RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11102
(87 letters)
>gnl|CDD|212566 cd11684, DHR2_DOCK, Dock Homology Region 2, a GEF domain, of
Dedicator of Cytokinesis proteins. DOCK proteins
comprise a family of atypical guanine nucleotide
exchange factors (GEFs) that lack the conventional Dbl
homology (DH) domain. As GEFs, they activate the small
GTPases Rac and Cdc42 by exchanging bound GDP for free
GTP. They are also called the CZH (CED-5, Dock180, and
MBC-zizimin homology) family, after the first family
members identified. Dock180 was first isolated as a
binding partner for the adaptor protein Crk. The
Caenorhabditis elegans protein, Ced-5, is essential for
cell migration and phagocytosis, while the Drosophila
ortholog, Myoblast city (MBC), is necessary for myoblast
fusion and dorsal closure. DOCKs are divided into four
classes (A-D) based on sequence similarity and domain
architecture: class A includes Dock1 (or Dock180), 2 and
5; class B includes Dock3 and 4; class C includes Dock6,
7, and 8; and class D includes Dock9, 10 and 11. All
DOCKs contain two homology domains: the DHR-1 (Dock
homology region-1), also called CZH1, and DHR-2 (also
called CZH2 or Docker). This alignment model represents
the DHR-2 domain of DOCK proteins, which contains the
catalytic GEF activity for Rac and/or Cdc42.
Length = 392
Score = 29.6 bits (67), Expect = 0.15
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 1 MTTLVSQAREYYEKCHCYEKLISVYTEL-------GDFEALESCARKL 41
L +A + ++K +E I++Y EL D+ L RK+
Sbjct: 60 KEALYKKAIDLFDKGKAWEFAIALYKELIPQYENNFDYAKLSEVHRKI 107
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 26.9 bits (60), Expect = 0.53
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 11/66 (16%)
Query: 16 HCYEKLISVYTELGDF-EALESC------ARKLPDSSPL----LKPMGEIFVKYGLCEQA 64
L V LGD+ EALE AR+L + P L + +++ G ++A
Sbjct: 6 AALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEA 65
Query: 65 VYVFDK 70
+ +K
Sbjct: 66 LEYLEK 71
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 27.2 bits (61), Expect = 0.91
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 4 LVSQAREYYEKCHCYEKLISVYTELGDFEALESCARKLPDS 44
L +A Y+K Y++ IS+ +L ++ A K D
Sbjct: 85 LYEEAVILYKKNGNYKEAISLLKKLKLYKDAIEYAVKSNDP 125
>gnl|CDD|232970 TIGR00424, APS_reduc, 5'-adenylylsulfate reductase,
thioredoxin-independent. This enzyme, involved in the
assimilation of inorganic sulfate, is closely related to
the thioredoxin-dependent PAPS reductase of Bacteria
(CysH) and Saccharomyces cerevisiae. However, it has its
own C-terminal thioredoxin-like domain and is not
thioredoxin-dependent. Also, it has a substrate
preference for 5'-adenylylsulfate (APS) over
3'-phosphoadenylylsulfate (PAPS) so the pathway does not
require an APS kinase (CysC) to convert APS to PAPS.
Arabidopsis thaliana appears to have three isozymes, all
able to complement E. coli CysH mutants (even in
backgrounds lacking thioredoxin or APS kinase) but
likely localized to different compartments in
Arabidopsis [Central intermediary metabolism, Sulfur
metabolism].
Length = 463
Score = 26.5 bits (58), Expect = 1.6
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 22 ISVYTELGDFEALESCARKLPDSSPLLKPMGEIFVKYG 59
V ++ + E E A+KL ++SP L+ M + K+G
Sbjct: 79 PEVEEKVVEVEDFEKLAKKLENASP-LEIMDKALEKFG 115
>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 = 25.7 bits (57), Expect = 1.8
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 53 EIFVKYGLCEQAVYVFDKNKHKS 75
E+F +YG E+ V+D+ +S
Sbjct: 18 EVFSRYGPIEKVQVVYDQKTGRS 40
>gnl|CDD|183401 PRK12283, PRK12283, tryptophanyl-tRNA synthetase; Reviewed.
