RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4687
(339 letters)
>gnl|CDD|218350 pfam04959, ARS2, Arsenite-resistance protein 2. Arsenite is a
carcinogenic compound which can act as a co-mutagen by
inhibiting DNA repair. Arsenite-resistance protein 2 is
thought to play a role in arsenite resistance.
Length = 211
Score = 178 bits (453), Expect = 5e-55
Identities = 64/111 (57%), Positives = 85/111 (76%)
Query: 229 MPNRCGIIHTRGSAPASKVTPQEITDYCSTFQNKMSSLVSSPQEPTPEELDQLGAKKTDA 288
MPNRCGIIH RG P +++T E+ ++ TF+ K+ L+S + + EE ++G K +
Sbjct: 1 MPNRCGIIHVRGPPPPNRITHGEVNEWIKTFEEKLGPLLSVKETLSEEEAKKMGRKDPEQ 60
Query: 289 EVEKFIAANTQEISTDKWLCPLSGKKFKGPDFIRKHIFNKHAEKVEEVKKE 339
EVEKF+ ANTQE++ DKWLCPLSGKKFKGP+F+RKHIFNKH +KVEEV+KE
Sbjct: 61 EVEKFVQANTQELAKDKWLCPLSGKKFKGPEFVRKHIFNKHGDKVEEVRKE 111
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 37 IFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRDVDIKEICWNL 96
+F+ NL P T+ ++ L ++ V I D + +V F D ++ L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59
Query: 97 NNIRLRDCEL 106
N L +L
Sbjct: 60 NGKELDGRKL 69
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 35.3 bits (82), Expect = 0.004
Identities = 15/71 (21%), Positives = 29/71 (40%)
Query: 36 SIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRDVDIKEICWN 95
++F+ NL P T+ E+ L ++ V + + + +V F + D ++
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 96 LNNIRLRDCEL 106
LN L L
Sbjct: 61 LNGKELDGRPL 71
>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 = 33.0 bits (76), Expect = 0.021
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 37 IFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRRGW--VTFRRDVDIKEICW 94
+F+ NL P T+ ++++L ++ + I D +G+ V F + D ++
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV---RDETGRSKGFAFVEFEDEEDAEKALE 57
Query: 95 NLNNIRLRDCEL 106
LN L EL
Sbjct: 58 ALNGKELGGREL 69
>gnl|CDD|205992 pfam13821, DUF4187, Domain of unknown function (DUF4187). This
family is found at the very C-terminus of proteins that
carry a G-patch domain, pfam01585. The domain is short
and cysteine-rich.
Length = 55
Score = 30.7 bits (70), Expect = 0.12
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 12/58 (20%)
Query: 176 EEEELLGKSEENTEETEQVDPNVLRVLDRLILYLRIVHSVDYYNHCEYPNEDEMPNRC 233
EEE+ E E+ L L+ YLR H+ ++ +Y +E+++ C
Sbjct: 2 EEED-----EFEELSPEER-------LQLLLSYLREEHNYCFWCGTKYEDEEDLLENC 47
>gnl|CDD|163667 cd07424, MPP_PrpA_PrpB, PrpA and PrpB, metallophosphatase domain.
