (94), Expect = 2e-04
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
++ V NL + V++DD+ +LF ++G L + + D+ + ++ G A V F A +A +
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMK 59
Query: 397 HLDGTVFLGR 406
+G GR
Sbjct: 60 QYNGVPLDGR 69
Score = 36.1 bits (84), Expect = 0.005
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG---SGLHRGFGFVEFITKNEAK 742
+K+LV N+ F +++ELF FG LK K V SG G V F + +A
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALK-----KAAVHYDRSGRSLGTADVVFERRADAL 55
Query: 743 RAMK 746
+AMK
Sbjct: 56 KAMK 59
Score = 35.7 bits (83), Expect = 0.007
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + NL+F ++D I+ F + G + V + + S+G V F R
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGR------SLGTADVVFERRADA 54
Query: 641 NQALKVLQNSSLD 653
+A+K LD
Sbjct: 55 LKAMKQYNGVPLD 67
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 40.0 bits (93), Expect = 3e-04
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
++FV LS TE+ + + F +G + + LP+D +T++ +GF VT+ E
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52
Score = 28.4 bits (63), Expect = 3.3
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALD 76
T+EQ+K F G + +++L T+ RR F F+ Y E+ Q L+
Sbjct: 11 TTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLE 59
Score = 28.1 bits (62), Expect = 3.6
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V + + +++E F AFGE++ + LP + RGF FV + + ++ ++
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMD-TKTNERRGFCFVTYTDEEPVQKLLE 59
Query: 747 A 747
+
Sbjct: 60 S 60
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 39.5 bits (93), Expect = 3e-04
Identities = 22/69 (31%), Positives = 38/69 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++R L T++DL KL + +G + +DK+T+K KG+ V F PE A +A + L
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62
Query: 399 DGTVFLGRM 407
+G +
Sbjct: 63 NGRGVQAQF 71
Score = 30.7 bits (70), Expect = 0.41
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV-TVARKKDPKSPGQFLSMGYGFVQFYTRES 639
T +YI+ L N+T++ + + + G I S + KK K GYGFV F + E+
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCK------GYGFVDFDSPEA 54
Query: 640 LNQALKVLQN 649
+A++ L
Sbjct: 55 ALKAIEGLNG 64
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 39.7 bits (93), Expect = 3e-04
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKA-FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ + NIP+ K ++++LF+ GE+ +V L K G RG G VEF K ++A+
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD--EEGKSRGCGVVEFKDKESVQKAL 58
Query: 746 KALCQSTHLYGRRLVL 761
+ + L GR+LV+
Sbjct: 59 ETM-NRYELKGRKLVV 73
Score = 30.5 bits (69), Expect = 0.54
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 338 RIFVRNLSYTVTEDDLTKLF-EKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
R+F+ N+ Y + DL LF EK G + V L D+E K++G +V F E +A
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKA 57
Score = 27.4 bits (61), Expect = 6.6
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEK-GTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y + + LK F EK G VT V+L EGK R + + ++ Q AL+ N +
Sbjct: 9 YDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKG 68
Query: 86 SRIKV 90
++ V
Sbjct: 69 RKLVV 73
>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 = 39.9 bits (94), Expect = 3e-04
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 343 NLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTV 402
L +VTE LT+ F +YGP+ V++ D+ +G ALV F E A A + G
Sbjct: 14 GLDESVTEQYLTRHFSRYGPVVHVVI------DRQRGQALVFFDKVEAAQAAVNEMKGRK 67
Query: 403 FLGRML 408
GR L
Sbjct: 68 LGGRKL 73
Score = 28.8 bits (65), Expect = 2.0
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
P +++ L+ + TE + RHF + GP+ V + R+ G V F E
Sbjct: 6 PTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQ-----------RGQALVFFDKVE 54
Query: 639 SLNQALKVLQNSSLDEHQIEL 659
+ A+ ++ L ++++
Sbjct: 55 AAQAAVNEMKGRKLGGRKLQV 75
>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 = 39.8 bits (93), Expect = 3e-04
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I++ +L + E +L K F ++G + V + K+T +K + + FL PE A A + +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 399 DGTVFLGRML--HLIP 412
+ + +G++L H++P
Sbjct: 62 NNYLLMGKVLQVHVLP 77
Score = 35.2 bits (81), Expect = 0.010
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I + ++P + E+++ F FG +K VR+ + +G + +GF++F+ A A K+
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSK-KTGNSKHYGFIQFLNPEVAAIAAKS 60
Query: 748 L 748
+
Sbjct: 61 M 61
Score = 33.6 bits (77), Expect = 0.036
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
+YI +L E ++++F + G + +V VAR K + S YGF+QF E
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGN-----SKHYGFIQFLNPEVAA 55
Query: 642 QALKVLQNSSLDEHQIELK 660
A K + N L +++
Sbjct: 56 IAAKSMNNYLLMGKVLQVH 74
Score = 32.1 bits (73), Expect = 0.15
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 31 QEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
+++LK F + GTV +V++ + + G + + FI + + A A NN + ++
Sbjct: 13 EKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72
Query: 90 V 90
V
Sbjct: 73 V 73
>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 = 39.5 bits (93), Expect = 3e-04
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 8/64 (12%)
Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
+KIL ++N+P + + +E LF F K VRL + RG FVEF T+ +A A
Sbjct: 2 NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-------RGIAFVEFETEEQATVA 54
Query: 745 MKAL 748
++AL
Sbjct: 55 LQAL 58
Score = 32.9 bits (76), Expect = 0.060
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
+I+ ++NLP T L+ LF F V LVP GI VEF + QA A +L
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGI-AFVEFETEEQATVALQALQGF 61
Query: 507 K 507
K
Sbjct: 62 K 62
Score = 32.9 bits (76), Expect = 0.065
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+F++NL T++ L LF ++ EV L +G A V F E AT A Q L
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58
Query: 399 DGT 401
G
Sbjct: 59 QGF 61
>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 = 39.8 bits (93), Expect = 3e-04
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV+NL Y +T D+L ++FE ++ LP K+ +KG A + F A +A +
Sbjct: 6 LFVKNLPYNITVDELKEVFED---AVDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALEEK 61
Query: 399 DGTVFLGR 406
G GR
Sbjct: 62 QGAEVDGR 69
Score = 36.0 bits (83), Expect = 0.006
Identities = 22/76 (28%), Positives = 45/76 (59%), Gaps = 6/76 (7%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V+N+P+ E++E+F+ + +RLP GS +G ++EF T+ EA++A++
Sbjct: 6 LFVKNLPYNITVDELKEVFEDAVD---IRLPSGKDGSS--KGIAYIEFKTEAEAEKALEE 60
Query: 748 LCQSTHLYGRRLVLEW 763
Q + GR +V+++
Sbjct: 61 K-QGAEVDGRSIVVDY 75
Score = 32.1 bits (73), Expect = 0.15
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++KNL +N T D ++ F+ + + KD S G +++F T
Sbjct: 5 TLFVKNLPYNITVDELKEVFEDA---VDIRLPSGKDGSSK------GIAYIEFKTEAEAE 55
Query: 642 QALKVLQNSSLD 653
+AL+ Q + +D
Sbjct: 56 KALEEKQGAEVD 67
Score = 30.6 bits (69), Expect = 0.44
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYF---KPLPLASVRT-TFLGMAYIGFKDEKNCNKAL 275
R T+ VKNLP + +LK F + L S + + G+AYI FK E KAL
Sbjct: 1 RDARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKAL 58
Score = 29.4 bits (66), Expect = 1.4
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFE 469
R R + VKNLPY +LK +FE
Sbjct: 1 RDARTLFVKNLPYNITVDELKEVFE 25
Score = 29.0 bits (65), Expect = 1.7
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
Y IT ++LK FE+ D++L +G + A+I + E +A+ AL+
Sbjct: 13 YNITVDELKEVFED---AVDIRLPSGKDGSSKGIAYIEFKTEAEAEKALE 59
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 39.5 bits (92), Expect = 3e-04
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+FV LS+ T+ DL + F K+G + + + ID T +++GF V F
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLF 47
Score = 36.0 bits (83), Expect = 0.006
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ L++++T+ ++ +F K G + T+ K DP + G+ S G+GFV F S+ +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTI--KIDPVT-GR--SRGFGFVLFKDAASVEK 55
Query: 643 ALKVLQNSSLDEHQIELKRS 662
L + LD I+ KR+
Sbjct: 56 VLD-QKEHKLDGRVIDPKRA 74
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 39.2 bits (92), Expect = 3e-04
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV +S +VT++ L +LF+ L L D T K+KGFA VT+ P A A +
Sbjct: 2 RLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60
Query: 398 LDG 400
L+G
Sbjct: 61 LNG 63
>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 = 39.8 bits (94), Expect = 4e-04
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVI--------LPIDKETDKTKGFALVTFLMPEH 390
++V L +T ++ ++F K G + E L D+ KG AL +L E
Sbjct: 4 VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENG-NLKGDALCCYLKEES 62
Query: 391 ATQAYQHLDGTVFLG 405
A Q LDGT
Sbjct: 63 VELAIQLLDGTEIGR 77
Score = 29.0 bits (66), Expect = 2.4
Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 10/77 (12%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK------SPGQFLSMGYGFVQF 634
T +Y+ L + T + F KCG I PK G G +
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIKEDP--ETGKPKIKLYRDENGNL--KGDALCCY 57
Query: 635 YTRESLNQALKVLQNSS 651
ES+ A+++L +
Sbjct: 58 LKEESVELAIQLLDGTE 74
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 39.2 bits (91), Expect = 4e-04
Identities = 26/70 (37%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILP-IDKETDKTKGFALVTFLMPEHATQAYQ 396
+IFVRNL + +T KL EK+ V+ I E K+KG V F PE A +A +
Sbjct: 1 QIFVRNLPFDLT---WQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACR 57
Query: 397 HLDGTVFLGR 406
++G GR
Sbjct: 58 LMNGIKINGR 67
Score = 30.0 bits (67), Expect = 0.77
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+I VRN+PF +++E F G + F + + +G +G G V F + A++A +
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME---NGKSKGCGTVRFDSPESAEKACR 57
Query: 747 ALCQSTHLYGRRL 759
L + GR +
Sbjct: 58 -LMNGIKINGREI 69
Score = 30.0 bits (67), Expect = 0.97
Identities = 21/85 (24%), Positives = 44/85 (51%), Gaps = 12/85 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPI--ASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
++++NL F+ T ++ F +CG + A + + K S G G V+F + ES
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGK---------SKGCGTVRFDSPESA 52
Query: 641 NQALKVLQNSSLDEHQIELKRSNRN 665
+A +++ ++ +I++ R +RN
Sbjct: 53 EKACRLMNGIKINGREIDV-RLDRN 76
>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 = 39.4 bits (92), Expect = 4e-04
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V N+ Y T ++L F G + V + DK + KGFA + F E + + L
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE-SVRTALAL 60
Query: 399 DGTVFLGRMLHLIP 412
D ++F GR + ++P
Sbjct: 61 DESLFRGRQIKVMP 74
Score = 35.9 bits (83), Expect = 0.006
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++Y+ N+++ +T + + HF CG + VT+ K P G+ +++F +ES+
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP-----KGFAYIEFSDKESVR 55
Query: 642 QALKVLQNSSLDEHQIEL 659
AL L S QI++
Sbjct: 56 TAL-ALDESLFRGRQIKV 72
Score = 29.0 bits (65), Expect = 1.9
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+ + A E+E F G + V L K SG +GF ++EF K + A+
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF--SGHPKGFAYIEFSDKESVRTAL 58
Score = 27.5 bits (61), Expect = 5.5
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 259 GMAYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
G AYI F D+++ AL ++S ++G+Q+ +
Sbjct: 42 GFAYIEFSDKESVRTALALDESLFRGRQIKV 72
>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 = 39.0 bits (91), Expect = 4e-04
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 10/67 (14%)
Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGR 757
++ ++E+LF+ FG L + K F FVEF +A +A++AL + + G
Sbjct: 13 REEDIEKLFEPFGPLVRCDIRKT---------FAFVEFEDSEDATKALEAL-HGSRIDGS 62
Query: 758 RLVLEWA 764
L +E+
Sbjct: 63 VLTVEFV 69
Score = 36.3 bits (84), Expect = 0.005
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 347 TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
T E+D+ KLFE +GPL + K FA V F E AT+A + L G+ G
Sbjct: 11 TTREEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKALEALHGSRIDGS 62
Query: 407 ML 408
+L
Sbjct: 63 VL 64
Score = 32.4 bits (74), Expect = 0.10
Identities = 13/63 (20%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
+E ++ FE G + ++ + FAF+ + + A AL+ + + + S +
Sbjct: 12 TREEDIEKLFEPFGPLVRCDIR-------KTFAFVEFEDSEDATKALEALHGSRIDGSVL 64
Query: 89 KVE 91
VE
Sbjct: 65 TVE 67
Score = 31.6 bits (72), Expect = 0.21
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 456 PYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY 514
P T D++ LFEPFG L R + + VEF A A +L ++ L
Sbjct: 9 PGTTREEDIEKLFEPFGPLVRCDIRKTF---AFVEFEDSEDATKALEALHGSRIDGSVLT 65
Query: 515 LEWA 518
+E+
Sbjct: 66 VEFV 69
Score = 30.1 bits (68), Expect = 0.70
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 14/77 (18%)
Query: 582 TLYIKNLNFNST-EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TL++ + +T E+ I + F+ GP+ + + + FV+F E
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT-------------FAFVEFEDSEDA 47
Query: 641 NQALKVLQNSSLDEHQI 657
+AL+ L S +D +
Sbjct: 48 TKALEALHGSRIDGSVL 64
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 39.3 bits (91), Expect = 4e-04
Identities = 26/72 (36%), Positives = 35/72 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NLS E L +LF +G + V + D T+K KGF VT + A A L
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 399 DGTVFLGRMLHL 410
+G R+L +
Sbjct: 64 NGYRLGDRVLQV 75
Score = 32.0 bits (72), Expect = 0.18
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I V N+ +A +S + +LF FG + V++ + + +GFGFV +EA A+ +
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKC-KGFGFVTMTNYDEAAMAIAS 62
Query: 748 L 748
L
Sbjct: 63 L 63
>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 = 39.3 bits (92), Expect = 4e-04
Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+S ++FV NL + +TED+L + F+++G + EV + + F V F PE
Sbjct: 2 DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56
Score = 36.2 bits (84), Expect = 0.006
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL + TED ++ FK+ G + V + K F GFV F E++ +
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNF-----GFVVFDDPEAVQK 60
Query: 643 ALKVLQNSSLDEHQ--IELKR 661
L +H+ +E K+
Sbjct: 61 ILANKPIYFRGDHRLNVEEKK 81
Score = 34.3 bits (79), Expect = 0.024
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
++ V N+P + E++E FK FG + VR+ K G G FGFV F
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKG-GGGRLPNFGFVVF 52
Score = 31.2 bits (71), Expect = 0.29
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
IT+++LK F+E G V +V++ G+ F F+ + + Q L + R
Sbjct: 15 ITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPIYFRGDHR 74
Query: 88 IKVE 91
+ VE
Sbjct: 75 LNVE 78
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 39.4 bits (92), Expect = 5e-04
Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM---VGSGLHRGFGFVEFITKNEAK 742
+ I+++NIPF ++ ++ ++ + G + LP +G+ RG F F + EA+
Sbjct: 2 TAIVIKNIPFSLRKEQLLDIIEDLG----IPLPYAFNYHFDNGVFRGLAFANFRSPEEAQ 57
Query: 743 RAMKALCQSTHLYGRRLVLEW 763
++AL + GRRL +E+
Sbjct: 58 TVVEAL-NGYEISGRRLRVEY 77
Score = 34.0 bits (78), Expect = 0.030
Identities = 16/72 (22%), Positives = 30/72 (41%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I ++N+ +++ ++ L + E G + +G A F PE A + L
Sbjct: 4 IVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEAL 63
Query: 399 DGTVFLGRMLHL 410
+G GR L +
Sbjct: 64 NGYEISGRRLRV 75
Score = 29.7 bits (67), Expect = 1.00
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ + +EQL E+ G Y + G FR AF + ++AQ ++ N +
Sbjct: 11 FSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEALNGYEISG 70
Query: 86 SRIKVE 91
R++VE
Sbjct: 71 RRLRVE 76
Score = 27.0 bits (60), Expect = 8.8
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 226 TIVVKNLPAGVKKKDLKAYFK----PLPLASV----RTTFLGMAYIGFK 266
IV+KN+P ++K+ L + PLP A F G+A+ F+
Sbjct: 3 AIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFR 51
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 39.3 bits (91), Expect = 5e-04
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP 388
++F+ LS+ + D L F K+G + E ++ D T +++GF VTF P
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51
Score = 34.3 bits (78), Expect = 0.025
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++I L++ ++ DS+R +F K G I V R DP + S G+GFV F S+++
Sbjct: 2 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMR--DPTTK---RSRGFGFVTFADPASVDK 56
Query: 643 AL 644
L
Sbjct: 57 VL 58
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 39.1 bits (91), Expect = 5e-04
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G ++ V IP + E+ LF+ G++ RL M SG +RG+ FV + TK EA+ A
Sbjct: 1 GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRL--MMEFSGENRGYAFVMYTTKEEAQLA 58
Query: 745 MKAL 748
++ L
Sbjct: 59 IRIL 62
Score = 32.2 bits (73), Expect = 0.14
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
+ +++L FE G + + +L G+ R +AF+ Y +++AQ A+ NN
Sbjct: 13 MYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNN 64
Score = 31.4 bits (71), Expect = 0.28
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + + ED+L LFE+ G + E L ++ + + +G+A V + E A A + L
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIRIL 62
Query: 399 D 399
+
Sbjct: 63 N 63
>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 = 39.2 bits (91), Expect = 5e-04
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ N+P Q + EEL + FG L+ F+ + +G +G+GFVE++ K+ A RA
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSET---TGHSKGYGFVEYMKKDSAARAKSD 60
Query: 748 LCQSTHLYGRRLVLEWAE 765
L L R L + W +
Sbjct: 61 LL-GKQLGSRTLYVHWTD 77
Score = 31.8 bits (72), Expect = 0.20
Identities = 18/70 (25%), Positives = 31/70 (44%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
+ NL T T+ +L +G L L + T +KG+ V ++ + A +A L G
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63
Query: 401 TVFLGRMLHL 410
R L++
Sbjct: 64 KQLGSRTLYV 73
Score = 29.5 bits (66), Expect = 1.4
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
++ + NLP + L PFG+L R + TG VE+++K+ A A +
Sbjct: 1 LLCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSD 60
Query: 503 LAYTKFKEVPLYLEWA 518
L + LY+ W
Sbjct: 61 LLGKQLGSRTLYVHWT 76
>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 = 39.1 bits (92), Expect = 5e-04
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVIL 368
+ +RNL VTE DL L +G + V+L
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLL 31
Score = 29.9 bits (68), Expect = 0.84
Identities = 17/47 (36%), Positives = 23/47 (48%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKA 498
++NLP +DL AL PFG + VL+ LVE AK+
Sbjct: 4 LRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKS 50
Score = 29.5 bits (67), Expect = 1.3
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+RN+P +S++ L FG++ V L + VE + AK +
Sbjct: 4 LRNLPPDVTESDLIALVSPFGKVTNVLLLRGK-------NQALVEMDSVESAKSMVD 53
>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 = 38.7 bits (91), Expect = 5e-04
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 581 TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
TTL ++N+ + HF K G I ++ V +P+S VQF T E
Sbjct: 2 TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQV--NYNPES---------ALVQFSTSEE 50
Query: 640 LNQALK 645
+A +
Sbjct: 51 AKKAYR 56
Score = 31.7 bits (73), Expect = 0.14
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 14/68 (20%)
Query: 25 FIYKITQEQLKAK-----FEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALD--- 76
+ I E F + GT+ ++Q+ Y E A + + ++A+ A
Sbjct: 5 EVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPES-----ALVQFSTSEEAKKAYRSPE 59
Query: 77 -YFNNTYV 83
FNN ++
Sbjct: 60 AVFNNRFI 67
Score = 31.4 bits (72), Expect = 0.26
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 686 SKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
+ + VRNIP + +++ E F FG + +++ + V+F T EAK+A
Sbjct: 2 TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNY-------NPESALVQFSTSEEAKKA 54
Query: 745 MK 746
+
Sbjct: 55 YR 56
Score = 27.9 bits (63), Expect = 4.2
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 447 KRIILVKNLP----YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 502
+ V+N+P T L F FG + + V + LV+F +AK A+ S
Sbjct: 1 NTTLEVRNIPPELNNITK---LNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYRS 57
Score = 26.7 bits (60), Expect = 9.0
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 11/61 (18%)
Query: 339 IFVRNL---SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+ VRN+ +T+ L + F K+G + + + + E+ ALV F E A +AY
Sbjct: 4 LEVRNIPPELNNITK--LNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAY 55
Query: 396 Q 396
+
Sbjct: 56 R 56
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 39.0 bits (90), Expect = 5e-04
Identities = 21/69 (30%), Positives = 33/69 (47%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++R L T+ DL KL + YG + +DK T++ KG+ V F P A +A L
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66
Query: 399 DGTVFLGRM 407
+M
Sbjct: 67 KANGVQAQM 75
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 38.9 bits (90), Expect = 6e-04
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRNL+ TVTE+ L K F ++G L V K K +A V F + A +A +
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEERDAAVRAMDEM 55
Query: 399 DGTVFLGRMLHLIPGKP 415
+G G + ++ KP
Sbjct: 56 NGKEIEGEEIEIVLAKP 72
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 38.9 bits (91), Expect = 6e-04
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 6/74 (8%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T LYI NL + E + K G + S + R D K S G GF + +RE
Sbjct: 1 TNLYISNLPLHMDEQDLETMLKPYGQVISTRILR--DSKG----QSRGVGFARMESREKC 54
Query: 641 NQALKVLQNSSLDE 654
+ L
Sbjct: 55 EDIISKFNGKYLKG 68
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 38.8 bits (90), Expect = 6e-04
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV LS E+ + + F +G + + LP+D +T+K +GF +TF
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITF 48
Score = 29.2 bits (65), Expect = 1.6
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI V + + ++ E F AFGE++ + LP + RGF F+ F + K+ M+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDN-KTNKRRGFCFITFKEEEPVKKIME 59
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 38.6 bits (90), Expect = 6e-04
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 8/66 (12%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R++VR +E + ++F YG + EV + FA V F E A +A
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDS 52
Query: 398 LDGTVF 403
+ G V
Sbjct: 53 VHGKVL 58
Score = 36.6 bits (85), Expect = 0.002
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
VR P +S + E+F +G +K V++ F FVEF + A RA ++
