RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2111
(63 letters)
>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 = 60.8 bits (148), Expect = 2e-14
Identities = 21/31 (67%), Positives = 26/31 (83%)
Query: 11 RAYRTLHGAWFNSKLVTVKYLRYERYHERFP 41
+A++ LHG WF+ +LVTVKYLR ERYH RFP
Sbjct: 62 KAFKALHGWWFDGRLVTVKYLRLERYHSRFP 92
>gnl|CDD|235127 PRK03467, PRK03467, hypothetical protein; Provisional.
Length = 144
Score = 27.3 bits (61), Expect = 0.33
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 33 YERYHERFPQAKALVAPL 50
+RY+ RFP A+AL AP+
Sbjct: 101 RKRYNRRFPVARALSAPV 118
>gnl|CDD|236834 PRK11067, PRK11067, outer membrane protein assembly factor YaeT;
Provisional.
Length = 803
Score = 27.3 bits (61), Expect = 0.46
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 10 RRAYRTLHGAWFNSKLV 26
RR R + GAW S LV
Sbjct: 366 RREMRQMEGAWLGSDLV 382
>gnl|CDD|235675 PRK06025, PRK06025, acetyl-CoA acetyltransferase; Provisional.
Length = 417
Score = 25.9 bits (57), Expect = 1.4
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 3 EVGWEKKRRAYRTLHGAWFNSKLVTVKYL--RYERYHERFPQ----AKALVAPLKPS 53
+G E +RRA R + F+ LV V HE FP+ A+ L A LKP+
Sbjct: 178 ALGLESQRRAARAIKEGRFDKSLVPVYRDDGSVALDHEEFPRPQTTAEGL-AALKPA 233
>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 = 25.6 bits (56), Expect = 1.6
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 12 AYRTLHGAWFNSKLVTVKYLRYERYHERFP 41
A++ L+G +F K++T ++ + Y
Sbjct: 426 AFQALNGRYFGGKMITAAFVVNDVYDMSCL 455
>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase.
Corresponds to Merops family A17. These proteins are
homologous to aspartic proteinases encoded by
retroposons and retroviruses.
Length = 159
Score = 25.4 bits (56), Expect = 1.7
Identities = 11/30 (36%), Positives = 12/30 (40%)
Query: 34 ERYHERFPQAKALVAPLKPSNDRRYSLQQA 63
E AK VAPLK + R L A
Sbjct: 105 EEIQVSLVAAKTRVAPLKTVSIPRLELCAA 134
>gnl|CDD|215634 PLN03211, PLN03211, ABC transporter G-25; Provisional.
Length = 659
Score = 25.6 bits (56), Expect = 1.8
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 7 EKKRRAYRTLHGAWFNSKLVTVKYLRYERYHERF 40
++ R + R WFN + ++ ER HE F
Sbjct: 375 KEHRSSDRISISTWFNQFSILLQRSLKERKHESF 408
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 24.7 bits (54), Expect = 2.9
Identities = 12/53 (22%), Positives = 20/53 (37%)
Query: 4 VGWEKKRRAYRTLHGAWFNSKLVTVKYLRYERYHERFPQAKALVAPLKPSNDR 56
+G +R+ ++ L + + E Y ER+ QA V L R
Sbjct: 135 LGSSVQRQEFQNLLEQMLEENNIPFVVIEGEDYLERYLQAVEAVEELLGEKQR 187
>gnl|CDD|212573 cd11700, DHR2_DOCK11, Dock Homology Region 2, a GEF domain, of
Class D Dedicator of Cytokinesis 11. Dock11, also
called Zizimin2 or activated Cdc42-associated GEF (ACG),
is an atypical guanine nucleotide exchange factor (GEF)
that lacks the conventional Dbl homology (DH) domain. As
a GEF, it activates the small GTPase Cdc42 by exchanging
bound GDP for free GTP. Dock11 is predominantly
expressed in lymphocytes and is found in high levels in
germinal center B lymphocytes after T cell dependent
antigen immunization. DOCK proteins are divided into
four classes (A-D) based on sequence similarity and
domain architecture; class D includes Dock9, 10 and 11.
All DOCKs contain two homology domains: the DHR-1 (Dock
homology region-1), also called CZH1 (CED-5, Dock180,
and MBC-zizimin homology 1), and DHR-2 (also called CZH2
or Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock11, which
contains the catalytic GEF activity for Cdc42. Class D
DOCKs also contain a Pleckstrin homology (PH) domain at
the N-terminus.
Length = 413
Score = 25.0 bits (54), Expect = 3.3
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 6 WEKKRRAYRTLHGAW 20
+EK + YRTLHGA+
Sbjct: 118 FEKLTQLYRTLHGAY 132
>gnl|CDD|233540 TIGR01709, typeII_sec_gspL, type II secretion system protein L.
This model represents GspL, protein L of the main
terminal branch of the general secretion pathway, also
called type II secretion. It transports folded proteins
across the bacterial outer membrane and is widely
distributed in Gram-negative pathogens [Protein fate,
Protein and peptide secretion and trafficking].
Length = 384
Score = 23.9 bits (52), Expect = 7.1
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 34 ERYHERFPQAKALVAPLKPSNDRRYSLQQA 63
E Y + FP+AK +V P L
Sbjct: 273 ETYRQLFPEAKKVVNPRTQFKAELSRLAAQ 302
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that 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. Like U2AF35, U2AFBPL 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 domain. .
Length = 105
Score = 23.4 bits (51), Expect = 9.8
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 11 RAYRTLHGAWFNSKLVTVKY 30
A++ +G W+ K +T ++
Sbjct: 84 AAFKMFNGRWYAGKQLTCEF 103
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
0.321 0.133 0.418
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,244,308
Number of extensions: 220608
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 13
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.3 bits)