PrpA and PrpB are bacterial type I serine/threonine and
tyrosine phosphatases thought to modulate the expression
of proteins that protect the cell upon accumulation of
misfolded proteins in the periplasm. The PPP
(phosphoprotein phosphatase) family, to which PrpA and
PrpB belong, is one of two known protein phosphatase
families specific for serine and threonine. This family
also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5,
PP6, PP7, Bsu1, RdgC, PrpE, and ApA4 hydrolase. The PPP
catalytic domain is defined by three conserved motifs
(-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family
is ancient with members found in all eukaryotes, and in
most bacterial and archeal genomes. Dephosphorylation
of phosphoserines and phosphothreonines on target
proteins plays a central role in the regulation of many
cellular processes. PPPs belong to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 207
Score = 31.9 bits (73), Expect = 0.34
Identities = 34/137 (24%), Positives = 51/137 (37%), Gaps = 27/137 (19%)
Query: 7 LMMLNSYNN--------IINGGESKNEPPPRALHRTSSIFLRNLAPTITKAEVENLCKRY 58
M +++ + NGGE + P L R ++ L L I EVE
Sbjct: 66 QMAIDALRAEPLDAVRWLANGGEWFLDLPDEELRRWLALKLEQLPLAI---EVE------ 116
Query: 59 SGFLRVAI--ADPQPDRRWFRRGWVTFRRDVDIKEICWNLNNIRLRDCELGAIVNRDLSR 116
+ +V I AD D G VT R DI+E+ W+ I+ + I D
Sbjct: 117 TEGGKVGIVHADYPSDDWSDGVGAVT-LRPEDIEELLWSRTRIQKAQTQ--PIKGVD--- 170
Query: 117 RVRTVSGLTSLKPVVQF 133
V G T +K ++
Sbjct: 171 --AVVHGHTPVKRPLRL 185
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 29.1 bits (66), Expect = 0.60
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 34 TSSIFLRNLAPTITKAEVENLCKRYSGFLR 63
+++F+ NL P T+ E+ L R GF R
Sbjct: 2 CNTLFVANLGPNTTEEELRQLFSRQPGFRR 31
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM2 of U1A/U2B"/SNF protein family,
containing Drosophila sex determination protein SNF and
its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs) connected by a variable, flexible linker.
SNF is an RNA-binding protein found in the U1 and U2
snRNPs of Drosophila where it is essential in sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). U1A is an RNA-binding protein associated with
the U1 snRNP, a small RNA-protein complex involved in
pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent on U2 snRNA binding. .
Length = 72
Score = 28.3 bits (64), Expect = 1.1
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 37 IFLRNLAPTITKAEVENLCKRYSGFLRV 64
+FL+NL TK +E L ++ GF V
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEV 32
>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 = 28.3 bits (63), Expect = 1.3
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 14/87 (16%)
Query: 36 SIFLRNLAPTITKAEVENLCKRYSGFLRV----AIADPQPDR-RWFRRGWVTFRRDVDIK 90
++F+RNLA ++T+ ++ + +S + + DP+ R + G+VTF D +
Sbjct: 1 TLFVRNLAFSVTQEDLTDF---FSDVAPIKHAVVVTDPETGESRGY--GFVTFAMLEDAQ 55
Query: 91 EICWNLNNIRLRDCELGAIVNRDLSRR 117
E L N +L G I+ D++ R
Sbjct: 56 EALAKLKNKKLH----GRILRLDIAER 78
>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 = 28.3 bits (64), Expect = 1.3
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 37 IFLRNLAPTITKAEVENLCKRY 58
+ LRNL P +T++++ L +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPF 23
>gnl|CDD|168300 PRK05934, PRK05934, type III secretion system protein; Validated.
Length = 341
Score = 29.8 bits (67), Expect = 1.8
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 124 LTSLKPVVQFDMKLSLWTDGQEPAQQPMSYTLSSKN------PVLQNITDYL 169
LT PV Q + LSL T+ + +S LS +L +ITDYL
Sbjct: 80 LTMFHPVAQATVALSLETEDDPMSPAEISVILSLPKAETLSPSLLHSITDYL 131
>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 = 27.8 bits (62), Expect = 2.1
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 37 IFLRNLAPTITKAEVENLCKRY 58
+F+ L ++TK E+E L K++
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKH 26
>gnl|CDD|192565 pfam10391, DNA_pol_lambd_f, Fingers domain of DNA polymerase
lambda. DNA polymerases catalyze the addition of dNMPs
onto the 3-prime ends of DNA chains. There is a general
polymerase fold consisting of three subdomains that
have been likened to the fingers, palm, and thumb of a
right hand. DNA_pol_lambd_f is the central
three-helical region of DNA polymerase lambda referred
to as the F and G helices of the fingers domain.