Sbjct: 4 VRPFPPDTSESAIREIFSPYGAVKEVKMIS---------NFAFVEFESLESAIRAKDSV 53
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 38.3 bits (90), Expect = 6e-04
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G + V NL +++ +L LF ++G + ++ + + K V F A A
Sbjct: 2 GTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALD 56
Query: 397 HLDGTVFLGRMLHL 410
L+G FLG L +
Sbjct: 57 ALNGRPFLGGRLKV 70
Score = 32.6 bits (75), Expect = 0.072
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLV 760
E+ LF FGE+K +R + FVEF A+ A+ AL L G RL
Sbjct: 17 ELRSLFSQFGEVKDIRETPL---RPSQK---FVEFYDIRAAEAALDALNGRPFL-GGRLK 69
Query: 761 LE 762
++
Sbjct: 70 VK 71
Score = 27.9 bits (63), Expect = 3.5
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY-TRESL 640
TL + NL+ ++ +R F + G + + ++ P P Q FV+FY R +
Sbjct: 3 TLLVFNLDSPISDQELRSLFSQFGEVKDI----RETPLRPSQK------FVEFYDIRAAE 52
Query: 641 NQALKVLQNSSLDEHQIELK 660
AL L ++++K
Sbjct: 53 A-ALDALNGRPFLGGRLKVK 71
>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 = 38.9 bits (91), Expect = 7e-04
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEV-ILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
+I + N+ V +DL L YG + +P ET VT+ PE A QA
Sbjct: 2 KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN----VTYESPEQAQQAVN 57
Query: 397 HLDGTVFLGRMLH 409
L+G + G L
Sbjct: 58 KLNGHEYEGSKLK 70
Score = 33.5 bits (77), Expect = 0.045
Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
KI + NIP + +++ L +G +K ++P K + ++ V + + +A++A
Sbjct: 1 RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN-----VTYESPEQAQQA 55
Query: 745 MKAL 748
+ L
Sbjct: 56 VNKL 59
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, 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. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 38.8 bits (90), Expect = 7e-04
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G +I + +P + E+ L + G++ +R+ M +G +RG+ FV F K EAK A
Sbjct: 1 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRM--MMDFNGNNRGYAFVTFSNKQEAKNA 58
Query: 745 MKAL 748
+K L
Sbjct: 59 IKQL 62
Score = 34.6 bits (79), Expect = 0.022
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IF+ L + ED+L L EK G + E+ + +D + +G+A VTF + A A + L
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQL 62
Query: 399 DG-TVFLGRML 408
+ + GR+L
Sbjct: 63 NNYEIRNGRLL 73
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 38.9 bits (90), Expect = 7e-04
Identities = 26/72 (36%), Positives = 35/72 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NLS E L +LF +G + V + D T+K KGF VT + A A L
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 399 DGTVFLGRMLHL 410
+G R+L +
Sbjct: 66 NGYRLGDRVLQV 77
Score = 31.6 bits (71), Expect = 0.25
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
TG I V N+ + +S + +LF FG + V++ + + +GFGFV +EA
Sbjct: 2 TGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDF-NTNKCKGFGFVTMTNYDEAAM 60
Query: 744 AMKAL 748
A+ +L
Sbjct: 61 AIASL 65
>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 = 38.7 bits (90), Expect = 8e-04
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V N+P E EEL +A+G ++ L V +G +G+GFVE++ K+ A +A L
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEV-TGHSKGYGFVEYMKKDSASKARLELL 62
Query: 750 QSTHLYGRRLVLEWAE 765
L L +W +
Sbjct: 63 GKQ-LGESTLFAQWMD 77
Score = 31.8 bits (72), Expect = 0.16
Identities = 16/60 (26%), Positives = 29/60 (48%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V NL + T ++ +L YG + L + T +KG+ V ++ + A++A L G
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63
Score = 31.0 bits (70), Expect = 0.41
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 502
++ V NLP + + L +G++ R + +TG VE+++K+ A A
Sbjct: 1 LLCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60
Query: 503 LAYTKFKEVPLYLEWA 518
L + E L+ +W
Sbjct: 61 LLGKQLGESTLFAQWM 76
>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 = 38.4 bits (90), Expect = 8e-04
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFALVTFLMPEH 390
I++ L VTED L +LF G + + + DKET + KG A VT+ P
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59
Query: 391 ATQAYQHLDGTVFLGRMLH 409
A A + +G F G +
Sbjct: 60 AQAAIEWFNGYEFRGNKIK 78
Score = 31.5 bits (72), Expect = 0.27
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIA 608
+YI L + TEDS+ F G I
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIK 26
>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 = 38.5 bits (90), Expect = 8e-04
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL+I NL +T +R F++ G I + + KK +P Y F+Q+ S+
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDI--KKQGGNP------AYAFIQYADIASVV 55
Query: 642 QALKVLQNSSLDEHQIEL 659
+A++ + L ++++L
Sbjct: 56 KAMRKMDGEYLGNNRVKL 73
Score = 33.5 bits (77), Expect = 0.036
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID-KETDKTKGFALVTFLMPEHATQAYQH 397
+F+ NL T T DL + FE++G I+ ID K+ +A + + +A +
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGE----IIDIDIKKQGGNPAYAFIQYADIASVVKAMRK 60
Query: 398 LDGTVFLGR 406
+DG +LG
Sbjct: 61 MDG-EYLGN 68
Score = 27.8 bits (62), Expect = 4.3
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T L+ FE G + D+ +K +G +AFI Y A+ + Y+ ++R+
Sbjct: 14 TTYSDLREAFERFGEIIDIDIK--KQGGNPAYAFIQYADIASVVKAMRKMDGEYLGNNRV 71
Query: 89 KV 90
K+
Sbjct: 72 KL 73
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 75
Score = 38.3 bits (90), Expect = 9e-04
Identities = 27/80 (33%), Positives = 33/80 (41%), Gaps = 17/80 (21%)
Query: 339 IFVRNLSYTVTEDDLTK-----LFEKYGPLAE-VILPIDKETDKTKGF--ALVTFLMPEH 390
+ V N+ V + K LF YG +A V LP F A V F PE
Sbjct: 1 LIVTNVPSEVFTNAELKAALESLFSSYGEIATFVYLP---------SFRRARVVFSSPEE 51
Query: 391 ATQAYQHLDGTVFLGRMLHL 410
A A L GTVF G +L +
Sbjct: 52 AALARIELHGTVFEGSVLRV 71
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 38.3 bits (89), Expect = 0.001
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ N + A+QSE+E LF +G + V + GF FV + +A+ A++
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRV---------DMKSGFAFVYMEDERDAEDAIRG 53
Query: 748 LCQSTHLY-GRRLVLEWAE 765
L RRL +EWA+
Sbjct: 54 LDNFEFGRQRRRLRVEWAK 72
Score = 34.8 bits (80), Expect = 0.013
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+F N Y + ++ +LF KYG + V D GFA V A A + L
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRV--------DMKSGFAFVYMEDERDAEDAIRGL 54
Query: 399 DGTVF 403
D F
Sbjct: 55 DNFEF 59
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 38.5 bits (89), Expect = 0.001
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V +P Q E+E+LF +G + R+ V +G+ RG GF+ F + EA+ A+
Sbjct: 3 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAEEAI 61
Query: 746 KAL 748
K L
Sbjct: 62 KGL 64
Score = 32.4 bits (73), Expect = 0.11
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+T+ +L +LF +YG + + +D+ T ++G + F A +A + L
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 399 DG 400
+G
Sbjct: 65 NG 66
>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 = 42.3 bits (99), Expect = 0.001
Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 16/93 (17%)
Query: 572 DEEREPEPDT-----TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLS 626
+ E E + D LY++NL +TE+ I + F + P V + +D
Sbjct: 220 EPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------- 270
Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEHQIEL 659
Y FV F RE +A+ L L+ +IE+
Sbjct: 271 --YAFVHFEDREDAVKAMDELNGKELEGSEIEV 301
Score = 41.1 bits (96), Expect = 0.002
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 9/110 (8%)
Query: 314 NIKAKHWKSQEDSVQFAEDIAESGRI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK 372
++ A W E+ V ED+ +I +VRNL T TE+ + K F ++ P +
Sbjct: 212 HVIAVDWAEPEEEVD--EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKV------E 263
Query: 373 ETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHLIPGKPKENEGNV 422
K + +A V F E A +A L+G G + + KP + + V
Sbjct: 264 RVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYV 313
Score = 39.6 bits (92), Expect = 0.006
Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 678 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 737
S V G ++ V IP + E+ LF+ G + +RL M SG +RG+ FV F
Sbjct: 51 SGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRL--MMDFSGQNRGYAFVTFCG 108
Query: 738 KNEAKRAMKAL 748
K EAK A+K L
Sbjct: 109 KEEAKEAVKLL 119
Score = 39.6 bits (92), Expect = 0.007
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + + ED+L LFEK GP+ E+ L +D + +G+A VTF E A +A + L
Sbjct: 61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAFVTFCGKEEAKEAVKLL 119
Query: 399 D 399
+
Sbjct: 120 N 120
Score = 35.7 bits (82), Expect = 0.11
Identities = 45/199 (22%), Positives = 80/199 (40%), Gaps = 27/199 (13%)
Query: 576 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
+P +++ + + ED + F+K GPI + + ++ GY FV F
Sbjct: 54 QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQN------RGYAFVTFC 107
Query: 636 TRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPF 695
+E +A+K+L N + R R L + ++ V IP
Sbjct: 108 GKEEAKEAVKLLNNYEI--------RPGRLLGVCISV-----------DNCRLFVGGIPK 148
Query: 696 QAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS-TH 753
K+ E+ E F E + V + +RGF FVE+ + A A + L
Sbjct: 149 NKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQ 208
Query: 754 LYGRRLVLEWAEEADNVED 772
L+G + ++WAE + V++
Sbjct: 209 LWGHVIAVDWAEPEEEVDE 227
Score = 29.6 bits (66), Expect = 8.2
Identities = 16/60 (26%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 25 FIYKIT----QEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
F+ KI +++L FE+ G + +++L G+ R +AF+ + +++A+ A+ NN
Sbjct: 62 FVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNN 121
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 38.5 bits (89), Expect = 0.001
Identities = 24/72 (33%), Positives = 35/72 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NL+ E L ++F +G + V + D T+K KGF VT + A A L
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 399 DGTVFLGRMLHL 410
+G R+L +
Sbjct: 66 NGYRLGDRVLQV 77
Score = 32.0 bits (72), Expect = 0.22
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
TG I V N+ A +S + ++F FG + V++ + + +GFGFV +EA
Sbjct: 2 TGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDF-NTNKCKGFGFVTMTNYDEAAM 60
Query: 744 AMKAL 748
A+ +L
Sbjct: 61 AIASL 65
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 38.2 bits (88), Expect = 0.001
Identities = 22/70 (31%), Positives = 32/70 (45%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V LS T DL LF KYG + + + + + + VT E AT+ HL
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63
Query: 399 DGTVFLGRML 408
T GRM+
Sbjct: 64 HRTELHGRMI 73
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end)
protein family. This subfamily corresponds to the RRM1
domain in the Spen (split end) 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 possesses 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 known as 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 = 38.0 bits (89), Expect = 0.001
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 687 KILVRNIPFQAKQSEVEE-LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+P + ++E+ L+ F KF + +++ G +V F +A+ A
Sbjct: 3 TLCVSNLPSKLSDEDIEDVLYHEFK--KFGDVSVRVLHDGEDERVAYVNFRHPEDAREAK 60
Query: 746 KALCQSTHLYGRRLVLEW 763
A L+ R L +E
Sbjct: 61 HA-KGRLVLFDRPLNVEP 77
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM2 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed
BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-1 is strongly expressed in all adult
and fetal tissues tested. Human CELF-1 is a nuclear and
cytoplasmic RNA-binding protein that regulates multiple
aspects of nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic dystrophy
protein kinase) gene; it preferentially targets UGU-rich
mRNA elements. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
binds specifically to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contains three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it preferentially binds
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contains three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are also
important for localization in the cytoplasm. The
splicing activation or repression activity of CELF-2 on
some specific substrates is mediated by RRM1/RRM2. Both,
RRM1 and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 38.1 bits (88), Expect = 0.001
Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + + + ++++ +F FG+++ R+ + GL RG FV F T+ A+ A+K
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIK 60
Query: 747 ALCQSTHLYG 756
A+ Q+ + G
Sbjct: 61 AMHQAQTMEG 70
Score = 32.7 bits (74), Expect = 0.10
Identities = 22/75 (29%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D L+I ++ E+ IR F G I + R D LS G FV F TR
Sbjct: 1 DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDG------LSRGCAFVTFTTRAM 54
Query: 640 LNQALKVLQNSSLDE 654
A+K + + E
Sbjct: 55 AQTAIKAMHQAQTME 69
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 38.1 bits (88), Expect = 0.001
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRNL+ TVTE+ L K F ++G L V K K +A + F + A +A + +
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 55
Query: 399 DGTVFLGRMLHLIPGKP 415
+G G + ++ KP
Sbjct: 56 NGKELEGENIEIVFAKP 72
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains 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 = 85
Score = 38.1 bits (88), Expect = 0.001
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
I++R +P A ++++ + G + + VRL + SG RGF FVEF +A R M+
Sbjct: 5 IMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNK-SSGQSRGFAFVEFNHLQDATRWME 63
Query: 747 ALCQSTHLYGRRLVLEWAE 765
A S + G+++ + +++
Sbjct: 64 ANQHSLMILGQKVSMHYSD 82
Score = 29.6 bits (66), Expect = 1.3
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLA-EVILPIDKETDKTKGFALVTFLMPEHAT-- 392
S I +R L TE D+ +++G EV L +K + +++GFA V F + AT
Sbjct: 2 SNIIMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRW 61
Query: 393 -QAYQH 397
+A QH
Sbjct: 62 MEANQH 67
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 38.1 bits (88), Expect = 0.001
Identities = 20/66 (30%), Positives = 36/66 (54%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E +F+ +L T+ DL + F +G + + IDK+T+ +K F V++ P+ A A
Sbjct: 3 EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62
Query: 395 YQHLDG 400
Q ++G
Sbjct: 63 IQAMNG 68
Score = 30.4 bits (68), Expect = 0.62
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 25 FIYKITQE----QLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFN 79
FIY + QE L F G V ++ + + F F+ Y D AQAA+ N
Sbjct: 8 FIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAMN 67
Query: 80 NTYVFSSRIKVE 91
+ + R+KV+
Sbjct: 68 GFQIGTKRLKVQ 79
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM3 of ACF, also termed APOBEC-1-stimulating
protein, 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. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 83
Score = 38.1 bits (88), Expect = 0.001
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 11/77 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY++NL ++TE++I + F P A V + +D Y FV F RE
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD-----------YAFVHFSNREDAVD 59
Query: 643 ALKVLQNSSLDEHQIEL 659
A+ L +D IE+
Sbjct: 60 AMNALNGKVIDGSPIEV 76
Score = 31.5 bits (71), Expect = 0.24
Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 331 EDIAESGRI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
ED S +I +VRNL + TE+ + K F P A + K + +A V F E
Sbjct: 2 EDTMSSVKILYVRNLMLSTTEETIEKEFNSIKPGAV------ERVKKIRDYAFVHFSNRE 55
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKP 415
A A L+G V G + + KP
Sbjct: 56 DAVDAMNALNGKVIDGSPIEVTLAKP 81
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 38.2 bits (88), Expect = 0.001
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V +P Q E+E+LF +G + R+ V +G+ RG GF+ F + EA+ A+
Sbjct: 6 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAEEAI 64
Query: 746 KAL 748
K L
Sbjct: 65 KGL 67
Score = 32.1 bits (72), Expect = 0.21
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+T+ +L +LF +YG + + +D+ T ++G + F A +A + L
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67
Query: 399 DG 400
+G
Sbjct: 68 NG 69
>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 = 38.0 bits (89), Expect = 0.001
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+Y+ NL+ +T D + F + G + V +A Q Y FV+F + S+
Sbjct: 6 TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD-----ETQPTR--YAFVEFAEQTSVI 58
Query: 642 QALKVLQNSSLDEHQIELKRSN 663
ALK L + +++ SN
Sbjct: 59 NALK-LNGAMFGGRPLKVNHSN 79
Score = 33.0 bits (76), Expect = 0.077
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I+V NL T T D L + F + G + V + D ET T+ +A V F A + L
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD-ETQPTR-YAFVEFAEQTSVINALK-L 63
Query: 399 DGTVFLGRML 408
+G +F GR L
Sbjct: 64 NGAMFGGRPL 73
Score = 31.1 bits (71), Expect = 0.40
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
I V N+ ++ E F GE+K+VR+ + FVEF + A+K
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD---ETQPTRYAFVEFAEQTSVINALK 62
>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 = 37.5 bits (87), Expect = 0.001
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 10/76 (13%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI V N+ Q E+ LF+A+G + + + R F FV + A RA++
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAV---------LSCAVMRQFAFVHLRGEAAADRAIE 52
Query: 747 ALCQSTHLYGRRLVLE 762
L L+GR+LV+E
Sbjct: 53 EL-NGRELHGRKLVVE 67
Score = 34.4 bits (79), Expect = 0.019
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IFV N+ ++++L LFE YG + + + FA V A +A +
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAV--------MRQFAFVHLRGEAAADRAIEE 53
Query: 398 LDGTVFLGRML 408
L+G GR L
Sbjct: 54 LNGRELHGRKL 64
Score = 29.4 bits (66), Expect = 1.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFG 472
I V N+ T +L+ALFE +G
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYG 25
Score = 28.2 bits (63), Expect = 2.4
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
+QE+L+A FE G V + R+FAF+ E A A++ N + ++
Sbjct: 13 SQEELRALFEAYGAVLSCAV-------MRQFAFVHLRGEAAADRAIEELNGRELHGRKLV 65
Query: 90 VE 91
VE
Sbjct: 66 VE 67
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 37.5 bits (87), Expect = 0.001
Identities = 16/62 (25%), Positives = 32/62 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV +LS VT+ L F + ++ + D ++ +++G+ V+F + A A +
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 399 DG 400
+G
Sbjct: 62 NG 63
Score = 35.6 bits (82), Expect = 0.007
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEW 763
F AF R+ M SG RG+GFV F ++ +A+ A+ + L R + W
Sbjct: 20 FSAFPSCSDARVMWDM-KSGRSRGYGFVSFRSQQDAENAINEM-NGKWLGSRPIRCNW 75
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 38.0 bits (88), Expect = 0.001
Identities = 21/57 (36%), Positives = 33/57 (57%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++FV L V E DLT+ F ++GP+ + + DK+T K +GF V F + A +A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57
Score = 31.0 bits (70), Expect = 0.43
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L + E + HF + GP+ V K G+GFV F +S ++
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGK-----KRGFGFVYFQNHDSADK 56
Query: 643 ALKVLQNSSLDEHQIELKRS 662
A V++ ++ H++E+K++
Sbjct: 57 AA-VVKFHPINGHRVEVKKA 75
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 37.7 bits (87), Expect = 0.002
Identities = 17/48 (35%), Positives = 31/48 (64%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV L+ TE+ + + F ++G + + LP+D +T+K +GF +TF
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITF 53
Score = 28.8 bits (64), Expect = 2.6
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
K KI V + +A + ++ E F FGE++ + LP + RGF F+ F ++
Sbjct: 1 KDPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMD-PKTNKRRGFVFITFKEEDPV 59
Query: 742 KRAMK 746
K+ ++
Sbjct: 60 KKVLE 64
Score = 28.4 bits (63), Expect = 3.3
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 578 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
+P +++ LN +TE+ IR +F + G I ++ + DPK+ + G+ F+ F
Sbjct: 2 DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELP--MDPKTNKR---RGFVFITFKEE 56
Query: 638 ESLNQALK 645
+ + + L+
Sbjct: 57 DPVKKVLE 64
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 37.7 bits (87), Expect = 0.002
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
++F+ LS+ T++ L + F ++G + E ++ D T +++GF VTF+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50
Score = 31.5 bits (71), Expect = 0.22
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + + +Q Q + E F FGE+K + + + + RGFGFV F+ + K
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-TKRSRGFGFVTFMDQAGVD---K 57
Query: 747 ALCQSTH 753
L QS H
Sbjct: 58 VLAQSRH 64
>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 = 37.7 bits (87), Expect = 0.002
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY++NL ++ED+I++ F + P V + +D Y FV F +RE
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-----------YAFVHFTSREDAVH 52
Query: 643 ALKVLQNSSLDEHQIEL 659
A+ L + L+ IE+
Sbjct: 53 AMNNLNGTELEGSCIEV 69
Score = 36.2 bits (83), Expect = 0.004
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++VRNL +ED + K F ++ P + K + +A V F E A A +L
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCV------ERVKKIRDYAFVHFTSREDAVHAMNNL 57
Query: 399 DGTVFLGRMLHLIPGKP 415
+GT G + + KP
Sbjct: 58 NGTELEGSCIEVTLAKP 74
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 37.3 bits (87), Expect = 0.002
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPI--DKETDKTKGFALVTFLMPEHATQAYQ 396
++V NL++ T++DL + G + + K K+KGFA V F A +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 397 HLDGTVFLGR 406
L+G F G+
Sbjct: 61 KLEGREFNGK 70
Score = 28.0 bits (63), Expect = 3.8
Identities = 13/71 (18%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ NL + +T++ + + G + ++ + + K+ G+ S G+ +V+F + +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSI-KFFEHKANGK--SKGFAYVEFASEAAAAA 57
Query: 643 ALKVLQNSSLD 653
+ L+ +
Sbjct: 58 VKEKLEGREFN 68
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 37.7 bits (87), Expect = 0.002
Identities = 22/62 (35%), Positives = 30/62 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IF+ NL E L ++F +G + V + D T+K KGF VT E A A L
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 399 DG 400
+G
Sbjct: 64 NG 65
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM1 of FCA, a gene controlling
flowering time in Arabidopsis, encoding a flowering time
control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains), and
a WW protein interaction domain. .