Length = 398
Score = 25.7 bits (57), Expect = 3.7
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 18 YEKLISVYTELGDFEALESCARKLPDSSP 46
Y +L + Y E GD EALE AR L
Sbjct: 195 YHELRNAYQEEGDDEALEQ-ARALLQEQQ 222
>gnl|CDD|219235 pfam06941, NT5C, 5' nucleotidase, deoxy (Pyrimidine), cytosolic
type C protein (NT5C). This family consists of several
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C
(NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a
ubiquitous enzyme in mammalian cells whose
physiological function is not known.
Length = 191
Score = 25.1 bits (55), Expect = 4.3
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 17 CYEKLISVYTELGDFEALESCARKLPDSSPLLKPMGEI 54
YEKL S Y G F LE +P + L+ + +
Sbjct: 55 LYEKLHSFYESPGFFLDLEP----IPGAREALRELADE 88
>gnl|CDD|236577 PRK09581, pleD, response regulator PleD; Reviewed.
Length = 457
Score = 25.2 bits (56), Expect = 4.5
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 13/40 (32%)
Query: 7 QAR---EYYEKCHCYEKLISVYTELGDFEALESCARKLPD 43
+A+ EYY V T EA+ C R+ PD
Sbjct: 19 EAKLLAEYYT----------VLTASSGAEAIAICEREQPD 48
>gnl|CDD|218128 pfam04523, Herpes_U30, Herpes virus tegument protein U30. This
family is named after the human herpesvirus protein, but
has been characterized in cytomegalovirus as UL47.
Cytomegalovirus UL47 is a component of the tegument,
which is a protein layer surrounding the viral capsid.
UL47 co-precipitates with UL48 and UL69 tegument
proteins, and the major capsid protein UL86. A
UL47-containing complex is thought to be involved in the
release of viral DNA from the disassembling virus
particle.
Length = 883
Score = 24.6 bits (54), Expect = 8.1
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 19 EKLISVYTELGDFEALESCARKLPDSSPLLKPMGEIFVKYGLCEQAVYVF 68
+K+ T LG +C+ K S + + ++ GL E+ +
Sbjct: 306 DKINDFMTTLGS-YLQIACSSKKQLSLSDILEIKRRLLRLGLTEETCATY 354
>gnl|CDD|220329 pfam09657, Cas_Csx8, CRISPR-associated protein Csx8 (Cas_Csx8).
Clusters of short DNA repeats with nonhomologous
spacers, which are found at regular intervals in the
genomes of phylogenetically distinct prokaryotic
species, comprise a family with recognisable features.
This family is known as CRISPR (short for Clustered,
Regularly Interspaced Short Palindromic Repeats). A
number of protein families appear only in association
with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry describes
proteins of unknown function which are encoded in the
midst of a cas gene operon.
Length = 441
Score = 24.5 bits (53), Expect = 8.2
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 4 LVSQAREYYEKCHCYEKLISVYTELGDFEALESC 37
L ++ +EY+E + + I ++ E+ DF +
Sbjct: 263 LKNRDKEYFETWYLRNESIKIFKEIEDFSYKDIR 296
>gnl|CDD|187875 cd09744, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as Csx8 family.
Length = 441
Score = 24.5 bits (53), Expect = 8.2
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 4 LVSQAREYYEKCHCYEKLISVYTELGDFEALESC 37
L ++ +EY+E + + I ++ E+ DF +
Sbjct: 263 LKNRDKEYFETWYLRNESIKIFKEIEDFSYKDIR 296
>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
protein; Provisional.
Length = 697
Score = 24.8 bits (54), Expect = 8.3
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 53 EIFVKYGLCEQAVYVFDKNKHKS 75
+++ K+G E A VFD+ K+
Sbjct: 368 DLYSKWGRMEDARNVFDRMPRKN 390
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 24.7 bits (55), Expect = 8.5
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 46 PLLKPMGEI 54
PLL PM EI
Sbjct: 128 PLLAPMSEI 136
>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region. This
region is composed of WD40 repeats.
Length = 429
Score = 24.5 bits (54), Expect = 9.5
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 8 AREYYEKCHCYEKLISVYTELGDFEALE 35
A E Y+K ++KL+ +Y G+ E L+
Sbjct: 352 AEEAYQKAKDFDKLLLLYLSTGNKEKLK 379
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
0.318 0.133 0.402
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: 4,205,921
Number of extensions: 322223
Number of successful extensions: 290
Number of sequences better than 10.0: 1
Number of HSP's gapped: 289
Number of HSP's successfully gapped: 17
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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 (21.7 bits)
S2: 53 (24.3 bits)