RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18100
(76 letters)
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), 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. .
Length = 96
Score = 58.1 bits (141), Expect = 4e-13
Identities = 28/69 (40%), Positives = 35/69 (50%), Gaps = 27/69 (39%)
Query: 5 ILDLNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEVKDECNTKYGEVVRV 64
+L NMVGPGEVD DLEPEVKEEC +KYG+V +V
Sbjct: 5 VLLRNMVGPGEVDEDLEPEVKEEC---------------------------SKYGKVTKV 37
Query: 65 IIHELPTTA 73
+I E+P +
Sbjct: 38 LIFEIPGAS 46
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 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), 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. The research indicates that
PUF60 binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 98
Score = 48.2 bits (115), Expect = 4e-09
Identities = 20/34 (58%), Positives = 26/34 (76%), Gaps = 1/34 (2%)
Query: 35 NMVGPGEVDSDLEPEVKDECNTKYGEVVRVIIHE 68
NMVGP ++D DLE EV +EC K+G V RVII++
Sbjct: 8 NMVGPEDLDDDLEGEVTEEC-GKFGAVNRVIIYQ 40
>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 = 46.1 bits (110), Expect = 2e-08
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 27/66 (40%)
Query: 5 ILDLNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEVKDECNTKYGEVVRV 64
++ NMV PGE+D DL+ E++EEC KYG+V+ V
Sbjct: 4 LVLRNMVTPGEIDEDLKDEIEEECE---------------------------KYGKVLNV 36
Query: 65 IIHELP 70
I+HE+
Sbjct: 37 IVHEVA 42
>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 = 40.8 bits (95), Expect = 1e-05
Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 35 NMVGPGEVDSDLEPEVKDECNTKYGEVVRVIIHELPTTAN 74
NMV P ++D LE E+++EC K+G V RVII+
Sbjct: 521 NMVTPQDIDEFLEGEIREECG-KFGVVDRVIINFEKQGEE 559
Score = 35.0 bits (80), Expect = 0.001
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 9 NMVGPGEVDSDLEPEVKEEC 28
NMV P ++D LE E++EEC
Sbjct: 521 NMVTPQDIDEFLEGEIREEC 540
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia 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. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 27.5 bits (62), Expect = 0.26
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 34 ENMVGPGEV-----DSDLEPEVKDECNTKYGEVVRVIIHELPTTANV 75
+NM P E D +++ +V +EC+ K+G V + + + V
Sbjct: 7 KNMFDPAEETEDEWDDEIKEDVLEECS-KFGPVEHIKVDKNSPEGVV 52
Score = 24.0 bits (53), Expect = 6.7
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 6/31 (19%)
Query: 9 NMVGPGEV-----DSDLEPEVKEECNTKYGE 34
NM P E D +++ +V EEC+ K+G
Sbjct: 8 NMFDPAEETEDEWDDEIKEDVLEECS-KFGP 37
>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 = 28.3 bits (63), Expect = 0.32
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 35 NMVGPGE-----VDSDLEPEVKDECNTKYGEVVRVII 66
NM P D+++ +VK+EC+ KYG VV + +
Sbjct: 369 NMFDPATEEEPNFDNEILDDVKEECS-KYGGVVHIYV 404
Score = 26.8 bits (59), Expect = 0.93
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 5/32 (15%)
Query: 9 NMVGPGE-----VDSDLEPEVKEECNTKYGEN 35
NM P D+++ +VKEEC+ G
Sbjct: 369 NMFDPATEEEPNFDNEILDDVKEECSKYGGVV 400
>gnl|CDD|213018 cd12142, SH3_D21-like, Src Homology 3 domain of SH3
domain-containing protein 21 (SH3D21) and similar
proteins. N-terminal SH3 domain of the uncharacterized
protein SH3 domain-containing protein 21, and similar
uncharacterized domains, it belongs to the CD2AP-like_3
subfamily of proteins. The CD2AP-like_3 subfamily is
composed of the third SH3 domain (SH3C) of CD2AP, CIN85
(Cbl-interacting protein of 85 kDa), and similar
domains. CD2AP and CIN85 are adaptor proteins that bind
to protein partners and assemble complexes that have
been implicated in T cell activation, kidney function,
and apoptosis of neuronal cells. They also associate
with endocytic proteins, actin cytoskeleton components,
and other adaptor proteins involved in receptor
tyrosine kinase (RTK) signaling. CD2AP and the main
isoform of CIN85 contain three SH3 domains, a
proline-rich region, and a C-terminal coiled-coil
domain. All of these domains enable CD2AP and CIN85 to
bind various protein partners and assemble complexes
that have been implicated in many different functions.
SH3C of both proteins have been shown to bind to
ubiquitin. SH3 domains are protein interaction domains
that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP
motifs. They play versatile and diverse roles in the
cell including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 24.3 bits (53), Expect = 3.3
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 41 EVDSDLEPEVKDECNTKYGEVVRVI 65
V D P DE K G+V+ VI
Sbjct: 3 RVLFDYNPVAPDELALKKGDVIEVI 27
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 25.0 bits (56), Expect = 4.3
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 57 KYGEVVRVI 65
KYG+ VRV+
Sbjct: 637 KYGDEVRVV 645
>gnl|CDD|165199 PHA02865, PHA02865, MHC-like TNF binding protein; Provisional.
Length = 338
Score = 24.4 bits (53), Expect = 6.7
Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 4 TILDLNMVGPGEVDSDLEPEVKEECNTKYGENMVGPGEVDSDLEPEV 50
T D + G + + P VK G+N DS V
Sbjct: 186 TANDYQKMAKGNIPKPVTPTVKVTGEEL-GDNTTLFCTFDSHYPSSV 231
>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7;
Provisional.
Length = 176
Score = 23.9 bits (52), Expect = 8.3
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 42 VDSDLEPEVKDECNTKYGEVVRVI 65
++ L +V+ +C KYG V+ VI
Sbjct: 26 IEDMLRSQVEGQCTRKYGYVICVI 49
>gnl|CDD|236064 PRK07589, PRK07589, ornithine cyclodeaminase; Validated.
Length = 346
Score = 24.1 bits (53), Expect = 8.9
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 3 ATILDLNMVGPG 14
ATIL +MV PG
Sbjct: 207 ATILTDDMVEPG 218
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.309 0.133 0.378
Gapped
Lambda K H
0.267 0.0511 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,776,586
Number of extensions: 287238
Number of successful extensions: 169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 164
Number of HSP's successfully gapped: 19
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 53 (24.7 bits)