Length = 80
Score = 37.6 bits (87), Expect = 0.002
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV ++ T+TE ++ +FE++G + EV + DK T +G V + + A +A +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60
Query: 398 LDGTVFL 404
L L
Sbjct: 61 LHNQRTL 67
Score = 34.6 bits (79), Expect = 0.022
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V ++P + EV +F+ G + V + K +G +G FV++ T++EA RA++
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDK-RTGHQQGCCFVKYSTRDEADRAIR 59
Query: 747 ALCQSTHLYG 756
AL L G
Sbjct: 60 ALHNQRTLPG 69
Score = 31.5 bits (71), Expect = 0.29
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ ++ TE +R F++ G + + VA KD ++ Q G FV++ TR+ ++
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNV--LEVAIIKDKRTGHQQ---GCCFVKYSTRDEADR 56
Query: 643 ALKVLQN 649
A++ L N
Sbjct: 57 AIRALHN 63
Score = 29.9 bits (67), Expect = 1.00
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
IT+++++ FEE G V +V + K G + F+ Y D+A A+ +N
Sbjct: 11 ITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRALHN 63
>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 = 37.6 bits (87), Expect = 0.002
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 9/89 (10%)
Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
ED++R L+I NL+ N +E +RR F K G I V + R P + Y
Sbjct: 2 EDDQRATR---NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKR------PARGQGGAYA 52
Query: 631 FVQFYTRESLNQALKVLQNSSLDEHQIEL 659
F++F + ++A + + + I++
Sbjct: 53 FLKFQNLDMAHRAKVAMSGRVIGRNPIKI 81
Score = 36.1 bits (83), Expect = 0.006
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG--FALVTFLMPEHATQAYQ 396
+F+ NL + V+E +L + F+KYG + EV++ K + +G +A + F + A +A
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVI---KRPARGQGGAYAFLKFQNLDMAHRAKV 67
Query: 397 HLDGTVFLGRMLHLIPGK 414
+ G V + + GK
Sbjct: 68 AMSGRVIGRNPIKIGYGK 85
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 37.3 bits (86), Expect = 0.002
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV LS+ ++ DL F K+G + + + +D T +++GF + F + +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 398 ----LDGTV 402
LDG +
Sbjct: 61 KEHRLDGRL 69
Score = 28.0 bits (62), Expect = 3.6
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V + + + ++++ F FGE+ + K +G RGFGF+ F +A K
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTI-KMDPNTGRSRGFGFILF---KDASSVEK 56
Query: 747 ALCQSTHLYGRRLV 760
L Q H RL+
Sbjct: 57 VLEQKEHRLDGRLI 70
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 37.3 bits (86), Expect = 0.002
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA----TQA 394
+F+ LS+ T+ DL F K+G + + L +D T +++GF V F E Q
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 395 YQHLDGTV 402
L+G V
Sbjct: 61 EHKLNGKV 68
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM2 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 = 37.2 bits (86), Expect = 0.002
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I+V + ++TE+ L + F + L + LP D + K + + F + AT A H+
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60
Query: 399 DG 400
G
Sbjct: 61 TG 62
>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 = 37.3 bits (87), Expect = 0.002
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV--ARKKDPKSPGQFLSMGYGFVQFYTRE 638
TTL+I +L+ TE+ ++ F++ G I S+ + R G +V TR+
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR-------------GCAYVCMETRQ 49
Query: 639 SLNQALKVLQNSSLDEHQIEL 659
++AL+ L+N L +I++
Sbjct: 50 DAHRALQKLRNVKLAGKKIKV 70
Score = 35.4 bits (82), Expect = 0.009
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV--ILPIDKETDKTKGFALVTFLMPEHATQ 393
S +++ +LS VTE+DL LFE+YG + + I P +G A V + A +
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP--------RGCAYVCMETRQDAHR 53
Query: 394 AYQHLDGTVFLGRML 408
A Q L G+ +
Sbjct: 54 ALQKLRNVKLAGKKI 68
Score = 33.1 bits (76), Expect = 0.073
Identities = 17/77 (22%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ + ++ + + +++ LF+ +GE++ + M+ RG +V T+ +A RA++
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSI----DMIPP---RGCAYVCMETRQDAHRALQK 57
Query: 748 LCQSTHLYGRRLVLEWA 764
L L G+++ + WA
Sbjct: 58 LRNVK-LAGKKIKVAWA 73
Score = 32.7 bits (75), Expect = 0.081
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
+ + +L + DLK LFE +G++ + ++PP G V + A A L
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRG-CAYVCMETRQDAHRALQKLRNV 61
Query: 507 KFKEVPLYLEWAP 519
K + + WAP
Sbjct: 62 KLAGKKIKVAWAP 74
Score = 29.2 bits (66), Expect = 1.4
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTTFL---GMAYIGFKDEKNCNKALNKNKS 280
T+ + +L V ++DLK F+ + S+ + G AY+ + ++ ++AL K ++
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSI--DMIPPRGCAYVCMETRQDAHRALQKLRN 60
>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 = 37.6 bits (87), Expect = 0.002
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 12/73 (16%)
Query: 571 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYG 630
ED++R + TL++ NL+ TE +RR F + G I V D K PG+ + YG
Sbjct: 1 EDDQR---ANRTLFLGNLDITVTETDLRRAFDRFGVITEV------DIKRPGRGQTSTYG 51
Query: 631 FVQFYTRESLNQA 643
F++F E+L+ A
Sbjct: 52 FLKF---ENLDMA 61
Score = 32.6 bits (74), Expect = 0.12
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 331 EDIAESGR-IFVRNLSYTVTEDDLTKLFEKYGPLAEV 366
ED + R +F+ NL TVTE DL + F+++G + EV
Sbjct: 1 EDDQRANRTLFLGNLDITVTETDLRRAFDRFGVITEV 37
Score = 29.1 bits (65), Expect = 2.0
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
+T+ L+ F+ G +T+V +K G+ + F+ + D A A + + + I
Sbjct: 19 VTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMSGKVLRRNPI 78
Query: 89 KV 90
K+
Sbjct: 79 KI 80
>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 = 37.2 bits (87), Expect = 0.003
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 13/88 (14%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASV---TVARKKDPKSP-----GQFLSMGYGFVQ 633
T+++ NL + + +++ FK+ GPI SV +V K+ + V
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61
Query: 634 FY----TRESLNQALKVLQNSSLDEHQI 657
Y ES +ALK L + + H I
Sbjct: 62 AYVVFKEEESAEKALK-LNGTEFEGHHI 88
Score = 35.7 bits (83), Expect = 0.009
Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 25/89 (28%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKP-----------LPLASVRTTFLGM-------------- 260
T+ V NLP KKKDLK FK +P+ +
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61
Query: 261 AYIGFKDEKNCNKALNKNKSFWKGKQLNI 289
AY+ FK+E++ KAL N + ++G + +
Sbjct: 62 AYVVFKEEESAEKALKLNGTEFEGHHIRV 90
Score = 34.9 bits (81), Expect = 0.020
Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 18/87 (20%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYG----------PLAEVILP-----IDKETDKTKGF--A 381
+FV NL T + DL KLF+++G P+ E LP I K+ K A
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 382 LVTFLMPEHATQAYQHLDGTVFLGRML 408
V F E A +A + +GT F G +
Sbjct: 63 YVVFKEEESAEKALKL-NGTEFEGHHI 88
Score = 29.2 bits (66), Expect = 2.0
Identities = 23/68 (33%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGD-----LGRVLVPPYGITGLVEFLQKNQAKAAFNS 502
R + V NLP T DLK LF+ FG V V + V ++K N
Sbjct: 1 RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60
Query: 503 LAYTKFKE 510
AY FKE
Sbjct: 61 NAYVVFKE 68
Score = 27.6 bits (62), Expect = 6.4
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRL 717
+ V N+P K+ ++++LFK FG ++ VR
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRF 32
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 36.7 bits (85), Expect = 0.003
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++V NL + E ++ LF KYGP+ ++ L K + G+A + F A A +
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57
Query: 398 LDGTVFLGRML 408
DG F G+ L
Sbjct: 58 RDGYDFDGQRL 68
Score = 30.5 bits (69), Expect = 0.41
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 17/81 (20%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFG-----ELKF-VRLPKKMVGSGLHRGFGFVEFITKNEA 741
+ V N+P ++ EVE+LF +G +LK R P G+ F+EF +A
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPP----------GYAFIEFEDARDA 51
Query: 742 KRAMKALCQSTHLYGRRLVLE 762
+ A++ G+RL +E
Sbjct: 52 EDAIRGR-DGYDFDGQRLRVE 71
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM2 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), 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 = 96
Score = 37.4 bits (87), Expect = 0.003
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V N++Y VT D L ++F K+G +L I T + AL+ F A A
Sbjct: 5 RVIVENMTYPVTLDVLHQIFSKFG----TVLKIITFTKNNQFQALIQFADAVSAQAAKLS 60
Query: 398 LDG 400
LDG
Sbjct: 61 LDG 63
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 37.0 bits (86), Expect = 0.003
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
I + LS T + F +G + E L +D T ++ G VTF
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF 47
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 36.9 bits (85), Expect = 0.003
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
IFV NL + V L ++F G + + DK+ K++G VTF P A QA
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKD-GKSRGMGTVTFEQPIEAVQAISMF 61
Query: 399 DGTVFLGRMLHL 410
+G R +H+
Sbjct: 62 NGQFLFDRPMHV 73
Score = 31.5 bits (71), Expect = 0.23
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+K+ ++LK F GTV +K +GK R + + + +A A+ FN ++F
Sbjct: 10 FKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFNGQFLFDR 69
Query: 87 RIKVE 91
+ V+
Sbjct: 70 PMHVK 74
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 36.9 bits (85), Expect = 0.003
Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFALVTFLMPEH 390
IFV+ L VT + + F++ G + + L D+ET K KG A V+F P
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64
Query: 391 ATQAYQHLDGTVFLGR 406
A A DG F G
Sbjct: 65 AKAAIDWFDGKEFSGN 80
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 36.6 bits (85), Expect = 0.004
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTF------LGMAYIGFKDEKNCNKALNKN 278
T+ ++ P VK+K ++ +F PL ++R G A++ K E++ KAL +N
Sbjct: 1 FTVKMRGAPFNVKEKHIREFFSPLKPVAIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRN 60
Query: 279 KSFWKGKQLNIY 290
K + G+ + ++
Sbjct: 61 KDYMGGRYIELF 72
Score = 35.0 bits (81), Expect = 0.011
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ +R PF K+ + E F + +R+ K G GF FV+ ++ + K+A+K
Sbjct: 3 VKMRGAPFNVKEKHIREFFSPL-KPVAIRIVKNDHGRKT--GFAFVDLKSEEDLKKALK 58
Score = 26.9 bits (60), Expect = 8.3
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+ ++ FN E IR F P+A + + + + G+ FV + E L
Sbjct: 2 TVKMRGAPFNVKEKHIREFFSPLKPVA-IRIVKNDHGRK------TGFAFVDLKSEEDLK 54
Query: 642 QALK 645
+ALK
Sbjct: 55 KALK 58
>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 = 36.6 bits (85), Expect = 0.004
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEK-YGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
++ V NL VTE + + F GP+ V+L + E K+ G A +TF AT+AY
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYN-EGGKSTGIANITFKRAGDATKAYD 59
Query: 397 HLDGTVFLGR 406
+G + G
Sbjct: 60 KFNGRIDDGN 69
Score = 36.6 bits (85), Expect = 0.004
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 29 ITQEQLKAKF-EEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVF-SS 86
+T+ Q++ F + G + V L Y GK A I + R A A D FN +
Sbjct: 11 VTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNR 70
Query: 87 RIKVE 91
++KVE
Sbjct: 71 KMKVE 75
Score = 30.1 bits (68), Expect = 0.86
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---------GMAYIGFKDEKNCNKALNK 277
++V NLP V + ++ YF + ++ L G+A I FK + KA +K
Sbjct: 2 VIVSNLPKDVTEAQIREYFVS-QIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 36.3 bits (84), Expect = 0.004
Identities = 23/57 (40%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
RI+V NL V E DL LF KYG + ++ L K FA V F P A A
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDA 54
Score = 28.6 bits (64), Expect = 1.9
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 10/62 (16%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG---FGFVEFITKNEAKR 743
+I V N+P ++ ++E+LF +G ++ + L + RG F FV F +A+
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNR-------RGLVPFAFVRFEDPRDAED 53
Query: 744 AM 745
A+
Sbjct: 54 AV 55
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 36.3 bits (84), Expect = 0.004
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
GS++ + IP + + LF++ G L RL M SGL+RGF + ++ + A A
Sbjct: 1 GSEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRL--MMTFSGLNRGFAYAKYSDRRGASAA 58
Query: 745 MKAL 748
+ L
Sbjct: 59 IATL 62
Score = 30.9 bits (70), Expect = 0.39
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 25 FIYKITQE----QLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
FI KI Q+ +L F+ GT+ + +L T G R FA+ Y A AA+ +N
Sbjct: 5 FIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLHN 64
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 36.3 bits (84), Expect = 0.004
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G + + NL TV+ + L +F+ YG + E+ +ET + V F A +A +
Sbjct: 2 GTLVIFNLDPTVSSETLRSIFQVYGDVKEL-----RETPCKREQRFVEFFDVRDAAKALR 56
Query: 397 HLDGTVFLGR 406
++G G+
Sbjct: 57 AMNGKEISGK 66
Score = 28.3 bits (63), Expect = 2.8
Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 9/76 (11%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+++ N+ + +F+ +G++K +R P K R FVEF +A +A++
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKELRETPCK-------REQRFVEFFDVRDAAKALR 56
Query: 747 ALCQSTHLYGRRLVLE 762
A+ + G+ +V+E
Sbjct: 57 AM-NGKEISGKPVVIE 71
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 36.5 bits (84), Expect = 0.004
Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
I++R +P ++++ EL ++F + VRL K+ +G+ RGF FVEF +A M
Sbjct: 8 IMLRGLPINITENDIRELIESFEGPQPADVRLMKRK--TGVSRGFAFVEFYHLQDATSWM 65
Query: 746 KALCQSTHLYGRRLVLEWA 764
+A + + G+ + + ++
Sbjct: 66 EANQKKLVIQGKTIAMHYS 84
Score = 33.8 bits (77), Expect = 0.042
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKY-GPLAEVILPIDKETDKTKGFALVTFLMPEH 390
D ES I +R L +TE+D+ +L E + GP + + ++T ++GFA V F +
Sbjct: 1 DEKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQD 60
Query: 391 ATQ 393
AT
Sbjct: 61 ATS 63
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 36.4 bits (84), Expect = 0.005
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V + QA + EVEE+F +G ++ + + + + RG FV++ +K A+ A+K
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQS--RGCAFVKYSSKEMAQAAIK 58
Query: 747 AL 748
AL
Sbjct: 59 AL 60
Score = 36.0 bits (83), Expect = 0.007
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV L+ TE ++ ++F YG + ++ + D E +++G A V + E A A +
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59
Query: 398 LDGT 401
L+G
Sbjct: 60 LNGV 63
Score = 33.3 bits (76), Expect = 0.069
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
T+++++ F G V D+ + + R AF+ Y ++ AQAA+ N Y
Sbjct: 12 TEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNGVYT 65
Score = 32.9 bits (75), Expect = 0.089
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ LN +TE + F G + + + R + S G FV++ ++E
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDE------MKQSRGCAFVKYSSKEMAQA 55
Query: 643 ALKVL 647
A+K L
Sbjct: 56 AIKAL 60
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, 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. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play 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 = 77
Score = 36.1 bits (83), Expect = 0.006
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49
Score = 28.0 bits (62), Expect = 4.4
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
KI V I ++ + + F+ +G+++ + + GSG RGF FV F
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 49
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 36.1 bits (83), Expect = 0.006
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IFVRNL + T L F + G + + I E K+KG +V F PE A +A +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVRFESPEVAERACRM 58
Query: 398 LDGTVFLGR 406
++G GR
Sbjct: 59 MNGYKLNGR 67
Score = 29.2 bits (65), Expect = 1.7
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 12/85 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPI--ASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
++++NL F+ T ++ F +CG + A + + K S G G V+F + E
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK---------SKGCGVVRFESPEVA 52
Query: 641 NQALKVLQNSSLDEHQIELKRSNRN 665
+A +++ L+ +I++ R +RN
Sbjct: 53 ERACRMMNGYKLNGREIDV-RIDRN 76
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated in
protein shuttling and protein-protein interactions. .
Length = 77
Score = 36.1 bits (83), Expect = 0.006
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL + +L + F YGPL V + GFA V F P A A +
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 55
Query: 398 LDGTVFLG 405
LDG V G
Sbjct: 56 LDGKVICG 63
Score = 29.2 bits (65), Expect = 1.6
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V N+ A + E+E F +G L+ V + + G F FVEF +A+ A++
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG------FAFVEFEDPRDAEDAVR 54
Query: 747 AL 748
L
Sbjct: 55 GL 56
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 39.2 bits (91), Expect = 0.007
Identities = 19/70 (27%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYI 585
KE + K ++ EEE E E++ +E+ ++D++ + +++ +ED+E E + D+TL+
Sbjct: 33 KKENAIRKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDD-DEDDEDEDDDDSTLH- 90
Query: 586 KNLNFNSTED 595
+ +S +D
Sbjct: 91 ---DDSSADD 97
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 35.7 bits (83), Expect = 0.007
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 349 TEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
+ED+L K+F KYG +++V++ K KG A+V F + A A ++ G
Sbjct: 17 SEDELRKIFSKYGDVSDVVVSS-----KKKGSAIVEFASKKAAEAAVENECG 63
>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 = 35.8 bits (83), Expect = 0.008
Identities = 17/57 (29%), Positives = 23/57 (40%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
++ V+ LP DL FG + V + P LVEF + AKA N
Sbjct: 3 PVVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNHAQ 59
Score = 29.3 bits (66), Expect = 1.5
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVIL 368
VR L VTE DL + ++GP++ V +
Sbjct: 7 VRGLPDGVTEADLVEALSEFGPISYVTM 34
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 36.2 bits (83), Expect = 0.008
Identities = 19/66 (28%), Positives = 35/66 (53%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E +F+ +L + DL ++F +G + + IDK+T+ +K F V++ P A A
Sbjct: 6 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65
Query: 395 YQHLDG 400
Q ++G
Sbjct: 66 IQAMNG 71
>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 = 35.7 bits (83), Expect = 0.008
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 15/80 (18%)
Query: 582 TLYIK----NLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
TLY+ E+ +RRHF + G I + V K G FV++ R
Sbjct: 3 TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSK-----------GIAFVRYKYR 51
Query: 638 ESLNQALKVLQNSSLDEHQI 657
S A + + + SLD ++
Sbjct: 52 ASAEFAKEAMADQSLDGGEV 71
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 35.4 bits (81), Expect = 0.009
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 10/61 (16%)
Query: 686 SKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
S++ + N+ K+S+VE +F +G K+VG +H+GF FV+++ + A+ A
Sbjct: 2 SRVFIGNLNTLVVKKSDVEAIFSKYG---------KIVGCSVHKGFAFVQYVNERNARAA 52
Query: 745 M 745
+
Sbjct: 53 V 53
Score = 33.4 bits (76), Expect = 0.045
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 336 SGRIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ R+F+ NL + V + D+ +F KYG + + KGFA V ++ +A A
Sbjct: 1 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAA 52
Query: 395 YQHLDGTVFLGRMLHL 410
DG + G++L +
Sbjct: 53 VAGEDGRMIAGQVLDI 68
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 35.7 bits (83), Expect = 0.009
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL---AEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
IFV +L+ VT+ L + F P A+V++ D T ++KG+ V F + +A
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVM--DPVTGRSKGYGFVRFGDEDERDRAL 61
Query: 396 QHLDGTVFLGR 406
++G R
Sbjct: 62 TEMNGVYCSSR 72
Score = 32.3 bits (74), Expect = 0.13
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 724 SGLHRGFGFVEFITKNEAKRAM 745
+G +G+GFV F ++E RA+
Sbjct: 40 TGRSKGYGFVRFGDEDERDRAL 61
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 35.9 bits (82), Expect = 0.009
Identities = 18/67 (26%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
+ + + ++V +P Q E++ LF + GE++ +L + + +G G+GFV +I +A
Sbjct: 1 EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYIDPKDA 59
Query: 742 KRAMKAL 748
++A+ L
Sbjct: 60 EKAINTL 66
Score = 32.4 bits (73), Expect = 0.12
Identities = 19/77 (24%), Positives = 37/77 (48%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L +T+++L LF G + L DK T ++ G+ V ++ P+ A +A L
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66
Query: 399 DGTVFLGRMLHLIPGKP 415
+G + + + +P
Sbjct: 67 NGLRLQTKTIKVSYARP 83
Score = 28.2 bits (62), Expect = 4.1
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T++ ++ F G I S + R K GQ S+GYGFV + +
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDK---ITGQ--SLGYGFVNYIDPKDA 59
Query: 641 NQALKVLQNSSLDEHQIEL 659
+A+ L L I++
Sbjct: 60 EKAINTLNGLRLQTKTIKV 78
>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 = 35.4 bits (82), Expect = 0.009
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+++ ++ + +ED ++ F CG + V + + S + FV+F ES
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD-------RQHSARFAFVEFADAESAL 54
Query: 642 QALKVLQNSSLDEHQIELKRS 662
AL L + L H + + S
Sbjct: 55 SALN-LSGTLLGGHPLRVSPS 74
Score = 34.6 bits (80), Expect = 0.018
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I V + +++EDDL + F G + V L D++ FA V F E A A L
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEFADAESALSALN-L 59
Query: 399 DGTVFLGRMLHLIPGK 414
GT+ G L + P K
Sbjct: 60 SGTLLGGHPLRVSPSK 75
Score = 34.3 bits (79), Expect = 0.024
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
++++ LK F G VT V+L + RFAF+ + + A +AL
Sbjct: 11 SLSEDDLKEFFSNCGEVTRVRLCGDRQHS-ARFAFVEFADAESALSAL 57
Score = 33.1 bits (76), Expect = 0.063
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
I V I + +++E F GE+ VRL F FVEF A A+
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRL---CGDRQHSARFAFVEFADAESALSALN 58
Score = 29.2 bits (66), Expect = 1.3
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKP------LPLASVRTTFLGMAYIGFKDEKNCNKALNKNK 279
TI V + + + DLK +F + L R A++ F D ++ ALN +
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNLSG 61
Query: 280 SFWKGKQLNI 289
+ G L +
Sbjct: 62 TLLGGHPLRV 71
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of 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 = 81
Score = 35.5 bits (82), Expect = 0.009
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L I L T++ R F GP+ + + R K G S G+GFV + + E
Sbjct: 1 TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDK---RTG--YSYGFGFVDYQSAEDA 55
Query: 641 NQALKVL 647
+A++ L
Sbjct: 56 QRAIRTL 62
Score = 33.1 bits (76), Expect = 0.077
Identities = 18/57 (31%), Positives = 29/57 (50%)
Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
L T+T+++ LF GP+ + DK T + GF V + E A +A + L+G
Sbjct: 8 LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNG 64
Score = 31.6 bits (72), Expect = 0.23
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRAMK 746
+++ +P E LF A G +K ++ + K +G GFGFV++ + +A+RA++
Sbjct: 3 LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKR--TGYSYGFGFVDYQSAEDAQRAIR 60
Query: 747 AL 748
L
Sbjct: 61 TL 62
Score = 28.9 bits (65), Expect = 1.8
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQL-KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSR 87
+T E+ ++ F G V + ++ + G F F+ Y + AQ A+ N + + R
Sbjct: 12 LTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKR 71
Query: 88 IKV 90
IKV
Sbjct: 72 IKV 74
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 35.3 bits (81), Expect = 0.009
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV+ LS TE+ L + F+ G +A I+ D++T +KGF V F E A A + +
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSIAARIV-TDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 399 DGTVFLGRMLHLIPGKPK 416
+ G + L KPK
Sbjct: 60 EDGEIDGNKVTLDFAKPK 77
Score = 31.1 bits (70), Expect = 0.33
Identities = 22/78 (28%), Positives = 44/78 (56%), Gaps = 8/78 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++K L+ ++TE++++ F G IA+ + +D S S G+GFV F + E
Sbjct: 2 TLFVKGLSEDTTEETLKESFD--GSIAA-RIVTDRDTGS-----SKGFGFVDFSSEEDAK 53
Query: 642 QALKVLQNSSLDEHQIEL 659
A + +++ +D +++ L
Sbjct: 54 AAKEAMEDGEIDGNKVTL 71
Score = 29.9 bits (67), Expect = 0.88
Identities = 14/42 (33%), Positives = 29/42 (69%), Gaps = 1/42 (2%)
Query: 724 SGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
+G +GFGFV+F ++ +AK A +A+ + + G ++ L++A+
Sbjct: 35 TGSSKGFGFVDFSSEEDAKAAKEAM-EDGEIDGNKVTLDFAK 75
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 35.4 bits (81), Expect = 0.010
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+++ LSY E D+ + F+ YG + EV D G+ V F A A
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEV--------DLKNGYGFVEFDDLRDADDAVYE 52
Query: 398 LDGTVFLG 405
L+G G
Sbjct: 53 LNGKDLCG 60
Score = 34.6 bits (79), Expect = 0.019
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ + + +QA++ +VE FK +G K++ L G+GFVEF +A A+
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYG---------KILEVDLKNGYGFVEFDDLRDADDAVY 51
Query: 747 ALCQSTHLYGRRLVLE 762
L L G R+++E
Sbjct: 52 EL-NGKDLCGERVIVE 66
Score = 27.6 bits (61), Expect = 6.1
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 13/52 (25%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
+YI L++ + E + R FK G I V L GYGFV+F
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKILEVD-------------LKNGYGFVEF 40
>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 = 35.6 bits (82), Expect = 0.010
Identities = 26/78 (33%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYG--------PLAEVILPIDKETDKTKGFALVTFLMPEH 390
I+V+ L+ VT ++L F+ G V + DKET K KG A V++ P
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 391 ATQAYQHLDGTVFLGRML 408
A A + DG F G L
Sbjct: 63 AKAAVEWFDGKDFQGSKL 80
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding
Raly-like protein (RALYL). This subgroup corresponds to
the RRM of RALYL, also termed heterogeneous nuclear
ribonucleoprotein C-like 3, or hnRNP core protein C-like
3, a putative RNA-binding protein that shows high
sequence homology with Raly, an RNA-binding protein
playing a critical role in embryonic development. The
biological role of RALYL remains unclear. Like Raly,
RALYL contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain. .
Length = 69
Score = 35.0 bits (80), Expect = 0.010
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 9/48 (18%)
Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K++++E +F +G K+VG +H+G+ FV++I++ A+ A+
Sbjct: 15 KKADIEAIFAKYG---------KIVGCSVHKGYAFVQYISERHARAAV 53
>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 = 35.5 bits (82), Expect = 0.010
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 8/71 (11%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPID-KETDKTKG--FALVTFLMPEHATQAY 395
+FV NL T+TE++L + FE+YG V+ +D K + +G +A V FL + A +A
Sbjct: 5 LFVGNLEITITEEELRRAFERYG----VVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAK 60
Query: 396 QHLDGTVFLGR 406
+ G ++GR
Sbjct: 61 VAMSGQ-YIGR 70
Score = 34.7 bits (80), Expect = 0.017
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ NL TE+ +RR F++ G + V + R GQ Y FV+F +L+
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKR----PPRGQ--GNAYAFVKF---LNLD 54
Query: 642 QALK 645
A +
Sbjct: 55 MAHR 58
Score = 34.3 bits (79), Expect = 0.021
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
IT+E+L+ FE G V DV +K G+ +AF+ + D A A + Y+ ++I
Sbjct: 14 ITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSGQYIGRNQI 73
Query: 89 KV 90
K+
Sbjct: 74 KI 75
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 35.5 bits (81), Expect = 0.010
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E LF + GE++ +L + + +G G+GFV +I +A++A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYIDPKDAEKAI 61
Query: 746 KAL 748
L
Sbjct: 62 NTL 64
Score = 31.2 bits (70), Expect = 0.37
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T++ R F G I S + R K GQ S+GYGFV + +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQ--SLGYGFVNYIDPKDA 57
Query: 641 NQALKVLQNSSLDEHQIEL 659
+A+ L L I++
Sbjct: 58 EKAINTLNGLRLQTKTIKV 76
Score = 30.9 bits (69), Expect = 0.41
Identities = 18/77 (23%), Positives = 36/77 (46%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L +T+++ LF G + L DK T ++ G+ V ++ P+ A +A L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 399 DGTVFLGRMLHLIPGKP 415
+G + + + +P
Sbjct: 65 NGLRLQTKTIKVSYARP 81
>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 = 35.1 bits (81), Expect = 0.013
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D L++ L+ TED +RR F+ G I T+ R D G S G FV+F +
Sbjct: 1 DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD----GN--SKGCAFVKFSSHAE 54
Query: 640 LNQALKVLQNS 650
A+ L S
Sbjct: 55 AQAAINALHGS 65
Score = 34.3 bits (79), Expect = 0.025
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT-KGFALVTFLMPEHATQAYQ 396
++FV LS TEDD+ +LFE +G + E I + D KG A V F A A
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECT--ILRGPDGNSKGCAFVKFSSHAEAQAAIN 60
Query: 397 HLDGT 401
L G+
Sbjct: 61 ALHGS 65
Score = 30.5 bits (69), Expect = 0.61
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 696 QAKQSEVEELFKAFG---ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQST 752
Q + +V LF+ FG E +R P G +G FV+F + EA+ A+ AL S
Sbjct: 12 QQTEDDVRRLFEPFGTIEECTILRGP-----DGNSKGCAFVKFSSHAEAQAAINALHGSQ 66
Query: 753 HLYG--RRLVLEWAE 765
+ G LV+++A+
Sbjct: 67 TMPGASSSLVVKFAD 81
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B). This
subgroup corresponds to the RRM of Setd1B, also termed
SET domain-containing protein 1B (Set1B), or lysine
N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits high
homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone H3
at Lys4. Set1B contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), an N- SET domain, and a
C-terminal catalytic SET domain followed by a post-SET
domain. .