Contacts with DNA involve this conserved
helix-hairpin-helix motif in the fingers region which
interacts with the primer strand. This motif is common
to several DNA binding proteins and confers a
sequence-independent interaction with the DNA backbone.
Length = 52
Score = 26.7 bits (60), Expect = 2.4
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 73 RRWFRRGWVTFRRDVDIKEICWNLN 97
R+W+R+G T D++E L
Sbjct: 16 RKWYRQGIRTLE---DLRENKAKLT 37
>gnl|CDD|219252 pfam06985, HET, Heterokaryon incompatibility protein (HET). This
family represents a conserved region approximately 150
residues long within various heterokaryon
incompatibility proteins that seem to be restricted to
ascomycete fungi. Genetic differences in specific het
genes prevent a viable heterokaryotic fungal cell from
being formed by the fusion of filaments from two
different wild-type strains. Many family members also
contain the pfam00400 repeat and the pfam05729 domain.
Length = 94
Score = 27.6 bits (62), Expect = 3.3
Identities = 5/11 (45%), Positives = 6/11 (54%)
Query: 71 PDRRWFRRGWV 81
+ WF RGW
Sbjct: 81 DESPWFTRGWT 91
>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 = 27.0 bits (60), Expect = 3.9
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 34 TSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQP 71
T ++F+ NL TIT+ E+ +RY V I P
Sbjct: 2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPR 39
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 28.7 bits (65), Expect = 4.2
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 8/49 (16%)
Query: 294 IAANTQE---ISTDKWLCPLSGKKFKGPDFIRKHIFNKHAEKVEEVKKE 339
+A + +STDK C L + IR + F K +++E
Sbjct: 119 VAQAGHQATIVSTDKGYCQLLSPTIQ----IRDY-FQKRWLDAPFIEQE 162
>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 = 27.2 bits (61), Expect = 5.1
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 76 FRRGWVTFRRDVDIKEICWNLNN 98
F GWV F K + +LNN
Sbjct: 54 FTEGWVEFEDKKVAKRVAESLNN 76
>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 = 26.8 bits (60), Expect = 5.1
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 34 TSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIADPQPDRRWFRR---GWVTF--RRDVD 88
T+++++ NL P +T+ + R+ V I P+ + R G+V F R D +
Sbjct: 1 TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60
>gnl|CDD|216447 pfam01346, FKBP_N, Domain amino terminal to FKBP-type
peptidyl-prolyl isomerase. This family is only found at
the amino terminus of pfam00254. This domain is of
unknown function.
Length = 124
Score = 27.6 bits (62), Expect = 5.5
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 245 SKVTPQEITDYCSTFQNKMSSLVSSPQEPTPEELDQLGAKKTDAEVEKFIAAN 297
K+T +EI FQ K+ Q + ++ A++ A E F+A N
Sbjct: 63 LKLTDEEIQKALQAFQKKL-------QAKQQAKAEKK-AEENKAAGEAFLAEN 107
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 28.0 bits (61), Expect = 6.8
Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 25 EPPPRALHRTSSIFLRNLAPTITKAEVENLCKRYSGFLRVAIA-DPQPDRRWFRRGWVTF 83
+ ++ +++F+ NL +T+ ++ L K++ RV + D + + +V F
Sbjct: 106 KSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR-GFAFVEF 164
Query: 84 RRDVDIKEICWNLNNIRL 101
+ ++ LN L
Sbjct: 165 ESEESAEKAIEELNGKEL 182
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.133 0.391
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: 17,419,706
Number of extensions: 1668402
Number of successful extensions: 1808
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1806
Number of HSP's successfully gapped: 27
Length of query: 339
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 241
Effective length of database: 6,590,910
Effective search space: 1588409310
Effective search space used: 1588409310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.4 bits)