RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7101
(130 letters)
>gnl|CDD|227925 COG5638, COG5638, Uncharacterized conserved protein [Function
unknown].
Length = 622
Score = 76.7 bits (188), Expect = 2e-17
Identities = 40/80 (50%), Positives = 54/80 (67%), Gaps = 1/80 (1%)
Query: 10 VEQSEGEDSAEEESTEGNAYHREKLRQYQLNRLKYYYAVVVFDSAESANKVYTECDGMEY 69
++ GED+ E GN + KLRQYQL RL+YYYAVV + E++ +Y+ CDG+EY
Sbjct: 225 SDRDAGEDALIEGDR-GNEFDMVKLRQYQLERLRYYYAVVECEDIETSKNIYSACDGVEY 283
Query: 70 ESSATRVDLRFVPDDTEFDE 89
E+SA +DLRFVPD FD+
Sbjct: 284 ENSANVLDLRFVPDSLTFDD 303
>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 = 28.6 bits (65), Expect = 0.17
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 33 KLRQYQLNRLKYYYAVVVFDSAESANKVYTECDG 66
+ + +L + K +A V F + E+A K +G
Sbjct: 10 NVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNG 43
>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 = 28.0 bits (63), Expect = 0.40
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYESSATRVD 77
+A V F+S E A K +G E + +V
Sbjct: 41 FAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 27.6 bits (62), Expect = 0.66
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYESSATRV 76
+A V F+S E A K +G E + +V
Sbjct: 43 FAFVEFESEEDAEKALEALNGKELDGRPLKV 73
>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 = 27.6 bits (62), Expect = 0.67
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYES 71
+A V F+ E A K +G E
Sbjct: 41 FAFVEFEDEEDAEKALEALNGKELGG 66
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 27.0 bits (60), Expect = 1.2
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 44 YYYAVVVFDSAESANKVYTECDG 66
+YA V F SA +A++ C+G
Sbjct: 46 GFYAFVKFYSARAASRAQKACNG 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 = 26.8 bits (60), Expect = 1.5
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYESSATRV 76
+A V + +AE A + +G + S RV
Sbjct: 46 FAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 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 = 98
Score = 26.8 bits (59), Expect = 2.0
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYESSATRVDL 78
+AVV +++AE A +V DG + S ++
Sbjct: 46 FAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSF 78
>gnl|CDD|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. RpoE is subunit E of
archaeal RNA polymerase. Archaeal cells contain a single
RNA polymerase made up of 12 subunits, which are
homologous to the 12 subunits (RPB1-12) of eukaryotic
RNA polymerase II. RpoE is homologous to Rpa43 of
eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA
polymerase II, and Rpc25 of eukaryotic RNA polymerase
III. RpoE is composed of two domains, the N-terminal RNP
(ribonucleoprotein) domain and the C-terminal S1 domain.
This S1 domain binds ssRNA and ssDNA. This family is
classified based on the C-terminal S1 domain. The
function of RpoE is not fully understood. In eukaryotes,
RPB7 and RPB4 form a heterodimer that reversibly
associates with the RNA polymerase II core.
Length = 99
Score = 26.1 bits (58), Expect = 2.8
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 103 NISPQADLMVHLPQIRDDHMKY 124
I P D ++H+ QI DD++ Y
Sbjct: 18 RIGP-VDGLLHISQIMDDYISY 38
>gnl|CDD|237883 PRK14991, PRK14991, tetrathionate reductase subunit A; Provisional.
Length = 1031
Score = 26.9 bits (60), Expect = 3.4
Identities = 12/34 (35%), Positives = 13/34 (38%), Gaps = 10/34 (29%)
Query: 83 DDTEFDEHFDPGKWPL----------SSSSNISP 106
D T E F +WPL SS S SP
Sbjct: 874 DGTPLREQFPESQWPLLLISFKSNLMSSMSIASP 907
>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7;
Provisional.
Length = 176
Score = 26.6 bits (59), Expect = 3.6
Identities = 9/43 (20%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 81 VPDDTEFDEHFDPGKWPLSSSS-NISPQADLMVHLPQIRDDHM 122
+P D +D + S I P ++ + L +R D
Sbjct: 113 IPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS 155
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 27.0 bits (60), Expect = 3.7
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 30 HREKLRQYQLNRLKYYYAVVVFDSAESANKVYT---ECDGMEYESSATRVDLRF 80
L + LN L+ V ++ A+ AN+V +G++ E A +D +F
Sbjct: 274 KECMLTEKLLNGLREINKVKIYGPADPANRVGVVSFTVEGIDSEEVADILDEKF 327
>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 = 25.2 bits (55), Expect = 4.9
Identities = 19/61 (31%), Positives = 28/61 (45%)
Query: 18 SAEEESTEGNAYHREKLRQYQLNRLKYYYAVVVFDSAESANKVYTECDGMEYESSATRVD 77
SA E+S + +R Q N YA V F+SAE A + C+ E E + R++
Sbjct: 12 SASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTEIEGRSIRLE 71
Query: 78 L 78
Sbjct: 72 F 72
>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 = 24.9 bits (55), Expect = 6.6
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYESSATRVD 77
+ V F+S E A + +GME + RVD
Sbjct: 43 FGFVYFESVEDAKEAKERLNGMEIDGRRIRVD 74
>gnl|CDD|149301 pfam08165, FerA, FerA (NUC095) domain. This is central domain A in
proteins of the Ferlin family.
Length = 66
Score = 24.6 bits (54), Expect = 7.3
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 97 PLSSSSNISPQADLMVHLPQIRDDHMKYISELAR 130
PL L + L ++RD+ + I E A
Sbjct: 30 PLPRLEGKPNATALDIQLRKLRDESLLQIREAAI 63
>gnl|CDD|222979 PHA03093, PHA03093, EEV glycoprotein; Provisional.
Length = 185
Score = 25.5 bits (56), Expect = 8.4
Identities = 7/38 (18%), Positives = 13/38 (34%), Gaps = 4/38 (10%)
Query: 52 DSAESANKVYTECDGMEYESSATRVDLRFVPDDTEFDE 89
+ + K C G+ Y+ S F + F +
Sbjct: 89 ADSTTQYKHKESCKGIVYDGSC----YIFHSEPKTFSD 122
>gnl|CDD|227277 COG4941, COG4941, Predicted RNA polymerase sigma factor containing
a TPR repeat domain [Transcription].
Length = 415
Score = 25.9 bits (57), Expect = 8.6
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 5 SPLELVEQSEGEDSAEEESTEGNAYHREKLR 35
+P EL+ E E+ E E+ + ++LR
Sbjct: 81 APPELLLSDEDEEMEEAEALDDEHIRDDRLR 111
>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 = 24.6 bits (54), Expect = 9.3
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 46 YAVVVFDSAESANKVYTECDGMEYESSATRVDL 78
+ V F+ ES K E DG ++ + RVD+
Sbjct: 44 FCYVEFEDVESL-KEALEYDGALFDDRSLRVDI 75
>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 = 24.6 bits (53), Expect = 9.4
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 38 QLNRLKYYYAVVVFDSAESANKVYTECDGMEYESSATRVD 77
Q +R +A V F++ + A + +GME + RVD
Sbjct: 45 QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 84
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
0.312 0.129 0.367
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: 6,429,830
Number of extensions: 535959
Number of successful extensions: 414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 39
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
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: 53 (24.1 bits)