Length = 93
Score = 35.4 bits (81), Expect = 0.014
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
L+ + E+ LT + +KYG + EV + + + K G A V F + A A QHL T
Sbjct: 10 LNDNIRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDAVQHLHNTSV 69
Query: 404 LGRMLHL 410
+G ++H+
Sbjct: 70 MGNIIHV 76
>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 = 36.8 bits (85), Expect = 0.014
Identities = 26/68 (38%), Positives = 38/68 (55%)
Query: 528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKN 587
E K +++E +EEE EE EEE +E ED ++ V + EE E++E+ D N
Sbjct: 41 EDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNIN 100
Query: 588 LNFNSTED 595
FNST+D
Sbjct: 101 DIFNSTQD 108
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 38.4 bits (90), Expect = 0.014
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD--- 580
AE K + + KEK+K G++ EEE++E +E ++ E EE EE++E E E
Sbjct: 419 AEKKREEEKKEKKKKAFAGKKKEEEEEE--EKEKKEEEKEEEEEEAEEEKEEEEEKKKKQ 476
Query: 581 TTL 583
TL
Sbjct: 477 ATL 479
Score = 31.0 bits (71), Expect = 2.9
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
+ +K K ++K EEE +E +++ +E+ ++ E E+ EE EE E E +
Sbjct: 409 TKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEE--EEKEKKEEEKEEEEEEAEEE 465
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 34.8 bits (80), Expect = 0.015
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFE-KYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
IFV +LS V E DL LF+ ++ + D T ++G+ V F +A
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Query: 398 LDGTVFLGRML 408
+ G GR +
Sbjct: 64 MQGVYCGGRPM 74
Score = 30.2 bits (68), Expect = 0.79
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 724 SGLHRGFGFVEFITKNEAKRAM 745
+G+ RG+GFV F +N+ +RA+
Sbjct: 40 TGVSRGYGFVRFSDENDQQRAL 61
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 34.5 bits (79), Expect = 0.015
Identities = 21/68 (30%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+++ LSY V E D+ + F YG L E+ D G+ V F A A
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEI--------DLKNGYGFVEFEDSRDADDAVYE 52
Query: 398 LDGTVFLG 405
L+G G
Sbjct: 53 LNGKDLCG 60
Score = 29.5 bits (66), Expect = 1.1
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ + + + ++ +++ F +G K++ L G+GFVEF +A A+
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYG---------KLLEIDLKNGYGFVEFEDSRDADDAVY 51
Query: 747 ALCQSTHLYGRRLVLEWA 764
L L G R+++E A
Sbjct: 52 EL-NGKDLCGERVIVEHA 68
>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 = 0.016
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
A+ +E K ++E E E E +EE+KE ED + +E+ E +EE E E + +
Sbjct: 46 ADEQEAKKSDDQETAEIE--EVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEES 102
Score = 37.0 bits (86), Expect = 0.021
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE--EDNQQGVPEVEENVEEDEERE 576
E V E KE + ++KE + +E EE ++EN E E + + E EE E + E+E
Sbjct: 63 EEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKE 121
Score = 33.9 bits (78), Expect = 0.23
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 525 EAKEKSKGKEKEK---NEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
E E + KE+EK N E+ E+ + +KE+ E+ + E + E E E
Sbjct: 58 ETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKT 114
Score = 31.2 bits (71), Expect = 1.6
Identities = 14/52 (26%), Positives = 32/52 (61%)
Query: 529 KSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
K + KE +E++ ++G+ EK++ +EE+N++ E + E++ E + E +
Sbjct: 66 KEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESN 117
>gnl|CDD|240962 cd12518, RRM_SRSF11, RNA recognition motif in serine/arginine-rich
splicing factor 11 (SRSF11) and similar proteins. This
subgroup corresponds to the RRM of SRSF11, also termed
arginine-rich 54 kDa nuclear protein (SRp54 or p54),
which belongs to a family of proteins containing regions
rich in serine-arginine dipeptides (SR proteins family).
It is involved in bridge-complex formation and splicing
by mediating protein-protein interactions across either
introns or exons. SRSF11 has been identified as a tau
exon 10 splicing repressor. It interacts with a
purine-rich element in exon 10, and suppresses exon 10
inclusion by antagonizing Tra2beta, an
SR-domain-containing protein that enhances exon 10
inclusion. SRSF11 is a unique SR family member and may
regulate the alternative splicing in a tissue- and
substrate-dependent manner. It can directly interact
with the U2 auxiliary factor 65-kDa subunit (U2AF65), a
protein associated with the 3' splice site. In addition,
unlike the typical SR proteins, SRSF11 associates with
other SR proteins but not with the U1 small nuclear
ribonucleoprotein U1-70K or the U2 auxiliary factor
35-kDa subunit (U2AF35). SREK1 has unique properties in
regulating alternative splicing of different pre-mRNAs;
it promotes the use of the distal 5' splice site in E1A
pre-mRNA alternative splicing. It also inhibits cryptic
splice site selection on the beta-globin pre-mRNA
containing competing 5' splice sites. SREK1 contains an
RNA recognition motif (RRM), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and one serine-arginine (SR)-rich domains (SR domains).
.
Length = 80
Score = 35.0 bits (80), Expect = 0.016
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVIL--PIDKETDKTKGFALVTFLMPEHATQAYQ 396
I V N+S + + + + LF G + E+ L P D T V F P+ A + Q
Sbjct: 2 IQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPDDSPLPVTSRVCFVKFHDPDSAVVS-Q 60
Query: 397 HLDGTVFLGRMLHLIP 412
HL TVF+ R L ++P
Sbjct: 61 HLTNTVFVDRALIVVP 76
>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 = 35.4 bits (82), Expect = 0.017
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM--------GY--GF 631
TL++ N+ TE+S++R F +CG + SV + K P S G+ +
Sbjct: 2 TLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAY 61
Query: 632 VQFYTRESLNQALK 645
V F SL++ALK
Sbjct: 62 VVFKKPSSLSRALK 75
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 38.4 bits (89), Expect = 0.019
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL 583
EAK+ KG + + G+ EEE++E EE+ E EE EE+EE E E +L
Sbjct: 844 EAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEE------EEEEEEEEEEEEENEEPLSL 896
Score = 37.3 bits (86), Expect = 0.036
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 12/54 (22%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP 577
+ S G + E+ EEE EE EEE++E E EE EE+E EP
Sbjct: 852 VDGGGGSDGGDSEEEEEEEEEEEEEEEE------------EEEEEEEEEENEEP 893
Score = 34.6 bits (79), Expect = 0.22
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 518 APEGVFAEAKEKSKGKEKE---KNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
V E E+ E + K +E+G +G +EE+ ++ E EE EE+EE
Sbjct: 824 DDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEE 883
Query: 575 REPE 578
E E
Sbjct: 884 EEEE 887
Score = 32.7 bits (74), Expect = 0.93
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 525 EAKEKSKGKEKEKNEEEGE-----EGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
EA+++ + + K +NE EGE +GE+E + ++ E VE + E E E
Sbjct: 666 EAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEG 725
Query: 580 D 580
Sbjct: 726 T 726
Score = 31.5 bits (71), Expect = 2.1
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE 573
E E V E + +++G E E E GEEGEE + E E +G EVE + E
Sbjct: 709 ETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGE---AEGKHEVETEGDRKE 763
Score = 30.0 bits (67), Expect = 6.2
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 506 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEE---EGEEGEEEKKENTAEEDNQQGV 562
T+ +EV E EG E + ++ + +E +E E E E + E +E +G
Sbjct: 710 TEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGE 769
Query: 563 PEVEENVEEDE 573
E E +EDE
Sbjct: 770 TEAEGKEDEDE 780
Score = 29.6 bits (66), Expect = 8.6
Identities = 18/66 (27%), Positives = 29/66 (43%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 575
E EG + KG+ + + E E E E E+ E + + EVE+ E + E
Sbjct: 692 EQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEG 751
Query: 576 EPEPDT 581
+ E +T
Sbjct: 752 KHEVET 757
Score = 29.6 bits (66), Expect = 9.3
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE-----EDNQQGVP--------E 564
A K++ +G+ + + ++ + E ++E AE + +++GV +
Sbjct: 803 HEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGD 862
Query: 565 VEENVEEDEEREPE 578
EE EE+EE E E
Sbjct: 863 SEEEEEEEEEEEEE 876
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 34.7 bits (79), Expect = 0.019
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++FV + E L FE+YG + + + D+++ K +GF VTF
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49
>gnl|CDD|241192 cd12748, RRM4_RBM12B, RNA recognition motif 4 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM4 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 76
Score = 34.7 bits (80), Expect = 0.019
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE--VILPIDKETDKTKGF--ALVTFLMPEHATQA 394
I+ RN + VT+ ++ K F + + E + L D DK G ALV F E A +A
Sbjct: 3 IYARNFPFDVTKVEVQKFFAPF-NIDEDDIYLLYD---DKGVGLGEALVKFKSEEQAMKA 58
Query: 395 YQHLDGTVFLG 405
+ L+G FLG
Sbjct: 59 -ERLNGQRFLG 68
Score = 30.5 bits (69), Expect = 0.51
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 688 ILVRNIPFQAKQSEVEELFKAF--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
I RN PF + EV++ F F E + L G GL G V+F ++ +A +A
Sbjct: 3 IYARNFPFDVTKVEVQKFFAPFNIDE-DDIYLLYDDKGVGL--GEALVKFKSEEQAMKA 58
Score = 29.7 bits (67), Expect = 0.93
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLA--SVRTTF------LGMAYIGFKDEKNCNKALNKN 278
I +N P V K +++ +F P + + + LG A + FK E+ KA N
Sbjct: 3 IYARNFPFDVTKVEVQKFFAPFNIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKAERLN 62
Query: 279 KSFWKGKQL 287
+ G ++
Sbjct: 63 GQRFLGTEV 71
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 34.5 bits (80), Expect = 0.019
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L + +L + F+++G + ID D + +A + + E A A + L
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRR----IDY--DPGRNYAYIEYESIEAAQAAKEAL 54
Query: 399 DGTVFLGRMLHL 410
G G L
Sbjct: 55 RGFPLGGPGRRL 66
Score = 28.3 bits (64), Expect = 2.6
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+E+E F FG ++ + R + ++E+ + A+ A +AL
Sbjct: 13 AELEREFDRFGAIRRIDYDP-------GRNYAYIEYESIEAAQAAKEAL 54
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 34.4 bits (79), Expect = 0.020
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG--FGFVEFITKNEAKRA 744
+I V N+P + ++E+LF +G ++ + L + RG F FVEF +A+ A
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNR-------RGPPFAFVEFEDPRDAEDA 53
Query: 745 MKA 747
+
Sbjct: 54 VYG 56
Score = 32.1 bits (73), Expect = 0.13
Identities = 25/71 (35%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI+V NL + D+ LF KYG I ID + + FA V F P A A
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGA----IRDIDLKNRRGPPFAFVEFEDPRDAEDAVYG 56
Query: 398 LDGTVFLGRML 408
DG + G L
Sbjct: 57 RDGYDYDGYRL 67
>gnl|CDD|241227 cd12783, RRM2_PTBP2, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM2 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and 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 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 101
Score = 35.4 bits (81), Expect = 0.020
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI + N+ Y VT D L ++F K+G + ++I T + AL+ + P +A QA
Sbjct: 5 RIIIDNMYYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYGDPVNAQQAKLA 60
Query: 398 LDG 400
LDG
Sbjct: 61 LDG 63
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 34.8 bits (81), Expect = 0.020
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF-ALVTFLMPEHATQAYQ 396
+ + NL Y VT D L ++F YG + ++++ +K G ALV F E A A +
Sbjct: 3 LVTISNLLYPVTVDVLHQVFSPYGAVEKILI-----FEKNTGVQALVQFDSVESAENAKK 57
Query: 397 HLDG 400
L+G
Sbjct: 58 ALNG 61
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 34.4 bits (79), Expect = 0.020
Identities = 17/66 (25%), Positives = 35/66 (53%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E +F+ +L + +L ++F +G + + +D+ T+++K F V+F P A A
Sbjct: 3 EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62
Query: 395 YQHLDG 400
Q ++G
Sbjct: 63 IQAMNG 68
Score = 28.3 bits (63), Expect = 3.8
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 25 FIYKITQE----QLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDY 77
FIY + QE +L F G V ++ + T + K F F+ + AQAA+
Sbjct: 8 FIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKC--FGFVSFDNPASAQAAIQA 65
Query: 78 FNNTYVFSSRIKVE 91
N + R+KV+
Sbjct: 66 MNGFQIGMKRLKVQ 79
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but 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. Some
family members also contain another RRM domain.
Length = 78
Score = 34.4 bits (79), Expect = 0.022
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
DL FE+YG L +P + T +++ FA V + A AY+ + G F
Sbjct: 15 DLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEEMHGRRFPDT 68
Score = 27.5 bits (61), Expect = 6.2
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
V + + ++ F+ +G L +P R F FVE+ + +A+ A + +
Sbjct: 4 VTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQS--RPFAFVEYESHRDAEDAYEEMH 61
Query: 750 QSTHLYGRR--LVLEWA 764
L ++WA
Sbjct: 62 GR-RFPDTGDTLHVQWA 77
>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 = 34.5 bits (80), Expect = 0.022
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 339 IFVRN--LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
+ V N L V+ ++L ++FEKYG + ++++P K + V++ E A AY
Sbjct: 4 LVVANGGLGNGVSREELLRVFEKYGTVEDLVMPPGKP------YCFVSYSSIEDAAAAYD 57
Query: 397 HLDGTV 402
L+G
Sbjct: 58 ALNGKE 63
Score = 30.3 bits (69), Expect = 0.65
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
+++E+L FE+ GTV D+ GK + F+ Y + A AA D N
Sbjct: 15 VSREELLRVFEKYGTVEDL---VMPPGK--PYCFVSYSSIEDAAAAYDALNG 61
>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 = 34.3 bits (79), Expect = 0.022
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 14/71 (19%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+YI NL + +E+ +R +K GPI + + ++K FV F S+
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEK-----------NIAFVHFL---SIAN 51
Query: 643 ALKVLQNSSLD 653
A+KV+ +
Sbjct: 52 AIKVVTTLPCE 62
Score = 29.7 bits (67), Expect = 1.1
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
S +++ NL + +E++L + EK+GP+ ++ I KE K A V FL +A +
Sbjct: 1 GASRNVYIGNLPESYSEEELREDLEKFGPIDQI--KIVKE----KNIAFVHFLSIANAIK 54
Query: 394 AYQHL 398
L
Sbjct: 55 VVTTL 59
Score = 28.6 bits (64), Expect = 2.5
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ + N+P + E+ E + FG + +++ K+ + FV F++ A + +
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-------KNIAFVHFLSIANAIKVVTT 58
Query: 748 LCQSTHLYGRRL 759
L RR+
Sbjct: 59 LPCEPDYASRRI 70
>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 = 38.0 bits (88), Expect = 0.023
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 519 PEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
P E++E+ +E+E+ EEE EE E+E +E E++ ++ EVE + +EE E
Sbjct: 432 PSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEE--EEVEADNGSEEEMEGS 489
Query: 579 PD 580
+
Sbjct: 490 SE 491
Score = 33.7 bits (77), Expect = 0.43
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQ--QGVPEVEENVEEDEEREPEPD 580
E +E+ + +E+E EEEGE+ EEE++ + +G E + + EE EE +
Sbjct: 449 EEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRN 507
Score = 33.3 bits (76), Expect = 0.55
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 540 EEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 581
+E EE E ++E EE+ ++ E EE EDEE E E +
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEA 478
Score = 31.8 bits (72), Expect = 1.8
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEE---D 572
A S+ E+E++ EE EE EEE++E E + ++G E EE E
Sbjct: 422 SKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNG 481
Query: 573 EEREPEPDT 581
E E E +
Sbjct: 482 SEEEMEGSS 490
Score = 31.4 bits (71), Expect = 2.1
Identities = 14/57 (24%), Positives = 23/57 (40%)
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
+K S E + E EE +E EE+ ++ + E E ++E E E
Sbjct: 422 SKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEA 478
>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 = 34.2 bits (78), Expect = 0.032
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 10/84 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D +Y+ NL N + + R F GP+ SV VAR +P G+ FV+F
Sbjct: 4 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR--NPP--------GFAFVEFEDPRD 53
Query: 640 LNQALKVLQNSSLDEHQIELKRSN 663
A++ L +L ++ ++ SN
Sbjct: 54 AADAVRELDGRTLCGCRVRVELSN 77
Score = 31.6 bits (71), Expect = 0.25
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL + +L + F YGPL V + GFA V F P A A +
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 60
Query: 398 LDGTVFLG 405
LDG G
Sbjct: 61 LDGRTLCG 68
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 34.2 bits (79), Expect = 0.034
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 688 ILVRNIPFQAK-QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V +P + S + +LF G+ F +L + +G RGF FVE+ T +A+ A +
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQL--AIAPNGQPRGFAFVEYATAEDAEEAQQ 62
Query: 747 AL 748
AL
Sbjct: 63 AL 64
Score = 32.2 bits (74), Expect = 0.16
Identities = 26/81 (32%), Positives = 36/81 (44%), Gaps = 5/81 (6%)
Query: 339 IFVRNLSYTVTEDD-LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+FV L T + L KLF + G L I + +GFA V + E A +A Q
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATAEDAEEAQQA 63
Query: 398 LDGTVFLG---RMLHLIPGKP 415
L+G G R+ PG+P
Sbjct: 64 LNGHSLQGSPIRVSFGNPGRP 84
Score = 30.7 bits (70), Expect = 0.66
Identities = 18/64 (28%), Positives = 27/64 (42%)
Query: 31 QEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKV 90
L+ F + G T QL G+ R FAF+ Y + A+ A N + S I+V
Sbjct: 17 VSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
Query: 91 EKCS 94
+
Sbjct: 77 SFGN 80
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 33.8 bits (77), Expect = 0.034
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FEKYG + + + D+++ K +GFA VTF
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 33.6 bits (77), Expect = 0.035
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 347 TVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
TE+D+++ F ++GP+ +V +P ++ + F VTF E
Sbjct: 10 RFTEEDVSEYFGQFGPVLDVRIPYQQK----RMFGFVTFENAE 48
Score = 32.8 bits (75), Expect = 0.074
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
T+E + F + G V DV++ Y + R F F+ + + + L N ++ SR++
Sbjct: 12 TEEDVSEYFGQFGPVLDVRIPY---QQKRMFGFVTFENAETVKRILSKGNPHFICGSRVR 68
Query: 90 V 90
V
Sbjct: 69 V 69
Score = 27.8 bits (62), Expect = 4.0
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 699 QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ +V E F FG + VR+P R FGFV F KR
Sbjct: 13 EEDVSEYFGQFGPVLDVRIPY-----QQKRMFGFVTFENAETVKR 52
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 34.1 bits (79), Expect = 0.036
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAE---VILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+RN+ T++ L +L +++G + LPID + G+A + F+ PE+A + Y+
Sbjct: 3 IRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYKA 62
Query: 398 LDG 400
+G
Sbjct: 63 FNG 65
Score = 28.7 bits (65), Expect = 2.7
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 689 LVRNIPFQAKQSEVEELFKAFG---ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
++RNIP + Q + +L G F+ LP + + G+ F+ F+ A++
Sbjct: 2 MIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDF-KNKCNVGYAFINFVNPEYAEK 58
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 37.5 bits (86), Expect = 0.036
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
E E++ + E+N EE EE EE E EE+ ++ V E+EENVEE+ E E
Sbjct: 1055 ENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAE 1108
Score = 35.9 bits (82), Expect = 0.095
Identities = 23/71 (32%), Positives = 37/71 (52%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
E E+ + E+ EE EE EE E EE +++ V E+EEN+EE+ E E +
Sbjct: 1032 ENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEEN 1091
Query: 585 IKNLNFNSTED 595
++ + N E+
Sbjct: 1092 VEEIEENVEEN 1102
Score = 34.8 bits (79), Expect = 0.26
Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 509 KEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE-VEE 567
KE+ E PE + A+ + +E EE+ EE EE E EE+ ++ V E VEE
Sbjct: 926 KELKNQNENVPEHLKEHAEANIEEDAEENVEEDAEENVEENVEENVEENVEENVEENVEE 985
Query: 568 NVEEDEEREPE 578
NVEE+ E E
Sbjct: 986 NVEENVEENVE 996
Score = 34.4 bits (78), Expect = 0.27
Identities = 30/97 (30%), Positives = 42/97 (43%), Gaps = 8/97 (8%)
Query: 493 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKEN 552
KNQ + L + E E V +A+E + +E EE EE EE E
Sbjct: 929 KNQNENVPEHLKEHAEANIEEDAE---ENVEEDAEENVEENVEENVEENVEENVEENVEE 985
Query: 553 TAEEDNQQGVPE-----VEENVEEDEEREPEPDTTLY 584
EE+ ++ V E +EENVEE+ E E + Y
Sbjct: 986 NVEENVEENVEENVEENIEENVEENVEENIEENVEEY 1022
Score = 34.0 bits (77), Expect = 0.35
Identities = 22/71 (30%), Positives = 36/71 (50%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
E E++ + E+N EE +E E+ E EE +++ V E+EEN EE+ E E + Y
Sbjct: 1005 ENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEY 1064
Query: 585 IKNLNFNSTED 595
+ E+
Sbjct: 1065 DEENVEEIEEN 1075
Score = 34.0 bits (77), Expect = 0.42
Identities = 22/76 (28%), Positives = 32/76 (42%)
Query: 509 KEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEEN 568
+ + Y E E + +E + +E EE EE EE +EN E + EEN
Sbjct: 1059 ENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEENAEEN 1118
Query: 569 VEEDEEREPEPDTTLY 584
EE ++ PE Y
Sbjct: 1119 AEEYDDENPEEHNEEY 1134
Score = 33.6 bits (76), Expect = 0.48
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPE-VEENVEEDEEREPE 578
E V +E + +E EE EE EE E EE+ ++ V E VEEN+EE+ E E
Sbjct: 965 ENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDE 1024
Query: 579 PDTTLYIKNLNFNSTED 595
+ +N+ E+
Sbjct: 1025 ENVEEVEENVEEYDEEN 1041
Score = 32.5 bits (73), Expect = 1.1
Identities = 24/71 (33%), Positives = 35/71 (49%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
E E++ + E+N EE EE EE E EE + VEEN+EE+ E E +
Sbjct: 1013 ENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEI 1072
Query: 585 IKNLNFNSTED 595
+N+ N E+
Sbjct: 1073 EENIEENIEEN 1083
Score = 32.1 bits (72), Expect = 1.6
Identities = 24/59 (40%), Positives = 31/59 (52%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
E V +E + +E EE EE EE E EE +++ V EVEENVEE +E E
Sbjct: 985 ENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVE 1043
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. The hnRNP H protein family
includes hnRNP H (also termed mcs94-1), hnRNP H2 (also
termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also
termed hnRNP 2H9), which represent a group of nuclear
RNA binding proteins that are involved in pre-mRNA
processing. These proteins have similar RNA binding
affinities and specifically recognize the sequence GGGA.
They can either stimulate or repress splicing upon
binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
the splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. For instance, members in this family can regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. The family also
includes a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. It may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 also contains
three potential RRMs responsible for the RNA binding,
and two auxiliary domains (an acidic alpha-helical
domain and an N-terminal alanine-rich region) that may
play a role in protein-protein interactions and provide
binding specificity. .
Length = 75
Score = 33.8 bits (78), Expect = 0.036
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
R +P++A ++++ F+ F L V + + G G VEF T +A AM
Sbjct: 6 RGLPYRATENDI---FEFFSPLNPVNVRIEYNADGRATGEADVEFATHEDAVAAMS 58
>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 = 34.0 bits (78), Expect = 0.036
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L+ E+ +R F G I TV R ++ + S G FV F +R+
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQ------SRGCAFVTFASRQCALN 57
Query: 643 ALKVLQNS 650
A+K + +S
Sbjct: 58 AIKAMHHS 65
Score = 32.1 bits (73), Expect = 0.16
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++FV LS E+D+ +F +G + E + D+ +++G A VTF
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTF 49
Score = 29.8 bits (67), Expect = 1.0
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V + + +++V +F FG ++ + + +G RG FV F ++ A A+K
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD--QNGQSRGCAFVTFASRQCALNAIK 60
Query: 747 ALCQSTHLYG--RRLVLEWAE 765
A+ S + G LV+++A+
Sbjct: 61 AMHHSQTMEGCSSPLVVKFAD 81
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 33.8 bits (78), Expect = 0.038
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
++ V IP + E+ E F E + V + + +RGF FVE+ + A A
Sbjct: 2 CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61
Query: 745 MKALCQST-HLYGRRLVLEWA 764
+ L L+G + ++WA
Sbjct: 62 RRKLVPGRILLWGHEVAVDWA 82
>gnl|CDD|240963 cd12519, RRM1_SREK1, RNA recognition motif 1 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subgroup corresponds to the RRM1 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), and is
involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 generally contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1; plays a modulatory role controlling SR
domain function by involvement in the inhibition of both
constitutive and alternative splicing and in the
selection of splice-site. .
Length = 80
Score = 33.8 bits (77), Expect = 0.040
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVIL--PIDKETDKTKGFALVTFLMPEHATQAYQ 396
I V NLS VT D + LF G + E+ L P + + + + P A Q
Sbjct: 2 IQVTNLSAAVTSDQMRTLFGFLGDIEELRLYPPDNAPLAFSSKVCYIKYREPSSVGVA-Q 60
Query: 397 HLDGTVFLGRMLHLIP 412
HL TVF+ R L ++P
Sbjct: 61 HLTNTVFIDRALIVVP 76
>gnl|CDD|235285 PRK04335, PRK04335, cell division protein ZipA; Provisional.
Length = 313
Score = 36.7 bits (85), Expect = 0.040
Identities = 24/74 (32%), Positives = 37/74 (50%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 575
E AP V A+++ + + E + E EE EE + A+ + PE E +E DE
Sbjct: 108 EEAPIPVQAQSQPQPEKVEPQVEEPRDEEVLEEPEPVAAKVPMAEVQPEEETEIEVDEPE 167
Query: 576 EPEPDTTLYIKNLN 589
EP+P+ L + LN
Sbjct: 168 EPKPEPELDVIVLN 181
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 33.4 bits (76), Expect = 0.042
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+F+ L+ E D+ + F+ YG + ++ D +GF V F P A A
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRI--------RDIDLKRGFGFVEFDDPRDADDAVYE 52
Query: 398 LDG 400
LDG
Sbjct: 53 LDG 55
Score = 33.0 bits (75), Expect = 0.058
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ + + A++ +VE FK +G ++ + L RGFGFVEF +A A+
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDI---------DLKRGFGFVEFDDPRDADDAVY 51
Query: 747 ALCQSTHLYGRRLVLEWA 764
L L R+ +E A
Sbjct: 52 EL-DGKELCNERVTIEHA 68
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains 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 = 87
Score = 33.8 bits (77), Expect = 0.042
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+ ++NLN +ST DSI P A ++ + + K L+ G+ F+Q T
Sbjct: 4 TIILRNLNPHSTMDSI---LSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAA 60
Query: 642 QALKVLQ 648
Q L++LQ
Sbjct: 61 QLLQILQ 67
Score = 28.8 bits (64), Expect = 2.6
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLA--EVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
I +RNL+ T D + Y L+ V + DK+T +GFA + A Q Q
Sbjct: 5 IILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQ 64
Query: 397 HL 398
L
Sbjct: 65 IL 66
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 33.8 bits (77), Expect = 0.047
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++ V N+P +SE++E F +FG + +R+ K VG L FGFV F +R +
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKL-PNFGFVVFDDSEPVQRILG 65
Query: 747 A 747
A
Sbjct: 66 A 66
Score = 27.2 bits (60), Expect = 7.6
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+S ++FV NL + + E +L + F +G + E+ + K F V F
Sbjct: 4 DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVF 54
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 33.4 bits (76), Expect = 0.047
Identities = 13/48 (27%), Positives = 28/48 (58%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++F+ LS+ ++ DLT+ ++G + + + D T +++GF V F
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLF 48
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 33.8 bits (77), Expect = 0.047
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + + +P Q +VE++F FG + R+ +GL RG F+ F ++EA+ A+
Sbjct: 1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQA-TGLSRGVAFIRFDKRSEAEEAI 59
Query: 746 KAL 748
+
Sbjct: 60 TSF 62
Score = 30.4 bits (68), Expect = 0.67
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++ L T+T+ D+ +F ++G + + +D+ T ++G A + F A +A
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 399 DG 400
+G
Sbjct: 63 NG 64
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 33.4 bits (77), Expect = 0.049
Identities = 17/65 (26%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 700 SEVEE--LFKAFGELKF--VRLPKKMVGS-GLHRGFGFVEFITKNEAKRAMKALCQSTHL 754
+V++ L++ F + ++ + K ++ G RG+GFV F ++E KRA+ + ++ L
Sbjct: 11 PDVDDYQLYEFFSK-RYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEMQGASGL 69
Query: 755 YGRRL 759
G+ +
Sbjct: 70 GGKPI 74
Score = 30.0 bits (68), Expect = 0.89
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGP---LAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
+FV +L+ V + L + F K P A+V+L + ++G+ V F +A
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVL---DQNGNSRGYGFVRFSDESEQKRAL 60
Query: 396 QHLDGTVFLG-RMLHLIPGKPK 416
+ G LG + + + PK
Sbjct: 61 TEMQGASGLGGKPIRVSLAIPK 82
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 33.6 bits (76), Expect = 0.049
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E + LF + GE++ +L + + +G G+GFV ++ N+A +A+
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYVDPNDADKAI 62
Query: 746 KAL 748
L
Sbjct: 63 NTL 65
Score = 31.6 bits (71), Expect = 0.27
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T++ + F G I S + R K GQ S+GYGFV +
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDK---ITGQ--SLGYGFVNYVDPNDA 58
Query: 641 NQALKVLQNSSLDEHQIEL 659
++A+ L L I++
Sbjct: 59 DKAINTLNGLKLQTKTIKV 77
Score = 30.9 bits (69), Expect = 0.52
Identities = 18/77 (23%), Positives = 35/77 (45%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V L +T+++ LF G + L DK T ++ G+ V ++ P A +A L
Sbjct: 6 LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65
Query: 399 DGTVFLGRMLHLIPGKP 415
+G + + + +P
Sbjct: 66 NGLKLQTKTIKVSYARP 82
>gnl|CDD|241226 cd12782, RRM2_PTBP1, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM2 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence shows that
the RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 100
Score = 33.9 bits (77), Expect = 0.050
Identities = 24/63 (38%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI V NL Y VT D L ++F K+G +L I T + AL+ + P A A
Sbjct: 6 RIIVENLFYPVTLDVLHQIFSKFG----TVLKIITFTKNNQFQALLQYADPVSAQHAKLS 61
Query: 398 LDG 400
LDG
Sbjct: 62 LDG 64
>gnl|CDD|241108 cd12664, RRM1_RAVER2, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM1 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 = 70
Score = 33.0 bits (75), Expect = 0.066
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KIL++N+P + EV +L K + ELK+ + + ++ FV + +A+ A++
Sbjct: 1 KILIKNLPQDSTNQEVHDLLKDY-ELKYCYVDR-------NKRTAFVTLLNGEQAQDAIR 52
Query: 747 ALCQSTHLYGRRLVLE 762
Q T + G+ + ++
Sbjct: 53 TFHQ-TSVRGKDINVQ 67
>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 = 32.9 bits (76), Expect = 0.067
Identities = 11/47 (23%), Positives = 27/47 (57%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
T + ++ FE+ G V +++++ + KF+ F+ + E+ A+ L+
Sbjct: 12 TLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLE 58
Score = 30.2 bits (69), Expect = 0.54
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+Y+K ++T D I+ F+K G + ++ + R D K G FV+F T E
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSV------FVEFKTEE--- 51
Query: 642 QALKVLQNSSLDEHQIELKRS 662
A K L+ L + EL
Sbjct: 52 DAKKFLEKEKLKYKEKELTVM 72
Score = 29.9 bits (68), Expect = 0.72
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 8/61 (13%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG---FVEFITKNEAKRAMK 746
V+ P A +++E F+ FG++ +R+ + L + F FVEF T+ +AK+ ++
Sbjct: 4 VKGFPKDATLDDIQEFFEKFGKVNNIRMRRD-----LDKKFKGSVFVEFKTEEDAKKFLE 58
Query: 747 A 747
Sbjct: 59 K 59
Score = 27.2 bits (61), Expect = 7.1
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPL-PLASVR------TTFLGMAYIGFKDEKNCNKALNKN 278
T+ VK P D++ +F+ + ++R F G ++ FK E++ K L K
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEKE 60
Query: 279 KSFWKGKQLNI 289
K +K K+L +
Sbjct: 61 KLKYKEKELTV 71
>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 = 32.8 bits (75), Expect = 0.067
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+I++RN+P + EV +L + ++K+ + K + V + ++A RA+
Sbjct: 1 RIVIRNLPADVTKQEVHDLLSDY-QVKYCDVDK-------SKRTAQVTLLNGDQASRAIA 52
Query: 747 ALCQS 751
L QS
Sbjct: 53 KLHQS 57
Score = 29.8 bits (67), Expect = 0.73
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI +RNL VT+ ++ L Y + + DK+K A VT L + A++A
Sbjct: 1 RIVIRNLPADVTKQEVHDLLSDYQ-VKYCDV------DKSKRTAQVTLLNGDQASRAIAK 53
Query: 398 LDGTVFLGRML 408
L + + R +
Sbjct: 54 LHQSSYKERKI 64
Score = 28.6 bits (64), Expect = 2.2
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
I+++NLP ++ L + + V T V L +QA A L + +K
Sbjct: 2 IVIRNLPADVTKQEVHDLLSDY-QVKYCDVDKSKRTAQVTLLNGDQASRAIAKLHQSSYK 60
Query: 510 EVPLYLEWAP 519
E + ++ P
Sbjct: 61 ERKISVQLQP 70
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 33.1 bits (75), Expect = 0.067
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
VRNLS V+ + L + F ++GP+ ++ +D + ++ G +V F A +A++
Sbjct: 4 VRNLSPYVSNELLEEAFSQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKAFERCTE 62
Query: 401 TVFL 404
VFL
Sbjct: 63 GVFL 66
>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 = 33.4 bits (77), Expect = 0.068
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGP----IASVTVARKKDPKSPGQFLSMGYGFVQFY 635
T+Y L T++ +R FK P I +++ + F + V
Sbjct: 2 KDTVYCGKLPKKVTDEDLREFFKDYNPQEIWIFRTRKSKRNPLQLHRHFTAA---LVTLD 58
Query: 636 TRESLNQALKVLQNSSLDEHQIELK 660
T E+L++ ++ L++ L+ +I LK
Sbjct: 59 TEETLDEIIESLKSKKLNGKKISLK 83
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 33.0 bits (76), Expect = 0.069
Identities = 20/61 (32%), Positives = 29/61 (47%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V +P K+ E+ LF+ F + RL K G + GFV+F + A AM A
Sbjct: 3 LFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMDA 62
Query: 748 L 748
L
Sbjct: 63 L 63
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 33.1 bits (75), Expect = 0.070
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 336 SGRIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ R+F+ NL + V + D+ +F KYG + + KG+A V + HA A
Sbjct: 1 NSRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGA 52
Query: 395 YQHLDGTVFLGRMLHL-IPGKPK 416
+G V G+ L + + G+PK
Sbjct: 53 VIGENGRVLAGQTLDINMAGEPK 75
Score = 30.4 bits (68), Expect = 0.57
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 9/48 (18%)
Query: 698 KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
K+S+VE +F +G ++VG +H+G+ FV++ + A+ A+
Sbjct: 15 KKSDVETIFSKYG---------RVVGCSVHKGYAFVQYSNERHARGAV 53
>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 = 32.9 bits (75), Expect = 0.071
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 694 PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTH 753
P + ++E F+ +G+L VR+ R F FV++ T+ +A +A+++ +
Sbjct: 9 PINTRTRDLERHFEPYGKLVNVRI---------RRNFAFVQYETQEDATKALES-TNMSK 58
Query: 754 LYGRRLVLEWA 764
+ R + +E+A
Sbjct: 59 VLDRVISVEYA 69
Score = 31.0 bits (70), Expect = 0.30
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 34 LKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE 91
L+ FE G + +V+++ R FAF+ Y ++ A AL+ N + V I VE
Sbjct: 17 LERHFEPYGKLVNVRIR-------RNFAFVQYETQEDATKALESTNMSKVLDRVISVE 67
Score = 29.8 bits (67), Expect = 0.77
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 14/72 (19%)
Query: 582 TLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TL++ N + N+ + RHF+ G + +V + R + FVQ+ T+E
Sbjct: 1 TLFVINFDPINTRTRDLERHFEPYGKLVNVRIRRN-------------FAFVQYETQEDA 47
Query: 641 NQALKVLQNSSL 652
+AL+ S +
Sbjct: 48 TKALESTNMSKV 59
>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 = 32.9 bits (76), Expect = 0.072
Identities = 21/67 (31%), Positives = 27/67 (40%), Gaps = 10/67 (14%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF---ALVTFLMPEHATQAY 395
+FV NL TE++L +LF + L + KG V F ATQA
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQ--PGFRRLKM-----HNKGGGPVCFVEFEDVSFATQAL 57
Query: 396 QHLDGTV 402
L G V
Sbjct: 58 NSLQGAV 64
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 32.9 bits (76), Expect = 0.079
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLF----EKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHAT 392
R++V NL +TE++L F G P+ + + K FA V F E AT
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEAT 62
Query: 393 QAYQHLDGTVFLGRML 408
A LDG +F G+ L
Sbjct: 63 AALA-LDGIIFKGQPL 77
Score = 28.7 bits (65), Expect = 2.5
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 26/85 (30%)
Query: 583 LYIKNLNFNSTEDSIRRHF----KKCG-------PIASVTVARKKDPKSPGQFLSMGYGF 631
LY+ NL TE+ + F G P+ SV + +K+ + F
Sbjct: 4 LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN-----------FAF 52
Query: 632 VQFYTRESLNQALK----VLQNSSL 652
V+F T E AL + + L
Sbjct: 53 VEFRTVEEATAALALDGIIFKGQPL 77
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 32.5 bits (74), Expect = 0.080
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
++V N+ ++ ++F A+GE+K +R P K R F+EF A+ A+K
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNK-------RHHKFIEFYDVRSAEAALK 56
Query: 747 ALCQSTHLYGRRLVLE 762
AL + + G+R+ LE
Sbjct: 57 AL-NRSEIAGKRIKLE 71
Score = 27.8 bits (62), Expect = 3.9
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G + V NL +V+ DDL ++F YG + E+ +ET + + F A A +
Sbjct: 2 GTLVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAALK 56
Query: 397 HLDGTVFLGRMLHL 410
L+ + G+ + L
Sbjct: 57 ALNRSEIAGKRIKL 70
>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 = 33.4 bits (76), Expect = 0.087
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
+EK GK N E EE ++ ++ EE+ + + EE E +EE E + T
Sbjct: 24 EEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEET 79
Score = 30.3 bits (68), Expect = 1.1
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 533 KEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
KEK++ EE E G+ E+N + E EE+ + + E +
Sbjct: 17 KEKKEVVEEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEE 64
Score = 28.4 bits (63), Expect = 5.0
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 529 KSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
+ G E E+N + + E E++E E+D ++ EE EE+EE E
Sbjct: 33 PANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETE 80
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 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 = 91
Score = 33.0 bits (76), Expect = 0.095
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 346 YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLG 405
DDL + EK+G + +V+ D+ D G A V F PE A + + L+G F G
Sbjct: 22 INELRDDLREECEKFGQVKKVV-VFDRHPD---GVASVKFKEPEEADRCIEALNGRWFAG 77
Query: 406 RMLH 409
R L
Sbjct: 78 RQLE 81
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 32.3 bits (73), Expect = 0.11
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NLS VTE + +LF + GP + +D T + V F HA + +
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 60 NGRKIMGK 67
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 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 = 80
Score = 32.4 bits (74), Expect = 0.11
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAAL 75
++T+EQL A F G V D ++ R FAFI + E+ A+AAL
Sbjct: 13 QVTEEQLAALFSNCGQVVDCRVCGDPNSVLR-FAFIEFTDEEGARAAL 59
>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM1 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 32.3 bits (73), Expect = 0.11
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFK-AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + NIPF K +++L K GE+ +V L M G RG VEF + K+A+
Sbjct: 1 RAFISNIPFDVKWQSLKDLVKEKVGEVTYVEL--LMDAEGKSRGCAVVEFKMEESMKKAV 58
Query: 746 KAL 748
+ L
Sbjct: 59 EVL 61
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 32.4 bits (74), Expect = 0.11
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFK--KCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTR 637
D + ++ L ++ TED I F+ V V ++ K+ G +VQF T
Sbjct: 1 DNVVRLRGLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKT-------GEAYVQFATP 53
Query: 638 ESLNQALK 645
E N+AL
Sbjct: 54 EMANKALL 61
Score = 31.6 bits (72), Expect = 0.18
Identities = 16/59 (27%), Positives = 27/59 (45%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ +R L Y+ TEDD+ F + + ++ + + G A V F PE A +A
Sbjct: 1 DNVVRLRGLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKA 59
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 32.3 bits (73), Expect = 0.13
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 11/77 (14%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+Y + TE +R+ F G I V V F GY FV+F + ES
Sbjct: 2 TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRV-----------FPDKGYSFVRFNSHESAA 50
Query: 642 QALKVLQNSSLDEHQIE 658
A+ + ++++ H ++
Sbjct: 51 HAIVSVNGTTIEGHVVK 67
>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 = 31.8 bits (73), Expect = 0.13
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 620
T+ +KNL ++TE+ IR+ FK CG I V + +
Sbjct: 1 LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV 40
Score = 28.8 bits (65), Expect = 1.8
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 226 TIVVKNLPAGVKKKDLKAYFK 246
T+ VKNLP + ++ +FK
Sbjct: 2 TVKVKNLPKDTTENKIRQFFK 22
Score = 26.8 bits (60), Expect = 8.6
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ V+NL TE+ + + F+ G + EV + + E A++ F + A A
Sbjct: 3 VKVKNLPKDTTENKIRQFFKDCGEIREVKIV-ESEGGL---VAVIEFETEDEALAA 54
>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional.
Length = 413
Score = 34.9 bits (80), Expect = 0.14
Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 3/65 (4%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP 577
+P +E S + +E GE ++ A N Q E E+ E E P
Sbjct: 189 SPGPPQSETPTSS-PPPQSPPDEPGEPQSPTPQQ--APSPNTQQAVEHEDEPTEPEREGP 245
Query: 578 EPDTT 582
Sbjct: 246 PFPGH 250
Score = 34.6 bits (79), Expect = 0.22
Identities = 10/66 (15%), Positives = 16/66 (24%), Gaps = 1/66 (1%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEE-DNQQGVPEVEENVEEDEE 574
+ P G +E+ EE E ++ E P + E
Sbjct: 89 QGGPSGSGSESVGSPTPSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHE 148
Query: 575 REPEPD 580
P
Sbjct: 149 PAPPES 154
Score = 33.8 bits (77), Expect = 0.35
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 6/65 (9%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEE--EKKENTAEE----DNQQGVPEVEENVEEDEEREPE 578
++ + + + +E E + T ++ + QQ V +E E + E P
Sbjct: 188 DSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPPF 247
Query: 579 PDTTL 583
P
Sbjct: 248 PGHRS 252
Score = 33.0 bits (75), Expect = 0.56
Identities = 11/60 (18%), Positives = 17/60 (28%), Gaps = 4/60 (6%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAE----EDNQQGVPEVEENVEEDEEREPEPD 580
+ E + EE E E + ++ E P E E + P P
Sbjct: 161 QQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQ 220
Score = 32.6 bits (74), Expect = 0.78
Identities = 14/69 (20%), Positives = 20/69 (28%), Gaps = 2/69 (2%)
Query: 515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
L + S E E+ NQQ ++ + ED
Sbjct: 118 LSPENTSGSSPESPASHS-PPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPS-HEDSP 175
Query: 575 REPEPDTTL 583
EPEP T+
Sbjct: 176 EEPEPPTSE 184
Score = 32.2 bits (73), Expect = 0.94
Identities = 8/56 (14%), Positives = 16/56 (28%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
+ G + E ++ + + ++ E E E E P P
Sbjct: 137 PPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGP 192
>gnl|CDD|241107 cd12663, RRM1_RAVER1, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM1 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 = 71
Score = 31.8 bits (72), Expect = 0.16
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KIL++ +P EV +L + ELK+ + K ++G FV + +A+ A+K
Sbjct: 2 KILIKGLPADISNQEVHDLLGDY-ELKYCFVDK-------YKGTAFVTLLNGEQAESAIK 53
Query: 747 ALCQSTHLYGRRLVLE 762
QS L R + ++
Sbjct: 54 EFHQS-VLRDREISVQ 68
Score = 27.2 bits (60), Expect = 6.2
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 44 VTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE 91
+ D +LKY K++ AF+ +QA++A+ F+ + + I V+
Sbjct: 21 LGDYELKYCFVDKYKGTAFVTLLNGEQAESAIKEFHQSVLRDREISVQ 68
>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 = 31.8 bits (72), Expect = 0.16
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V N+P +A + E+ LF+ +G K++ + + +GFV K A A++
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYG---------KVLECDIIKNYGFVHMDDKTAADEAIR 52
Query: 747 AL 748
L
Sbjct: 53 NL 54
Score = 29.8 bits (67), Expect = 0.74
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV NL TE ++ LFE+YG + E D K + V A +A ++
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHMDDKTAADEAIRN 53
Query: 398 L 398
L
Sbjct: 54 L 54
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 31.9 bits (72), Expect = 0.17
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFK-AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ + NIP+ K +++L + GE+ +V L K G RG G VEF + K+A+
Sbjct: 1 RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKD--AEGKSRGCGVVEFKDEEFVKKAL 58
Query: 746 KALCQSTHLYGRRL 759
+ + + L GR L
Sbjct: 59 EVMNKYD-LNGRPL 71
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 32.1 bits (73), Expect = 0.17
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
+FV + + E ++ F KYG + EV + D+ T +KG+ V+F
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFY 54
Score = 29.8 bits (67), Expect = 1.2
Identities = 17/80 (21%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
K + + V I + ++E+ F +G +K V++ +G+ +G+GFV F +
Sbjct: 2 KIMPNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR--TGVSKGYGFVSFYDDVDV 59
Query: 742 KRAMKALCQSTHLYGRRLVL 761
++ ++ + +G++L L
Sbjct: 60 QKIVE---SQINFHGKKLKL 76
Score = 28.2 bits (63), Expect = 3.9
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
T+++ ++ E IR F K G + V + + +S GYGFV FY
Sbjct: 7 TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTG------VSKGYGFVSFY 54
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 32.2 bits (74), Expect = 0.19
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 352 DLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLH 409
D+ ++G + ++++ D D G V F E A A Q L+G + GR L+
Sbjct: 41 DVFLELSRFGEIEDLVV-CDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLY 97
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 31.8 bits (72), Expect = 0.20
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 686 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
SK+L +RN+P++ + E+ EL K FG ++ G +R FVEF N+A
Sbjct: 2 SKVLHLRNLPWECTEEELIELCKPFG-----KIVNTKCNVGANRNQAFVEFADLNQA 53
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 32.5 bits (74), Expect = 0.20
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEE 548
A A+EK++ KE+EK +EE +E EEE
Sbjct: 72 AAAEEKAEEKEEEKKKEEEKEEEEE 96
Score = 29.0 bits (65), Expect = 3.1
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE 555
AP A A E+ +++E E++ EE +EE++E
Sbjct: 65 APAAAAAAAAEEKAEEKEE--EKKKEEEKEEEEEEALA 100
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 34.6 bits (79), Expect = 0.21
Identities = 19/78 (24%), Positives = 33/78 (42%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
E +E+EK E E E E+ E + + + + EE +E++E EPE +
Sbjct: 104 SGAENETVEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPK 163
Query: 585 IKNLNFNSTEDSIRRHFK 602
+L N+ E +
Sbjct: 164 RGSLEENNGEFMTHKLKH 181
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48
(RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 32.3 bits (74), Expect = 0.22
Identities = 21/75 (28%), Positives = 34/75 (45%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
ES + V+ + E +L +LF YG + E L + ++ L+ F + A A
Sbjct: 9 ESRYLLVQGVPALGVEKELLELFALYGTIEEYRLLDEYPCEEFTEVYLIKFETIQSARFA 68
Query: 395 YQHLDGTVFLGRMLH 409
+ LD F G +LH
Sbjct: 69 KRKLDERSFFGGLLH 83
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 31.6 bits (72), Expect = 0.22
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKG-FALVTF 385
+FV +E+ L F +GP+ VI+ DK KG +A+V F
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIM------DKDKGVYAIVEF 46
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 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 = 89
Score = 32.0 bits (72), Expect = 0.23
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 2/87 (2%)
Query: 687 KILVRNIPFQAKQSEV-EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ + IP K+ E+ EE+ K + V + +RGF FVE+ + A A
Sbjct: 3 RLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62
Query: 746 KALCQS-THLYGRRLVLEWAEEADNVE 771
+ L L+G ++ ++WAE +V+
Sbjct: 63 RKLMPGRIQLWGHQIAVDWAEPEIDVD 89
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 31.5 bits (72), Expect = 0.24
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAE-VILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+F+ NL V E L F +G + + + D +T +KGFA +++ E + A +
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 398 LDGTVFLGRMLH 409
++G R +
Sbjct: 64 MNGQYLCNRPIT 75
Score = 28.0 bits (63), Expect = 5.1
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 704 ELFKAFGELKFVRLPKKM--VGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
+ F AFG + ++ PK M +G +GF F+ + + + A++A+ +L R + +
Sbjct: 20 DTFSAFGVI--LQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAM-NGQYLCNRPITV 76
Query: 762 EWAEEAD 768
+A + D
Sbjct: 77 SYAFKKD 83
Score = 27.6 bits (62), Expect = 7.0
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I NL+ E + F G I T +DP + S G+ F+ + + E+ +
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQ-TPKIMRDPDTGN---SKGFAFISYDSFEASDA 59
Query: 643 ALKVLQNSSLDEHQI 657
A++ + L I
Sbjct: 60 AIEAMNGQYLCNRPI 74
>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 = 31.2 bits (71), Expect = 0.24
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYG-PLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++ NLS V E DL +LFE++ P++ V++ K G+A V A +A +
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLV-------KKGGYAFVDCPDQSWADKAIEK 53
Query: 398 LDGTVFLGRMLHLIPGKPK 416
L+G + G+++ + PK
Sbjct: 54 LNGKILQGKVIEVEHSVPK 72
Score = 29.6 bits (67), Expect = 1.0
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 13/81 (16%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
LYI NL+ + E +R+ F++ P++SV V + GY FV + +
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG------------GYAFVDCPDQSWAD 48
Query: 642 QALKVLQNSSLDEHQIELKRS 662
+A++ L L IE++ S
Sbjct: 49 KAIEKLNGKILQGKVIEVEHS 69
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 31.6 bits (71), Expect = 0.25
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TLY+ NL+ + TE I + F + GP S + + P Y FV+FY
Sbjct: 1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-------YCFVEFYEHRDAA 53
Query: 642 QALKVL 647
AL +
Sbjct: 54 AALAAM 59
>gnl|CDD|241191 cd12747, RRM2_RBM12, RNA recognition motif 2 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM2 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 75
Score = 31.3 bits (71), Expect = 0.26
Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALC 749
+ +PF + ++ + F + + L K VG + G V+F + ++ A+K
Sbjct: 6 LHGLPFSVLEHDIRDFFHGLR-IDAIHLLKDHVGR--NNGNALVKFYSPHDTFEALK--- 59
Query: 750 QSTHLYGRRLV 760
++ L G+R +
Sbjct: 60 RNRMLMGQRYI 70
>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 = 33.6 bits (77), Expect = 0.27
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
+ EK EK+ E E E+ +EE +++ EE+ + E +E+ ++D++
Sbjct: 143 TEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEE---EEEDEDFDDDDD 194
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 31.1 bits (71), Expect = 0.28
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 346 YTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTV 402
Y +TE+ L K F +G + I+ +K K VTF E A +A L+GT
Sbjct: 12 YGLTEEILKKAFSPFGNI------INISMEKEKNCGFVTFEKMESADRAIAELNGTT 62
Score = 28.0 bits (63), Expect = 4.4
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
Y +T+E LK F G + ++ ++ K + F+ + + + A A+ N T V
Sbjct: 12 YGLTEEILKKAFSPFGNIINISME-----KEKNCGFVTFEKMESADRAIAELNGTTVQGV 66
Query: 87 RIKV 90
++KV
Sbjct: 67 QLKV 70
>gnl|CDD|241228 cd12784, RRM2_ROD1, RNA recognition motif 2 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM2 of ROD1 coding protein Rod1, a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein and negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It might
play a role controlling differentiation in mammals. Rod1
contains four repeats of RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and does have RNA binding
activities. .
Length = 103
Score = 31.9 bits (72), Expect = 0.28
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI V NL Y VT + L ++F K+G +L I T + AL+ + P +A A
Sbjct: 7 RIIVENLFYPVTLEVLHQIFSKFG----TVLKIITFTKNNQFQALLQYADPMNAHHAKMA 62
Query: 398 LDG 400
LDG
Sbjct: 63 LDG 65
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 31.9 bits (73), Expect = 0.32
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
I V + +ED + F +G +AE+ D T G L+ +
Sbjct: 5 IVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKY 51
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 34.2 bits (78), Expect = 0.34
Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 21/98 (21%)
Query: 487 LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEE-- 544
L+E QK+ ++A N+ + KE + K +EK +EE
Sbjct: 3916 LLETEQKSNEQSAANNESDLVSKE-------------DDNKALEDKDRQEKEDEEEMSDD 3962
Query: 545 -GEEEKKENTAEEDNQQGVPEVE-----ENVEEDEERE 576
G +++ + +E+N Q PE E E+++ DE+
Sbjct: 3963 VGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEG 4000
Score = 34.2 bits (78), Expect = 0.38
Identities = 15/76 (19%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVP-EVEENVEEDEEREPEPDTT 582
+ A +S KE + + E+ + ++KE+ E + G+ E++ +++E+ + P +
Sbjct: 3927 SAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENED 3986
Query: 583 LYI-KNLNFNSTEDSI 597
L + ++L + E +
Sbjct: 3987 LDLPEDLKLDEKEGDV 4002
Score = 29.6 bits (66), Expect = 10.0
Identities = 17/74 (22%), Positives = 30/74 (40%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
+ KS E +EE ++G + E EED +G + E+ +E P +
Sbjct: 4104 KMDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEAMS 4163
Query: 585 IKNLNFNSTEDSIR 598
+ + S D +R
Sbjct: 4164 EADRQYQSLGDHLR 4177
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 31.2 bits (71), Expect = 0.35
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+L++ +L E+ I+R F G + SV + R K P GY FV+F +
Sbjct: 1 SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGP-----AGYCFVEFADEATA 55
Query: 641 NQALKVL 647
+ L L
Sbjct: 56 ERCLHKL 62
Score = 28.8 bits (65), Expect = 2.1
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 724 SGLHRGFGFVEFITKNEAKRAMKAL 748
+G G+ FVEF + A+R + L
Sbjct: 38 TGGPAGYCFVEFADEATAERCLHKL 62
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 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 = 92
Score = 31.4 bits (71), Expect = 0.35
Identities = 14/65 (21%), Positives = 26/65 (40%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIK 89
L+ F + T QL +G+ + FA + Y + A+ + + S I+
Sbjct: 16 DVGDLREAFSKIHAPTFCQLACGQDGQLKGFAVLEYESAEMAEMVQQQADGLSLAGSHIR 75
Query: 90 VEKCS 94
V C+
Sbjct: 76 VSFCA 80
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2). MSSP-1 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence CT(A/T)(A/T)T, and stimulates
DNA replication in the system using SV40 DNA. MSSP-1 is
identical with Scr2, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-1 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with c-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 85
Score = 31.2 bits (70), Expect = 0.35
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
+ + + N+P + E+E + K FG++ R+ + G+ GF +E K EA
Sbjct: 1 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 56
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 30.9 bits (70), Expect = 0.37
Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 9/81 (11%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRE 638
P +++ NL + TE+ + H + G I +V V K V+F T E
Sbjct: 6 PTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQ---------ALVEFATEE 56
Query: 639 SLNQALKVLQNSSLDEHQIEL 659
+AL SSL+ I L
Sbjct: 57 QATEALACKHASSLNGSTIRL 77
Score = 29.4 bits (66), Expect = 1.5
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
I V NL VTE+D+ ++G + V + E++ K ALV F E AT+A
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKV---FESNGKKQ-ALVEFATEEQATEA 61
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 33.2 bits (76), Expect = 0.39
Identities = 14/52 (26%), Positives = 24/52 (46%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
E E+ KE E EE+ + E+ + E +E+ + E E E+ + E
Sbjct: 11 ENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDE 62
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 30.7 bits (69), Expect = 0.39
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++++ NLS VT +DL +LF + LP+ + G+A V + A +A +
Sbjct: 3 KLYIGNLSPAVTAEDLRQLF------GDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIET 56
Query: 398 LDGTVFL-GRMLHLIPGKPKE 417
L G V L G+++ + PK+
Sbjct: 57 LSGKVELHGKVMEVDYSVPKK 77
Score = 28.8 bits (64), Expect = 2.4
Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
E+L + FG+ K + ++ SG + FV++ +N A RA++ L L+G+ + +
Sbjct: 15 AEDLRQLFGDRKLPLTGQVLLKSG----YAFVDYPDQNWAIRAIETLSGKVELHGKVMEV 70
Query: 762 EWA 764
+++
Sbjct: 71 DYS 73
>gnl|CDD|201213 pfam00406, ADK, Adenylate kinase.
Length = 186
Score = 32.7 bits (75), Expect = 0.39
Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 19/98 (19%)
Query: 691 RNIPFQAKQSEVEELFKAFGELKFV--------RLPKKMVGSGLHRGFGFVEFITKNEAK 742
R +P QA+ +EE+ + +L +V L +++ G +H G + N K
Sbjct: 84 RTVP-QAE--ALEEMLEYGIKLDYVIEFDVPDEVLVERLTGRRIHPNSGRSYHLEFNPPK 140
Query: 743 RAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRY 780
K L R DN E ++KR Y
Sbjct: 141 VPGKDDVTGEPLSQR--------SDDNEETVKKRLETY 170
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 33.6 bits (77), Expect = 0.39
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 530 SKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP 577
K EKE +EE EE +EEKKE EE+ E + EE EE++
Sbjct: 28 EKEVEKEVPDEEEEEEKEEKKE---EEEKTTDKEEEVDEEEEKEEKKK 72
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which 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 heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 30.8 bits (69), Expect = 0.42
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV-ILPIDKETDKTKGFALVTFLMPEHAT 392
+ S + VR L +V E DL + EK+GP+ V ++P ++ ALV F M E A
Sbjct: 1 SVSPVVHVRGLCESVVEADLVEALEKFGPICYVMMMPFKRQ-------ALVEFEMVESAK 53
Query: 393 Q 393
+
Sbjct: 54 K 54
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 30.5 bits (69), Expect = 0.42
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + +P+ A + +V+E F ++ F++ +G + G V+F T +AK A+
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGLDVEDVIFLKRH-----NGRNNGNAIVKFATFQDAKEAL 56
Query: 746 KALCQSTHLYGRRLV 760
K + L G R +
Sbjct: 57 K---RHRELMGSRYI 68
Score = 28.2 bits (63), Expect = 3.6
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA---Y 395
+F+ L YT E D+ + F + +VI G A+V F + A +A +
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGLD-VEDVIFLKRHNGRNN-GNAIVKFATFQDAKEALKRH 59
Query: 396 QHLDGTVFLGRML 408
+ L G+ ++ ML
Sbjct: 60 RELMGSRYIELML 72
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 30.7 bits (70), Expect = 0.43
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 342 RNLSYTVTEDDLTKLFEKYGP---LAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
R L Y+ T D+ F P + IL + + G A V F E A +A
Sbjct: 7 RGLPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRA 62
Score = 28.8 bits (65), Expect = 2.1
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 688 ILVRNIPFQAKQSEVEELFKAF-------GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
I +R +P+ A +++ F + FV P G G FV F T+ +
Sbjct: 4 IRMRGLPYSATAADILAFFGGLCPVVGGPDGILFVTGP-----DGRPTGDAFVLFETEED 58
Query: 741 AKRAMK 746
A+RA+
Sbjct: 59 AQRALG 64
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 30.8 bits (69), Expect = 0.43
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 11/77 (14%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+Y + TE +R+ F G I + V F GY F++F T ES
Sbjct: 2 TVYCGGIASGLTEQLMRQTFSPFGQIMEIRV-----------FPEKGYSFIRFSTHESAA 50
Query: 642 QALKVLQNSSLDEHQIE 658
A+ + ++++ H ++
Sbjct: 51 HAIVSVNGTTIEGHVVK 67
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 31.1 bits (71), Expect = 0.44
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 14/79 (17%)
Query: 686 SKILVRNIPFQAKQSE-VEELFKAFGELKFVRL--PKKMVGSGL------HRGFG----- 731
++ N+P + E V ELF G + +R+ P + + L H G
Sbjct: 1 RTVVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECA 60
Query: 732 FVEFITKNEAKRAMKALCQ 750
VEF A++A++ L
Sbjct: 61 VVEFEKLEAARKAVEELSA 79
>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM2 of RBM46, also termed
cancer/testis antigen 68 (CT68). It 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 = 85
Score = 31.1 bits (70), Expect = 0.45
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGE--LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
++ + +IP + K+ E+ E K E + + P +RGF FVE+ + A A
Sbjct: 4 RLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSA-TDRTKNRGFAFVEYESHRAAAMA 62
Query: 745 MKALCQST-HLYGRRLVLEWAE 765
+ L T L+G + ++WA
Sbjct: 63 RRKLIPGTFQLWGHTIQVDWAC 84
>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 = 30.3 bits (69), Expect = 0.49
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 34 LKAKFEEKGTVT--DVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRIKVE 91
LK + G VT DV EG + + ++ + AL + T R++VE
Sbjct: 17 LKDFGRQAGDVTYADVDRDQEGEG------VVEFTSQEDMERALRKLDGTEFRGRRVRVE 70
Score = 29.9 bits (68), Expect = 0.66
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-PPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
++V LP DLK GD+ V G+VEF + + A L T+F
Sbjct: 3 VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTEF 62
Query: 509 K 509
+
Sbjct: 63 R 63
Score = 29.9 bits (68), Expect = 0.66
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKR 661
G G V+F ++E + +AL+ L + ++ ++
Sbjct: 38 GEGVVEFTSQEDMERALRKLDGTEFRGRRVRVEE 71
>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 = 30.8 bits (70), Expect = 0.49
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 13/74 (17%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF-YTRESLN 641
+Y+ + ++T +R+ F+ G I +T+ + D YGFV + Y +
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDD--------GDNYGFVTYRYACD--- 53
Query: 642 QALKVLQNSSLDEH 655
A + +++ + D
Sbjct: 54 -AFRAIEHGNDDPT 66
Score = 30.0 bits (68), Expect = 0.92
Identities = 11/53 (20%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
T+ +L+ +F+ G + ++ L + +G + F+ Y A A+++ N+
Sbjct: 13 DTTRSELRQRFQPFGEIEEITLHFRDDGD--NYGFVTYRYACDAFRAIEHGND 63
Score = 28.4 bits (64), Expect = 3.3
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
I+V + T +L + F+ +G + E+ L + D + VT+ A +A +H
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN---YGFVTYRYACDAFRAIEH 60
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 86
Score = 31.0 bits (70), Expect = 0.51
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T+ ++N+ ++ DSI P AS++V+ + K + G+ FVQ + +
Sbjct: 4 TIILRNIAPHTVVDSI---LSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEAS 60
Query: 642 QALKVLQ 648
Q L++LQ
Sbjct: 61 QLLQILQ 67
Score = 29.8 bits (67), Expect = 1.1
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLA--EVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
I +RN++ D + Y L+ + L DK+T + +GFA V A+Q Q
Sbjct: 5 IILRNIAPHTVVDSILSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64
Query: 397 HLDG 400
L
Sbjct: 65 ILQA 68
>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 = 33.2 bits (76), Expect = 0.53
Identities = 38/172 (22%), Positives = 61/172 (35%), Gaps = 29/172 (16%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ VRNL V E DL + +GP++ V++ K ALV F E A
Sbjct: 5 VHVRNLPQDVVEADLVEALIPFGPVSYVMML------PGKRQALVEFEDEESAKACVNFA 58
Query: 399 -DGTVFL-GRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIIL---VK 453
+++ G+ + I N ++ +L V+
Sbjct: 59 TSVPIYIRGQPAF------------FNYSTSQEIKRDG----NSDFDSAGPNKVLRVIVE 102
Query: 454 NLPYRTLPTDLKALFEPFGDLGRVLV--PPYGITGLVEFLQKNQAKAAFNSL 503
N Y L +F P+G + R++ LVEF N A+ A +L
Sbjct: 103 NPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAAL 154
Score = 32.5 bits (74), Expect = 1.0
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 501
++ V+NLP + DL PFG + V++ P LVEF + AKA N
Sbjct: 3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVN 56
Score = 31.7 bits (72), Expect = 1.9
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF-ALVTFLMPEHATQAYQ 396
R+ V N Y +T D L ++F YG + ++ K F ALV F A A
Sbjct: 98 RVIVENPMYPITLDVLYQIFNPYGKVLRIVT-----FTKNNVFQALVEFESVNSAQHAKA 152
Query: 397 HLDG 400
L+G
Sbjct: 153 ALNG 156
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 30.4 bits (69), Expect = 0.55
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+++V N+ + ++++ + GE+ + K+ G VEF T ++ KRA++
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQ------RPNEGVVEFATYSDMKRAIE 55
Query: 747 ALCQSTHLYGRRLVL 761
L T L GR++ L
Sbjct: 56 KL-DGTELNGRKIKL 69
Score = 28.5 bits (64), Expect = 2.2
Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V NLS V+ DL K G EV + +G +V F +A +
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAG---EVTYADAHKQRPNEG--VVEFATYSDMKRAIEK 56
Query: 398 LDGTVFLGRMLHLI 411
LDGT GR + LI
Sbjct: 57 LDGTELNGRKIKLI 70
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3). MSSP-2 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence T(C/A)TT, and stimulates DNA
replication in the system using SV40 DNA. MSSP-2 is
identical with Scr3, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-2 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-2 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 30.8 bits (69), Expect = 0.55
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
+ + + N+P + E+E + K FG++ R+ + G+ GF +E K EA
Sbjct: 1 TNLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEA 56
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 30.4 bits (68), Expect = 0.55
Identities = 17/70 (24%), Positives = 28/70 (40%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V LS DL LF KYG + + + + K + +VT + HL
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 399 DGTVFLGRML 408
T G+ +
Sbjct: 62 HRTELHGQQI 71
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 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 = 85
Score = 30.6 bits (69), Expect = 0.56
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 339 IFVRNLSYTVTEDDLTKLF--EKYGPLAE-----VILPIDKETDKT----KGFALVTFLM 387
+++ NLS+T T++ L + F + + + V +P K K KGFA V F
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 388 PEHATQAYQHLDGTVFLGRML 408
E AT+A L + GR L
Sbjct: 61 QE-ATKAAIALSEKILNGRKL 80
Score = 27.1 bits (60), Expect = 8.6
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHF--KKCGPIASVTVARKKDP----KSPGQFLSMGYGFVQFYT 636
++I NL+F +T++ +R+ F K I + R P K G + G+ +V F +
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 637 RESLNQAL 644
+E+ A+
Sbjct: 61 QEATKAAI 68
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 30.6 bits (69), Expect = 0.57
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
I++RNLS +++ +L K FE +G + E + I +K + +T+ EHA
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEK---YGFITYRHSEHA 54
>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 = 30.2 bits (68), Expect = 0.57
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ N++ +TE I F CG I+++ + + ++ + F +
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKISNLDLTNDGESQT---------ATITFEKPSAAKT 51
Query: 643 ALKVLQNSSLDEHQIEL 659
AL +L N+ L I++
Sbjct: 52 AL-LLDNALLGGKVIQV 67
>gnl|CDD|114629 pfam05917, DUF874, Helicobacter pylori protein of unknown function
(DUF874). This family consists of several hypothetical
proteins specific to Helicobacter pylori. The function
of this family is unknown.
Length = 417
Score = 32.9 bits (74), Expect = 0.64
Identities = 24/102 (23%), Positives = 50/102 (49%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
EG+ + +EK+K E+E ++ E+EK++ + + E E+ E+E+++
Sbjct: 168 EGIELANSQIKAEQEKQKTEQEKQKTEQEKQKTSNIANKNAIELEQEKQKTENEKQDLIK 227
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 621
+ +IK N E+ + KK G A + + + + K+P
Sbjct: 228 EQKDFIKEAEQNCQENHNQFFIKKLGIKAGIAIEIEAECKTP 269
>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 = 32.7 bits (74), Expect = 0.71
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 13/78 (16%)
Query: 517 WAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKE-------------NTAEEDNQQGVP 563
P+ K+ +K E +++EEE EE EEE+ E N+ E D+ G
Sbjct: 117 QLPKKAGNAGKKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNGTSTNSTEVDHGNGSS 176
Query: 564 EVEENVEEDEEREPEPDT 581
+ E +EE E +
Sbjct: 177 GGDNGEEGEEESVTEAEA 194
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 33.1 bits (76), Expect = 0.73
Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 4/93 (4%)
Query: 507 KFKEVPLYL---EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVP 563
+E+ LY ++ E ++ E+ K ++ E EK AE+ +
Sbjct: 429 GAEEIILYFLLKKFLEEEAILKSLEEFKQSIVKEAALSILEEIREKVLEQAEQGCENQ-E 487
Query: 564 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS 596
EV++ V + ++ PE DT L ++ L N
Sbjct: 488 EVKKEVPKKVKKIPEVDTYLLLEELGINEETYE 520
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 31.9 bits (73), Expect = 0.73
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 525 EAKEKSKGKEKEKNEEEG-------EEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
E K + +E E+ E E EE EE+ E ++ Q + E+E ++E EER
Sbjct: 2 EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEERY 60
Score = 30.0 bits (68), Expect = 3.6
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 539 EEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
EE+ E+ EEE +E EE + V E E + E E
Sbjct: 2 EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQ 43
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A). This
subgroup corresponds to the RRM of Setd1A, also termed
SET domain-containing protein 1A (Set1A), or lysine
N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is localized
to euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1A contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. In contrast to Set1B, Set1A
additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 30.3 bits (68), Expect = 0.79
Identities = 20/66 (30%), Positives = 31/66 (46%)
Query: 344 LSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVF 403
L+ V E L + K+G + EV + + +T K G A V F A +HL T
Sbjct: 10 LNDNVREPFLADMCRKFGEVEEVEILLHPKTRKHLGLARVLFTSTRGAKDTVKHLHNTSV 69
Query: 404 LGRMLH 409
+G ++H
Sbjct: 70 MGNIIH 75
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 30.8 bits (70), Expect = 0.82
Identities = 13/40 (32%), Positives = 15/40 (37%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEED 557
AP A + E E E EEEK+E EE
Sbjct: 60 APAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEES 99
>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 = 32.6 bits (74), Expect = 0.91
Identities = 17/73 (23%), Positives = 27/73 (36%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY 584
E +E S +E E + E E GEEE ++ ++ + + E E P T
Sbjct: 234 EGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESDDDSETPGEGARPARPFTSTGGE 293
Query: 585 IKNLNFNSTEDSI 597
F + D
Sbjct: 294 PDYKVFTTAFDET 306
Score = 29.1 bits (65), Expect = 9.5
Identities = 12/60 (20%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 525 EAKEKSKGKEKEKNEEEGEE----GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
E E+ + ++EE+G++ E++++ E + Q+G E + E E +
Sbjct: 198 ELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEE 257
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM2 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 86
Score = 30.3 bits (68), Expect = 0.91
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLA--EVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
I +RN++ D + Y LA + L DK+T + +GFA V A+Q Q
Sbjct: 5 IILRNIAPHTVVDSILTALAPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64
Query: 397 HLDG 400
L
Sbjct: 65 ILQS 68
>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 = 30.0 bits (67), Expect = 0.91
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPF-GDLGRVL-VPPYGITGLVEFLQKNQAKAAFNSLAY 505
R + V LP P +L LF PF G G ++ + G V F +++A+AA N+L
Sbjct: 2 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 61
Query: 506 TKFK-EVPLYL 515
+F E+P L
Sbjct: 62 IRFDPEIPQTL 72
>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein.
Length = 198
Score = 31.7 bits (72), Expect = 0.92
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE---REPEPDTT 582
+KSK K+KEK EE ++ + ++ E+N+ EE+ + E
Sbjct: 64 TTKKSKKKDKEKLT---EEEKKPESDDDKTEENENDPDNNEESGDSQESASANSLSDIDN 120
>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 = 0.92
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 463 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN----SLAYTKFKEVPLYL 515
L L +PFG + L+ +E +A A N A K V +YL
Sbjct: 17 QLLQLAKPFGTIVNHLILNKINEAFLEMSTHEEAVAMVNYYQTKPALVFGKPVRVYL 73
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 30.0 bits (67), Expect = 0.92
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKT-KGFALVTFLMPEHATQAYQHLD 399
V+NLS V+ + L + F ++GP+ ++ +D T KGF V F A +A +
Sbjct: 4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGF--VEFAAKPAARKALERCA 61
Query: 400 GTVFL 404
FL
Sbjct: 62 DGAFL 66
>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 = 30.3 bits (69), Expect = 0.94
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 18/73 (24%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGRV-LVP--------------PYGIT---GLVEF 490
I+ + +P R P L+ L +G++GR+ L P G VEF
Sbjct: 2 IVYLSRIPPRMNPAKLRQLLSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEF 61
Query: 491 LQKNQAKAAFNSL 503
K AK SL
Sbjct: 62 EDKKVAKRVAESL 74
>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 = 32.5 bits (74), Expect = 0.96
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 521 GVFAEAKEKSKGKE-KEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
G+ +AK+ K+ K+ ++E +E ++ E +E +++ E E+ +DEE E
Sbjct: 141 GIETKAKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSD 200
Query: 580 DTTL 583
Sbjct: 201 SEDY 204
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 30.1 bits (68), Expect = 1.0
Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 10/68 (14%)
Query: 687 KIL-VRNIPFQAKQSEVEELFKAFG-------ELKFVRLPKKMVGSGLHRGFGFVEFITK 738
K+L + N+P Q E+E F +G LK V S GF F +
Sbjct: 1 KVLYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPD-EDAYVSS-KDSISGFAVFQSH 58
Query: 739 NEAKRAMK 746
EA A+
Sbjct: 59 EEAMEALA 66
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily may share similar expression patterns
and functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation. It directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 29.6 bits (67), Expect = 1.0
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEK-YGPLAEVILPIDKETDKTKGFALVTF 385
+FV L +T +L + E+ YG + V + D+ G A VTF
Sbjct: 3 VFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTF 50
>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 = 1.1
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V + V+ +L ++FEK G + I + +KG +V+F A +AY+ L
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVKG----IFVKKLLSKGIVIVSFHDLRQAIKAYKDL 59
Query: 399 DGTVFLGR 406
G
Sbjct: 60 QSKRAFGD 67
Score = 28.5 bits (64), Expect = 2.3
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 448 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLV 479
R + V +P ++LK +FE GD+ + V
Sbjct: 2 RYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFV 33
>gnl|CDD|219714 pfam08066, PMC2NT, PMC2NT (NUC016) domain. This domain is found at
the N-terminus of 3'-5' exonucleases with HRDC domains,
and also in putative exosome components.
Length = 91
Score = 29.9 bits (68), Expect = 1.1
Identities = 14/67 (20%), Positives = 35/67 (52%), Gaps = 8/67 (11%)
Query: 650 SSLDEHQIELKRS-----NRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEE 704
SSL I+ RS +++L+ ++ + +++ + S+ IP ++++ +VE+
Sbjct: 9 SSLAAQDIDFYRSFDPEFSQSLDEQSQRLLSLINDLLQSADSR---GRIPDRSEEDDVED 65
Query: 705 LFKAFGE 711
+KA +
Sbjct: 66 QWKAVSD 72
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 32.3 bits (73), Expect = 1.3
Identities = 6/48 (12%), Positives = 14/48 (29%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 581
E+E+ + + + + P + DE P+
Sbjct: 372 EREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEK 419
Score = 31.9 bits (72), Expect = 1.5
Identities = 8/54 (14%), Positives = 14/54 (25%), Gaps = 1/54 (1%)
Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
+E+ + + E + E E E+ P PD
Sbjct: 373 REQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEP-EVPEKAAPIPD 425
Score = 30.3 bits (68), Expect = 4.7
Identities = 7/68 (10%), Positives = 17/68 (25%), Gaps = 3/68 (4%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE--- 574
P + +A + + + E + + E + + +E
Sbjct: 375 QPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPDELAV 434
Query: 575 REPEPDTT 582
P D
Sbjct: 435 AGPGDDPA 442
>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 = 1.3
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK- 509
V L RT D+ +L E FG + + ++PP G + + + A A L+ K
Sbjct: 9 VGQLDKRTTQQDVTSLLEEFGPIESINMIPPRG-CAYIVMVHRQDAYRALQKLSRGNVKV 67
Query: 510 -EVPLYLEWA 518
+ + + WA
Sbjct: 68 NQKSIKIAWA 77
>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM3 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, like other hnRNP H protein family members,
hnRNP H3 has an extensive glycine-rich region near the
C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 75
Score = 29.6 bits (66), Expect = 1.3
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+R +PF+A +S++ F L +R+ + G G VEF+T +A AM
Sbjct: 5 MRGLPFRATESDIANFF---SPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAM 57
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM2 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contain two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 88
Score = 29.7 bits (66), Expect = 1.3
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
+ + + N+P + E+E + K FG + R+ + +G+ RG GF
Sbjct: 2 TNLYISNLPVSMDEQELENMLKPFGHVISTRILRD--ANGVSRGVGF 46
>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 = 30.4 bits (69), Expect = 1.4
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
KE+ + + + E + EE E + E+D +G PE E+E
Sbjct: 70 KERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEY 117
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 31.8 bits (73), Expect = 1.4
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 489 EFLQKNQAKA-AFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEE 547
+ L K A+A A + K + L+ A + + +E+E+ EEE EE
Sbjct: 262 DILSKAVAQALALAAALADK-DALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEE 320
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 29.2 bits (66), Expect = 1.4
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 227 IVVKNLPAGVKKKDLKAYFKPLPLA--------SVRTTFLGMAYIGFKDEKNCNKALNKN 278
I +KN+P V K ++ A+F + +A LG AY+ F E++ +A +
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLH 61
Query: 279 KSFWKGK 285
+ KG+
Sbjct: 62 RKKLKGR 68
Score = 28.1 bits (63), Expect = 3.6
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 688 ILVRNIPFQAKQSEVEELFK--AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
I ++NIPF + EV F A E L +G G +VEF+++ +A RA
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHIL---YDKTGKTLGEAYVEFVSEEDAMRAE 58
Query: 746 K 746
+
Sbjct: 59 R 59
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 97
Score = 29.8 bits (67), Expect = 1.4
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGF-ALVTFLMPEHATQAYQHLD 399
+ N+ Y VT D L +F +G + ++ + +K GF AL+ + A A + L+
Sbjct: 8 IENMQYAVTVDVLHTVFSAFGFVQKIAI-----FEKNGGFQALIQYPDVPTAVNAKEALE 62
Query: 400 G 400
G
Sbjct: 63 G 63
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 31.6 bits (72), Expect = 1.4
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 532 GKEKEKNEEEGEEGEEEKKENTAEEDNQQGV--PEVEENVEEDEERE 576
G ++E EE E+ EEE++E+ E + + EE ++DE +
Sbjct: 273 GGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
>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 = 30.7 bits (68), Expect = 1.4
Identities = 21/48 (43%), Positives = 27/48 (56%)
Query: 533 KEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
+ E EEE E EEE +E E+ + PE EE EE+ E EPEP+
Sbjct: 60 PDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPE 107
Score = 29.5 bits (65), Expect = 3.3
Identities = 18/53 (33%), Positives = 26/53 (49%)
Query: 528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
+ E+E+ E EEGEEE + E+ + EE E + E EPEP+
Sbjct: 59 DPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPE 111
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 30.0 bits (68), Expect = 1.4
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEE 548
A A + + +E+E+ EEE EE EEE
Sbjct: 71 AAAAAEEEEEEEEEEEEEEEESEEE 95
Score = 28.1 bits (63), Expect = 5.8
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEE 548
A A A + +E+E+ EEE EE EE
Sbjct: 64 AAAAAAAAAAAAEEEEEEEEEEEEEEEESEE 94
Score = 27.7 bits (62), Expect = 7.7
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEE 547
A A A E+ + +E+E+ EEE E EE
Sbjct: 66 AAAAAAAAAAEEEEEEEEEEEEEEEESEEE 95
Score = 27.7 bits (62), Expect = 8.7
Identities = 16/37 (43%), Positives = 20/37 (54%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTA 554
AP A A + E+E+ EEE EE EEE+ E A
Sbjct: 60 APVAAAAAAAAAAAAAEEEEEEEEEEEEEEEESEEEA 96
>gnl|CDD|227199 COG4862, MecA, Negative regulator of genetic competence,
sporulation and motility [Posttranslational
modification, protein turnover, chaperones / Signal
transduction mechanisms / Cell motility and secretion].
Length = 224
Score = 31.2 bits (71), Expect = 1.4
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 535 KEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE------EREPEPDTTLYIKNL 588
K K E EG + +E + E+ ++G+ ++EE ++ E E E EPD YI L
Sbjct: 77 KSKIEGEGPDDLDEFLDMPDEDGAEEGLEQLEEKFDDVEKEEQGDEAEKEPDYLYYI--L 134
Query: 589 NFNSTEDSI 597
F ED I
Sbjct: 135 RFADFEDVI 143
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 75
Score = 29.3 bits (66), Expect = 1.5
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V+N+PF A E+ + F + + V L +G G V F T EA A++
Sbjct: 3 VKVQNLPFTATIEEILDFFYGYRVIPGSVSL--LYNDNGAPTGEATVAFDTHREAMAAVR 60
Query: 747 AL 748
L
Sbjct: 61 EL 62
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 31.5 bits (71), Expect = 1.5
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
+ A + E+E+ EE + EEE+ E + +G E+ E EE+ E
Sbjct: 163 DNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAE 217
Score = 31.1 bits (70), Expect = 2.1
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
+ W + EA + E EEE E + ++E EE E + E+EE
Sbjct: 156 IVWDNDEDNDEAPPAQPDVDNE--EEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEE 213
Query: 575 REPEPD 580
E E
Sbjct: 214 EEAEGS 219
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 30.4 bits (69), Expect = 1.6
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 575
K+K K K+K K + EE E K + ++ ++G + +E E E+
Sbjct: 94 KQKKKKKKKAKKGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIMEK 142
>gnl|CDD|151339 pfam10891, DUF2719, Protein of unknown function (DUF2719). This
family of proteins with unknown function appears to be
restricted to Nucleopolyhedrovirus.
Length = 81
Score = 29.5 bits (66), Expect = 1.6
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 90 VEKCSNLGDTTKPKSWSKYAPDSSAYQKL 118
+KC N T+PK+WS Y S+ Y L
Sbjct: 53 ADKCPNNFAVTQPKTWSNYTNCSALYYPL 81
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein (hnRNP) H protein family.
This subfamily corresponds to the RRM2 of hnRNP H
protein family which includes hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'),
hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation. hnRNP
H3 may be involved in the splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. .
Length = 77
Score = 29.3 bits (66), Expect = 1.6
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL--------GMAYIGFKDEKNCNKALN 276
+ ++ LP G K+++ +F L + T G AY+ F +++ +AL
Sbjct: 1 GVVRLRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALG 60
Query: 277 KNK 279
K+K
Sbjct: 61 KHK 63
>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 = 29.0 bits (65), Expect = 1.7
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 621
L++ NL N E+ I HFK+ G + SV + K+
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGG 40
Score = 27.8 bits (62), Expect = 5.1
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
V N+P ++ + E FK +G ++ V LPK+ G+ FV+F+ A++A A
Sbjct: 4 VGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA---AFVDFVDIKSAQKAHNA 59
>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 = 29.2 bits (66), Expect = 1.7
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V+NLS V+ + L + F ++G + ++ +D + ++ G +V F A A +
Sbjct: 4 VKNLSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIKRCSE 62
Query: 401 TVFL 404
FL
Sbjct: 63 GCFL 66
Score = 28.0 bits (63), Expect = 3.9
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 449 IILVKNLPYRTLPTDLKALFEPFGDLGR--VLVPPYGIT---GLVEFLQKNQAKAAFN 501
+ VKNL L+ F FG++ R V+V G + G+VEF +K A+AA
Sbjct: 1 ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIK 58
>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 = 29.0 bits (65), Expect = 1.8
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
++V LP DLK GD+ V G TG+VEFL+ K A L +KF+
Sbjct: 3 VIVSGLPPTGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFLRYEDMKYAVKKLDDSKFR 61
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 29.1 bits (66), Expect = 1.8
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E ++ ++NL + L K +K P + K + FA VTF E +A
Sbjct: 4 EIFKVEIKNLPKYIGFKQLKKFLKKQL-----FKPHKIKLLKRQDFAFVTFRSEEERQKA 58
Query: 395 YQHLDGTVFLGRML 408
+ LDG + GR+L
Sbjct: 59 LEILDGFKWKGRVL 72
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin or
neuroguidin, which blocks translation initiation through
interfering with the assembly of eIF-4E and eIF-4G.
Although CPEB-1 is mainly located in cytoplasm, it can
shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to high sequence similarity, members in
this subfamily may share similar expression patterns and
functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
CPEB-2 impedes target RNA translation at elongation; it
directly interacts with the elongation factor, eEF2, to
reduce eEF2/ribosome-activated GTP hydrolysis in vitro
and inhibit peptide elongation of CPEB2-bound RNA in
vivo. CPEB-3 is a sequence-specific translational
regulatory protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 112
Score = 29.6 bits (66), Expect = 2.0
Identities = 28/122 (22%), Positives = 44/122 (36%), Gaps = 15/122 (12%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY-- 395
++FV L + +TE D+ F ++G L V P K+ + + +
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFGSLQ-VDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNL 455
QH G VFL E E +V + C SE + F S V+
Sbjct: 61 QHPKGYVFL----------LFEKERSVRSLLLAC-SEEEGGLFRITSS-SSTDSKRVQIR 108
Query: 456 PY 457
P+
Sbjct: 109 PW 110
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 31.6 bits (71), Expect = 2.0
Identities = 13/57 (22%), Positives = 30/57 (52%)
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
A+E ++ +++ E+ +E+ + +E+ ++ E++ +EDEE E D T
Sbjct: 141 AEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFT 197
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 31.2 bits (70), Expect = 2.0
Identities = 26/79 (32%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 522 VFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 581
E KE S+G +KE+ +EE E E K+E ++ ++ G EE E+DE E E T
Sbjct: 282 AEIENKEVSEG-DKEQQQEEVENAEAHKEEVQSDRPDEIG----EEKEEDDENEENERHT 336
Query: 582 TLYIKNLNFNSTEDSIRRH 600
L LN +R
Sbjct: 337 ELLADELNELEKGIEEKRR 355
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 31.2 bits (71), Expect = 2.1
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
+ KE+ + K++ + E ++ ++E++E EED +VE D+E E
Sbjct: 76 EKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIE 128
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 31.5 bits (72), Expect = 2.1
Identities = 16/33 (48%), Positives = 17/33 (51%), Gaps = 9/33 (27%)
Query: 365 EVILPIDKETDKTKGFALVTF---------LMP 388
EVI+ IDKE KG AL TF LMP
Sbjct: 99 EVIVQIDKEERGNKGAALTTFISLAGSYLVLMP 131
>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 = 2.1
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKK-CGPIASVT 611
TL++ NL ++TE +R+ F G I SV
Sbjct: 2 TLFLVNLPVDTTERHLRKLFGSGGGIIESVV 32
>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase PARP-10, RNA recognition motif 2
in PARP-14, RNA recognition motif in N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35),
RNA-binding protein 43 (RBM43) and similar proteins.
This subfamily corresponds to the RRM1 and RRM2 of
PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi),
interferon-induced 35 kDa protein (IFP 35) and
RNA-binding protein 43 (RBM43). PARP-10 is a novel
oncoprotein c-Myc-interacting protein with
poly(ADP-ribose) polymerase activity. It is localized to
the nuclear and cytoplasmic compartments. In addition to
PARP activity, PARP-10 is also involved in the control
of cell proliferation by inhibiting c-Myc- and
E1A-mediated cotransformation of primary cells. PARP-10
may also play a role in nuclear processes including the
regulation of chromatin, gene transcription, and
nuclear/cytoplasmic transport. PARP-10 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two overlapping C-terminal domains composed of
a glycine-rich region and a region with homology to
catalytic domains of PARP enzymes (PARP domain). In
addition, PARP-10 contains two ubiquitin-interacting
motifs (UIM). PARP-14, also termed aggressive lymphoma
protein 2, is a member of the B aggressive lymphoma
(BAL) family of macrodomain-containing PARPs. Like
PARP-10, PARP-14 also includes two RRMs at the
N-terminus. Nmi, also termed N-myc and STAT interactor,
is an interferon inducible protein that interacts with
c-Myc, N-Myc, Max and c-Fos, and other transcription
factors containing bHLH-ZIP, bHLH or ZIP domains.
Besides binding Myc proteins, Nmi also associates with
all the Stat family of transcription factors except
Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma)
stimulation, Nmi can enhance Stat-mediated
transcriptional activity through recruiting the Stat1
and Stat5 transcriptional coactivators, CREB-binding
protein (CBP) and p300. IFP 35 is an interferon-induced
leucine zipper protein that can specifically form
homodimers. Distinct from known bZIP proteins, IFP 35
lacks a basic domain critical for DNA binding. In
addition, IFP 35 may negatively regulate other bZIP
transcription factors by protein-protein interaction.
For instance, it can form heterodimers with B-ATF, a
member of the AP1 transcription factor family. Both Nmi
and IFP35 harbor one RRM. RBM43 is a putative
RNA-binding protein containing one RRM, but its
biological function remains unclear. .
Length = 74
Score = 28.8 bits (65), Expect = 2.1
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKY-----GPLAEVILPIDKETDKTKGFALVTF 385
+ V L TV++D L FE G + V + KG ALVTF
Sbjct: 1 RCVLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQY------LREKGSALVTF 48
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 28.8 bits (64), Expect = 2.4
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 690 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
V+N+P +EE F FG+++ R + G G G VEF K A++A+
Sbjct: 4 VKNLPQFVSNELLEEAFSMFGQVE--RAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 28.7 bits (65), Expect = 2.7
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFG--FVEFITKNEAKRAMKAL 748
EE K +G++ V +P+ G G FVEF +A++A AL
Sbjct: 30 EECGK-YGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLAL 76
Score = 28.7 bits (65), Expect = 2.9
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 351 DDLTKLFEKYGPLAEVILPIDKETDKTK---GFALVTFLMPEHATQAYQHLDGTVFLGR 406
+D+ + KYG + V++P + G V F E A +A L G F GR
Sbjct: 26 EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGR 84
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. 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 RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 28.7 bits (65), Expect = 2.8
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 350 EDDLTKLFEKYGPLAEVIL---PIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGR 406
+D++ + EKYG + VI+ + D + F V F + A +A + L+G F GR
Sbjct: 20 KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIF--VEFSDADEAIKAVRALNGRFFGGR 77
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 31.0 bits (70), Expect = 2.8
Identities = 13/48 (27%), Positives = 23/48 (47%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDT 581
E + E EG + EE + + + ++G + E E+ E E + DT
Sbjct: 248 EAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDT 295
Score = 30.6 bits (69), Expect = 3.7
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEE--DEEREPEPDTT 582
E ++S+ E E + EGEEGE + E + + ++ E +E+ E ++ R P T
Sbjct: 255 EGSDESEEDEAEATDGEGEEGEMDAAEASEDSESD----ESDEDTETPGEDARPATPFTE 310
Query: 583 L 583
L
Sbjct: 311 L 311
>gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional.
Length = 815
Score = 30.9 bits (70), Expect = 2.9
Identities = 10/49 (20%), Positives = 25/49 (51%)
Query: 528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
E+S K K++ +++ K A ++ ++ +EE++ ++ RE
Sbjct: 34 EQSPKKAKKEKKQDDSGNGNGKSAEDAVKEFEEFCKAIEEHLSIEQMRE 82
>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM1 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 75
Score = 28.4 bits (63), Expect = 3.1
Identities = 8/28 (28%), Positives = 21/28 (75%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVIL 368
VRN+ + ++E+DL +L + +G + ++++
Sbjct: 5 VRNVGHEISENDLLQLVQPFGVVTKLVM 32
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 30.6 bits (69), Expect = 3.1
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 519 PEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
P G E +G+ + + E+GEE E E+ E EE+ ++ E E + EE
Sbjct: 56 PYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEE 111
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 30.8 bits (70), Expect = 3.2
Identities = 23/139 (16%), Positives = 43/139 (30%), Gaps = 12/139 (8%)
Query: 470 PFGD--LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPL--YLEWAPEGVFAE 525
P+G+ + + + + + K + K ++P L A+
Sbjct: 41 PYGEELVDYLEEEDPTLRDPQISVVSSVTKLSKGPKDEPKQVKIPRQSGLSEEVAEAEAK 100
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYI 585
A + K+ +E E EE E +E + V+E D I
Sbjct: 101 ATSVAAEATTPKSIQELVEALEELLEELLKE------TASDPVVQELVSIFN--DLIDSI 152
Query: 586 KNLNFNSTEDSIRRHFKKC 604
K N +S+ K+
Sbjct: 153 KEDNLKDDLESLIASAKEE 171
>gnl|CDD|153105 cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding
domain. Rubrerythrin-like domain, similar to
rubrerythrin, a nonheme iron binding domain found in
many air-sensitive bacteria and archaea, and member of a
broad superfamily of ferritin-like diiron-carboxylate
proteins. Rubrerythrin is thought to reduce hydrogen
peroxide as part of an oxidative stress protection
system. The rubrerythrin protein has two domains, a
binuclear metal center located within a four-helix
bundle of the rubrerythrin domain, and a rubredoxin
domain. The Rubrerythrin-like domains in this CD are
singular domains (no C-terminus rubredoxin domain) and
are phylogenetically distinct from rubrerythrin domains
of rubrerythrin-rubredoxin proteins.
Length = 123
Score = 29.2 bits (66), Expect = 3.5
Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 521 GVFAEAKEKSKGKEKEKNEE--EGEEGEEEKKENTAEEDNQQGVPEVEENVEE---DEER 575
FAE K KE E EGE G E K++ A E +G+ E + E DE R
Sbjct: 51 ARFAELLGKVSEDTKENLEMMLEGEAGANEGKKDAATEAKAEGLDEAHDFFHEAAKDEAR 110
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 30.7 bits (70), Expect = 3.6
Identities = 13/61 (21%), Positives = 34/61 (55%)
Query: 520 EGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
+ + + + E++EEE E+G +++ E ++D ++ +V+ + EE++E + +
Sbjct: 304 DEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDS 363
Query: 580 D 580
D
Sbjct: 364 D 364
Score = 30.7 bits (70), Expect = 3.9
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 524 AEAKEKSKGKEKEK----NEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
E E+ K E E+ EE ++ EEE + +A++ + + P+ ++N + E E
Sbjct: 265 KEEAERLKKLEAERLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEE 324
Query: 580 D 580
+
Sbjct: 325 E 325
Score = 30.0 bits (68), Expect = 6.1
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 517 WAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
+G E +E G + +++EE+ ++ EE++E+ D ++ + + + E+DEE E
Sbjct: 315 GLGQGEEDEEEE-EDGVD-DEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEE 372
Query: 577 PEPDT 581
E
Sbjct: 373 EEEKE 377
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 29.7 bits (67), Expect = 3.7
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEE---NVE-EDEEREPE 578
++E EE+ ++ +++E +D Q + EE V ++EE +PE
Sbjct: 13 DEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPE 61
>gnl|CDD|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM2 of ACF, also termed APOBEC-1-stimulating
protein, 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. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 85
Score = 28.5 bits (63), Expect = 3.7
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 687 KILVRNIPFQAKQSEV-EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ V IP K+ E+ E+ K + V + +RGF FVE+ + A A
Sbjct: 4 RLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYESHRAAAMAR 63
Query: 746 KALCQS-THLYGRRLVLEWAE 765
+ L L+G + ++WAE
Sbjct: 64 RKLLPGRIQLWGHPIAVDWAE 84
>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 = 30.1 bits (68), Expect = 3.8
Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 536 EKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT-LYIKNLNF 590
E E E + +E++++ E+++ + E EE+ E + + P+ DTT L++K +F
Sbjct: 36 EDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEVKASPDADTTILFVKPEDF 91
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 30.5 bits (69), Expect = 3.9
Identities = 11/49 (22%), Positives = 24/49 (48%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 582
E E + EE E+E++E +ED ++ E+++ E + + +
Sbjct: 382 EDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDS 430
>gnl|CDD|204097 pfam08926, DUF1908, Domain of unknown function (DUF1908). This
domain is found in a set of hypothetical/structural
eukaryotic proteins.
Length = 282
Score = 30.2 bits (68), Expect = 3.9
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF 709
SS V+ + S+ + +PFQ Q ++ L K F
Sbjct: 50 SSTVSSSSSSQERLHQLPFQPTQDDLHFLSKHF 82
>gnl|CDD|132849 cd07210, Pat_hypo_W_succinogenes_WS1459_like, Hypothetical patatin
similar to WS1459 of Wolinella succinogenes.
Patatin-like phospholipase. This family predominantly
consists of bacterial patatin glycoproteins. The patatin
protein accounts for up to 40% of the total soluble
protein in potato tubers. Patatin is a storage protein,
but it also has the enzymatic activity of a lipid acyl
hydrolase, catalyzing the cleavage of fatty acids from
membrane lipids. Members of this family have also been
found in vertebrates.
Length = 221
Score = 30.0 bits (68), Expect = 3.9
Identities = 13/68 (19%), Positives = 21/68 (30%), Gaps = 6/68 (8%)
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN------EAKRAMKALCQSTHL 754
E+ EL + F + GL G F + ++ E R A+
Sbjct: 53 EMAELLLSLERKDFWMFWDPPLRGGLLSGDRFAALLREHLPPDRFEELRIPLAVSVVDLT 112
Query: 755 YGRRLVLE 762
L+L
Sbjct: 113 SRETLLLS 120
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 29.1 bits (65), Expect = 4.0
Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 515 LEW--------APEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVE 566
LEW P A E ++ E +E+ +E E + A+E+ + E
Sbjct: 50 LEWTEAGRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDE 109
Query: 567 ENVEEDEEREPEPD 580
E D E E +
Sbjct: 110 TADEADAEAEEADE 123
>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional.
Length = 193
Score = 29.7 bits (66), Expect = 4.2
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 529 KSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
K+K KE ++ + + E E EK + EE +Q ++ E +E+ E PE
Sbjct: 7 KNKAKEPKRRDID-ELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPE 55
Score = 28.5 bits (63), Expect = 9.7
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 534 EKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
E+EK ++E EE E+K E+ EE Q E+ E +E++ E
Sbjct: 23 EREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQKPKE 67
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 30.5 bits (69), Expect = 4.3
Identities = 12/66 (18%), Positives = 24/66 (36%)
Query: 530 SKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLN 589
+ E +EE E+ +E +E E+ ++G E+ E + K
Sbjct: 366 DFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKESA 425
Query: 590 FNSTED 595
+S +
Sbjct: 426 SDSDSE 431
>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family. This
family includes the HABP4 family of hyaluronan-binding
proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1.
HABP4 has been observed to bind hyaluronan (a
glucosaminoglycan), but it is not known whether this is
its primary role in vivo. It has also been observed to
bind RNA, but with a lower affinity than that for
hyaluronan. PAI-1 mRNA-binding protein specifically
binds the mRNA of type-1 plasminogen activator inhibitor
(PAI-1), and is thought to be involved in regulation of
mRNA stability. However, in both cases, the sequence
motifs predicted to be important for ligand binding are
not conserved throughout the family, so it is not known
whether members of this family share a common function.
Length = 106
Score = 28.5 bits (64), Expect = 4.4
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 522 VFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEE----DNQQGVPEVEENVEEDEE 574
E + + KE EE E EEE KE T EE ++ V + +E
Sbjct: 49 EVEEKQAVEEEANKEGVVEEEEVEEEEDKEMTLEEYEKALQEKRKALPALKVRKAKE 105
Score = 28.1 bits (63), Expect = 7.1
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
+ E ++ E++ EEE E EE K+ EE N++GV E EE VEE+E++E
Sbjct: 29 SVKDEIAELTEEQGEEEEKNEVEE--KQAVEEEANKEGVVE-EEEVEEEEDKE 78
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 30.4 bits (69), Expect = 4.5
Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 528 EKSKGKEKEKNEEEGEE-GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
E+ +GK+++ EE+ EE G + +K + E+D +Q P D+E+EP+P
Sbjct: 315 EQPQGKDEKDLEEKPEEPGPDPEKPDEGEDDAEQSGPRGHPTPGNDDEKEPDP 367
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 28.3 bits (64), Expect = 4.6
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 16/85 (18%)
Query: 338 RIFVRNLSYTV-------TEDDLTK--LFEKYGPLAEVILPIDKET-----DKTKGFALV 383
R+ RNL Y V E+ L K F +YG + +++ I++ T A V
Sbjct: 1 RVIQRNLVYVVGLPPRLADEEVLKKPEYFGQYGKIKKIV--INRNTSYNGSQGPSASAYV 58
Query: 384 TFLMPEHATQAYQHLDGTVFLGRML 408
T+ E A + Q +DG GR+L
Sbjct: 59 TYSRKEDALRCIQAVDGFYLDGRLL 83
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 28.4 bits (64), Expect = 4.6
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEG 545
A + +E+ + +EKE++EEE G
Sbjct: 73 AAAAAEEKKEEEEEEEEKEESEEEAAAG 100
Score = 28.4 bits (64), Expect = 4.7
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEE 547
A A A + K +E+E+ EE+ E EE
Sbjct: 67 AAAAAAAAAAAEEKKEEEEEEEEKEESEEE 96
Score = 28.4 bits (64), Expect = 4.7
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAE 555
A A + E++K EEE EE +EE +E A
Sbjct: 68 AAAAAAAAAAEEKKEEEEEEEEKEESEEEAAA 99
Score = 28.0 bits (63), Expect = 7.9
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEEE 548
A A A ++ K++E+ EEE +E EE
Sbjct: 65 AAAAAAAAAAAAAEEKKEEEEEEEEKEESEE 95
Score = 27.6 bits (62), Expect = 9.5
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 518 APEGVFAEAKEKSKGKEKEKNEEEGEEGEE 547
A A ++K + +E+E+ EE EE
Sbjct: 70 AAAAAAAAEEKKEEEEEEEEKEESEEEAAA 99
>gnl|CDD|216289 pfam01080, Presenilin, Presenilin. Mutations in presenilin-1 are a
major cause of early onset Alzheimer's disease. It has
been found that presenilin-1 binds to beta-catenin
in-vivo. This family also contains SPE proteins from
C.elegans.
Length = 403
Score = 30.2 bits (68), Expect = 4.7
Identities = 16/65 (24%), Positives = 25/65 (38%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 575
E EKS E +E + E E + + A E++ PEV+ N E+
Sbjct: 258 SAPTSHSTLELPEKSSTPELSDDESDSSETESQSDSSLAPEEDAAEQPEVQSNSLPSNEK 317
Query: 576 EPEPD 580
E +
Sbjct: 318 REEEE 322
>gnl|CDD|130998 TIGR01943, rnfA, electron transport complex, RnfABCDGE type, A
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the A subunit [Energy
metabolism, Electron transport].
Length = 190
Score = 29.6 bits (67), Expect = 4.9
Identities = 9/37 (24%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 234 AGVKKK----DLKAYFKPLPLASVRTTFLGMAYIGFK 266
AG++++ D+ F+ P+A + + +A++GF+
Sbjct: 151 AGIRERLDLSDVPKAFRGSPIALITAGLMSLAFMGFQ 187
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.5 bits (68), Expect = 5.0
Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 518 APEGVFAEAKEKSKGKE-KEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
A E + EA+E K +E K+K EE ++ EE KK EE+N+ E ++ EED+++
Sbjct: 1690 AAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKA---EEENKIKAEEAKKEAEEDKKKA 1746
Query: 577 PE 578
E
Sbjct: 1747 EE 1748
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 30.3 bits (68), Expect = 5.2
Identities = 14/57 (24%), Positives = 25/57 (43%)
Query: 524 AEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
E E K K++ + + EE +EE E ++D ++ + V+ DE D
Sbjct: 275 LEDDEPDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVD 331
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), 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 and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large number
of non-snRNP proteins, including polypyrimidine tract
binding protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an important
role in virus replication. U1A contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and may
be free to bind other proteins. U1A also contains a
proline-rich region, and a nuclear localization signal
(NLS) in the central domain that is responsible for its
nuclear import. .
Length = 89
Score = 28.1 bits (62), Expect = 5.5
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 12/74 (16%)
Query: 579 PDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQF 634
P+ T+YI NLN +D +++ F + G I + V+R + G FV F
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR--------GQAFVIF 53
Query: 635 YTRESLNQALKVLQ 648
S AL+ +Q
Sbjct: 54 KEVSSATNALRSMQ 67
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 27.7 bits (62), Expect = 5.5
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 11/56 (19%)
Query: 597 IRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL 652
IR +F++ G SV V + GFV+F TRE+ + + + L
Sbjct: 19 IRDYFEQFGKSKSVIVNHRA-----------KCGFVRFETREAAEKFAAAISENGL 63
>gnl|CDD|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM3 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 101
Score = 28.3 bits (63), Expect = 6.0
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 18/89 (20%)
Query: 581 TTLYIKNL-NFNSTE---DSIRRHFKKCGPIASVTVARKKDPKSPGQFL----------S 626
TTL IKN+ N S + D + H +C + + P S F+ +
Sbjct: 2 TTLMIKNIPNKYSQKLLLDMLDTHCIQC----NQHIEDSSQPVSSYDFVYLPIDFKNKCN 57
Query: 627 MGYGFVQFYTRESLNQALKVLQNSSLDEH 655
+GY FV F + E+ + K N +E
Sbjct: 58 LGYAFVNFTSPEATWRFYKAFHNQQWEEF 86
>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 = 30.0 bits (68), Expect = 6.3
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 1/67 (1%)
Query: 527 KEKSKGKEKEKNEE-EGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYI 585
KE S+ +E+E+ + E E E K +E + + P + +ED ++ + D +
Sbjct: 227 KETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEIL 286
Query: 586 KNLNFNS 592
K
Sbjct: 287 KEKKDEE 293
>gnl|CDD|165442 PHA03171, PHA03171, UL37 tegument protein; Provisional.
Length = 499
Score = 29.6 bits (66), Expect = 6.3
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 516 EWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEV 565
E + A E + E+E N+ E + E E+++ EE+ + PEV
Sbjct: 69 ERPRDLTAALFAEAGEEAEEEDNDRECPDTEAEEEDE--EEEIEAPDPEV 116
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 28.6 bits (64), Expect = 6.3
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 519 PEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQ 560
PEG + G + EEE EE E EK++ + E QQ
Sbjct: 81 PEGP----AGTTSGTGHTRQEEEEEEEENEKQQQSDEAQVQQ 118
>gnl|CDD|240732 cd12286, RRM_Man1, RNA recognition motif in inner nuclear membrane
protein Man1 (Man1) and similar proteins. This
subfamily corresponds to the RRM of Man1, also termed
LEM domain-containing protein 3 (LEMD3), an integral
protein of the inner nuclear membrane that binds to
nuclear lamins and emerin, thus playing a role in
nuclear organization. It is part of a protein complex
essential for chromatin organization and cell division.
It also functions as an important negative regulator for
the transforming growth factor (TGF) beta/activin/Nodal
signaling pathway by directly interacting with
chromatin-associated proteins and transcriptional
regulators, including the R-Smads, Smad1, Smad2, and
Smad3. Moreover, Man1 is a unique type of left-right
(LR) signaling regulator that acts on the inner nuclear
membrane. Man1 plays a crucial role in angiogenesis. The
vascular remodeling can be regulated at the inner
nuclear membrane through the interaction between Man1
and Smads. Man1 contains an N-terminal LEM domain, two
putative transmembrane domains, a MAN1-Src1p C-terminal
(MSC) domain, and a C-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The LEM domain interacts
with the DNA and chromatin-binding protein
Barrier-to-Autointegration Factor, and is also necessary
for efficient localization of MAN1 in the inner nuclear
membrane. Research has indicated that C-terminal
nucleoplasmic region of Man1 exhibits a DNA binding
winged helix domain and is responsible for both DNA- and
Smad-binding. .
Length = 92
Score = 27.7 bits (62), Expect = 6.5
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 341 VRNL-SYTVTEDDLTK------LFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
+RN+ V + + EK G I+ I + +G + PE A +
Sbjct: 4 IRNMFDPEVERGEDWHVRIQDAILEKCGDNNG-IVHIQVDKASREGCVYIKCSSPEDAGK 62
Query: 394 AYQHLDGTVFLGRML 408
A++ L G F GR++
Sbjct: 63 AFKALHGWWFDGRLV 77
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 29.7 bits (67), Expect = 6.8
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 527 KEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 580
+E K + EK +E E EE+K E A E + E+ E + E+ + + E +
Sbjct: 201 EEYEKEVKAEKKRQELERVEEKKLEKMAPE--ASRLDEMSEGLLEESDDDGEEE 252
>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32. This family
consists of several mammalian specific proacrosin
binding protein sp32 sequences. sp32 is a sperm specific
protein which is known to bind with with 55- and 53-kDa
proacrosins and the 49-kDa acrosin intermediate. The
exact function of sp32 is unclear, it is thought however
that the binding of sp32 to proacrosin may be involved
in packaging the acrosin zymogen into the acrosomal
matrix.
Length = 243
Score = 29.2 bits (65), Expect = 6.9
Identities = 11/52 (21%), Positives = 20/52 (38%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
++ G + K + +E K + +E + EE EE+ E E
Sbjct: 181 QSSLSLGGSVQVKAPKPKQEQLLSKLQEYLQEHKTEEKQPQEEQEEEEVEEE 232
>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 = 29.4 bits (66), Expect = 7.0
Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEE----DEEREPEPD 580
+ + KE +++ E EE ++ ED+ E+E E + P+ D
Sbjct: 221 SEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSD 280
Score = 29.4 bits (66), Expect = 7.8
Identities = 11/64 (17%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 515 LEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 574
++ A E + E + ++ E ++ E+ ++++ E + + + + EE E
Sbjct: 206 MDMAEE--LGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMES 263
Query: 575 REPE 578
E E
Sbjct: 264 GEME 267
>gnl|CDD|219461 pfam07543, PGA2, Protein trafficking PGA2. A Saccharomyces
cerevisiae member of this family (PGA2) is an ER protein
which has been implicated in protein trafficking.
Length = 139
Score = 28.6 bits (64), Expect = 7.0
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 528 EKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQ---GVPEVEENVEEDEEREPEPD 580
K++ KE EK E EE E+K + + G E + + EEDEE P
Sbjct: 39 AKAQEKEHEKERAEREEAREKKAKISPNALRGGATAGHGEEDTDDEEDEEDFATPS 94
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 29.3 bits (65), Expect = 7.0
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE-EREPEPDTT 582
E E + +EK E+ EE E E++E T EE + E+ +E+DE E E + D T
Sbjct: 140 ERMEWERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEI---IEQDESETESDDDKT 195
>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 = 27.7 bits (61), Expect = 7.1
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 449 IILVKNL-PYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
++LV NL P R P L LF +GD+ RV ++ LV+ NQA+ A + L
Sbjct: 1 VLLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQ 60
Query: 507 KFKEVPL 513
K PL
Sbjct: 61 KLHGKPL 67
>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional.
Length = 196
Score = 29.1 bits (65), Expect = 7.1
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 525 EAKEKSKGKEKEKN-----EEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 579
E EK KE+EK+ E EG E ++ + QQ V E+EE ++ +++E E
Sbjct: 2 EEVEKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVEA 61
Query: 580 DTTLYI 585
L I
Sbjct: 62 QEYLDI 67
>gnl|CDD|176558 cd08621, PI-PLCXDc_like_2, Catalytic domain of uncharacterized
hypothetical proteins similar to eukaryotic
phosphatidylinositol-specific phospholipase C, X domain
containing proteins. This subfamily corresponds to the
catalytic domain present in a group of uncharacterized
hypothetical proteins found in bacteria and fungi, which
are similar to eukaryotic phosphatidylinositol-specific
phospholipase C, X domain containing proteins
(PI-PLCXD). The typical eukaryotic
phosphoinositide-specific phospholipase C (PI-PLC, EC
3.1.4.11) has a multidomain organization that consists
of a PLC catalytic core domain, and various regulatory
domains. The catalytic core domain is assembled from two
highly conserved X- and Y-regions split by a divergent
linker sequence. In contrast, eukaryotic PI-PLCXDs
contain a single TIM-barrel type catalytic domain, X
domain, and are more closely related to bacterial
PI-PLCs, which participate in Ca2+-independent PI
metabolism, hydrolyzing the membrane lipid
phosphatidylinositol (PI) to produce phosphorylated
myo-inositol and diacylglycerol (DAG). Although the
biological function of eukaryotic PI-PLCXDs still
remains unclear, it may distinct from that of typical
eukaryotic PI-PLCs.
Length = 300
Score = 29.3 bits (66), Expect = 7.4
Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 20/77 (25%)
Query: 279 KSFWKGKQLNIY-KYSKDNSAKYSGAADDNNNASMENIKAKHWKSQEDSVQFAEDIAESG 337
+ G Q +Y YS N+ + A+D +S F +DI
Sbjct: 190 GGIYDGPQFTVYDSYS--NTDDTNYMAEDQ---------LAKLRSHRRPS-FGDDI---- 233
Query: 338 RIFVRNLSYTVTEDDLT 354
F+ LS+T+T LT
Sbjct: 234 -FFL--LSWTLTPQALT 247
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 29.6 bits (66), Expect = 7.6
Identities = 10/52 (19%), Positives = 22/52 (42%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 576
KE + E +K E E + E +K + A + ++++ + E+
Sbjct: 268 SPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESKASEKEA 319
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 29.6 bits (67), Expect = 7.7
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAEE 556
+ K +E+E+ +EE EE EEE +E EE
Sbjct: 342 VNPEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372
>gnl|CDD|217477 pfam03291, Pox_MCEL, mRNA capping enzyme. This family of enzymes
are related to pfam03919.
Length = 327
Score = 29.3 bits (66), Expect = 7.7
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 312 MENIKAKHWKSQEDSVQFAEDIAES--GRIFVRNLS--------YTVTEDDLTKLFEKYG 361
++ K + + V F +D G +V NL Y V + L +L E+YG
Sbjct: 199 ATFVEHKSFGNSIYYVSFEKDPPRPPFGIKYVYNLEDMVTDVPEYLVPFETLVELAEEYG 258
>gnl|CDD|218637 pfam05558, DREPP, DREPP plasma membrane polypeptide. This family
contains several plant plasma membrane proteins termed
DREPPs as they are developmentally regulated plasma
membrane polypeptides.
Length = 201
Score = 28.9 bits (64), Expect = 7.8
Identities = 16/61 (26%), Positives = 21/61 (34%)
Query: 519 PEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 578
E AE ++K KEKE EE ++ EE A E + E
Sbjct: 138 EEAPAAETEKKPAVKEKEIVVEEEKKEEEAVPVAAAPSTKAPETKVEETPAKAPAAPAAE 197
Query: 579 P 579
P
Sbjct: 198 P 198
>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional.
Length = 449
Score = 29.4 bits (66), Expect = 8.0
Identities = 14/70 (20%), Positives = 30/70 (42%)
Query: 509 KEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEEN 568
K+ Y + A + AE + + +E + E E E+ + + ++ P E+
Sbjct: 371 KDSAEYDQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDE 430
Query: 569 VEEDEEREPE 578
E+++E E
Sbjct: 431 FEDEDELEEA 440
>gnl|CDD|150302 pfam09590, Env-gp36, Lentivirus surface glycoprotein. This
protein is found in feline immunodeficiency retrovirus.
It represents the surface glycoprotein which is found
in the polyprotein C-terminal to the Env protein.
Length = 591
Score = 29.5 bits (66), Expect = 8.3
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 28 KITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHRE 68
I Q +L+ E KG +T+ +L GK+RR ++ Y E
Sbjct: 53 VILQPKLQ---ELKGEITEGKLHEINAGKYRRLRYLRYSDE 90
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 28.9 bits (65), Expect = 8.4
Identities = 15/64 (23%), Positives = 29/64 (45%)
Query: 514 YLEWAPEGVFAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEENVEEDE 573
Y E + +K K K+K+K +++ ++ E+K E AE+ + E +
Sbjct: 78 YEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSETLSTLS 137
Query: 574 EREP 577
E +P
Sbjct: 138 ELKP 141
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 27.2 bits (60), Expect = 9.0
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+S ++FV NL + V + +L + F++YG + E+ + K F V F E
Sbjct: 2 DSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSE 53
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 29.2 bits (65), Expect = 9.1
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 525 EAKEKSKGKEKEKNEEEGEEGEEEKK 550
E E S+ E+EKNEEEG ++ KK
Sbjct: 315 EQDEDSEESEEEKNEEEGGLSKKGKK 340
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 27.4 bits (60), Expect = 9.2
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 523 FAEAKEKSKGKEKEKNEEEGEEGEEEKKENTAEEDNQQGVPEVEE 567
F E +E S + ++ E++ +E EE+ E+ E+D++ VP E
Sbjct: 5 FLEGEEDSD-SDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPSFGE 48
>gnl|CDD|177802 PLN00221, PLN00221, tubulin alpha chain; Provisional.
Length = 450
Score = 29.0 bits (65), Expect = 9.9
Identities = 30/90 (33%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 470 PFGDLGRVLVPPYGI---TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL-EWAPEGVFAE 525
P GDL +V I T + E + K F+ L Y K V Y+ E EG F+E
Sbjct: 364 PGGDLAKVQRAVCMISNSTAVAEVFSRIDHK--FD-LMYAKRAFVHWYVGEGMEEGEFSE 420
Query: 526 AKEKSKGKEKEKNEEEGEEGEEEKKENTAE 555
A+E EK+ EE G E E + + E
Sbjct: 421 AREDLAALEKDY-EEVGAESAEGEGDEGEE 449
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
0.313 0.131 0.372
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: 39,727,314
Number of extensions: 3912543
Number of successful extensions: 8511
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7059
Number of HSP's successfully gapped: 1510
Length of query: 787
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 682
Effective length of database: 6,280,432
Effective search space: 4283254624
Effective search space used: 4283254624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 63 (27.9 bits)