RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16431
(87 letters)
>gnl|CDD|107241 cd06492, p23_mNUDC_like, p23-like NUD (nuclear distribution)
C-like domain of mammalian(m) NUDC and similar
proteins. Mammalian(m) NUDC associates both with the
dynein complex and also with an anti-inflammatory
enzyme, platelet activating factor acetylhydrolase I,
PAF-AH(I) complex, through binding mNUDF, the
regulatory beta subunit of PAF-AH(I). mNUDC is
important for cell proliferation both in normal and
tumor tissues. Its expression is elevated in various
cell types undergoing mitosis or stimulated to
proliferate, with high expression levels observed in
leukemic cells and tumors. For a leukemic cell line,
human NUDC was shown to activate the thrombopoietin
(TPO) receptor (Mpl) by binding to its extracellular
domain, and promoting cell proliferation and
differentiation.
Length = 87
Score = 34.6 bits (80), Expect = 9e-04
Identities = 12/14 (85%), Positives = 14/14 (100%)
Query: 1 MEKINKMEWWSKLV 14
+EKINKMEWWS+LV
Sbjct: 74 LEKINKMEWWSRLV 87
>gnl|CDD|107286 cd06291, PBP1_Qymf_like, Ligand binding domain of the lacI-like
transcription regulator from a novel metal-reducing
bacterium Alkaliphilus Metalliredigens (strain Qymf) and
its close homologs. This group includes the ligand
binding domain of the lacI-like transcription regulator
from a novel metal-reducing bacterium Alkaliphilus
Metalliredigens (strain Qymf) and its close homologs.
Qymf is a strict anaerobe that could be grown in the
presence of borax and its cells are straight rods that
produce endospores. This group is a member of the
LacI-GalR family repressors that are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 265
Score = 28.3 bits (64), Expect = 0.41
Identities = 8/27 (29%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 54 EMGLPTSDEQKKQDVLKKFMEQHPEMD 80
E+ D +KK+++ K+ +E++P++D
Sbjct: 150 EIQENFDDAEKKEEI-KELLEEYPDID 175
>gnl|CDD|182731 PRK10788, PRK10788, periplasmic folding chaperone; Provisional.
Length = 623
Score = 28.4 bits (64), Expect = 0.42
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 42 LVEKMMYDQRQKEMGLPTSDEQKKQ 66
L+++ + DQ +E+GL SDEQ KQ
Sbjct: 95 LIDEALLDQYARELGLGISDEQVKQ 119
>gnl|CDD|107224 cd06467, p23_NUDC_like, p23_like domain of NUD (nuclear
distribution) C and similar proteins. Aspergillus
nidulas (An) NUDC is needed for nuclear movement.
AnNUDC is localized at the hyphal cortex, and binds
NUDF at spindle pole bodies (SPBs) and in the cytoplasm
at different stages in the cell cycle. At the SPBs it
is part of the dynein molecular motor/NUDF complex that
regulates microtubule dynamics. Mammalian(m) NUDC
associates both with the dynein complex and also with
an anti-inflammatory enzyme, platelet activating factor
acetylhydrolase I, PAF-AH(I) complex, through binding
mNUDF, the regulatory beta subunit of PAF-AH(I). mNUDC
is important for cell proliferation both in normal and
tumor tissues. Its expression is elevated in various
cell types undergoing mitosis or stimulated to
proliferate, with high expression levels observed in
leukemic cells and tumors. For a leukemic cell line,
human NUDC was shown to activate the thrombopoietin
(TPO) receptor (Mpl) by binding to its extracellular
domain, and promoting cell proliferation and
differentiation. This group also includes the human
broadly immunogenic tumor associated antigen, CML66,
which is highly expressed in a variety of solid tumors
and in leukemias. In normal tissues high expression of
CML66 is limited to testis and heart.
Length = 85
Score = 26.7 bits (60), Expect = 0.63
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 1 MEKINKMEWWSKLV 14
+EK N+ EWW LV
Sbjct: 72 LEKRNEGEWWPSLV 85
>gnl|CDD|238097 cd00168, SCP, SCP: SCP-like extracellular protein domain, found
in eukaryotes and prokaryotes. This family includes
plant pathogenesis-related protein 1 (PR-1), which
accumulates after infections with pathogens, and may
act as an anti-fungal agent or be involved in cell wall
loosening. This family also includes CRISPs, mammalian
cysteine-rich secretory proteins, which combine SCP
with a C-terminal cysteine rich domain, and allergen 5
from vespid venom. Roles for CRISP, in response to
pathogens, fertilization, and sperm maturation have
been proposed. One member, Tex31 from the venom duct of
Conus textile, has been shown to possess proteolytic
activity sensitive to serine protease inhibitors. The
human GAPR-1 protein has been reported to dimerize, and
such a dimer may form an active site containing a
catalytic triad. SCP has also been proposed to be a
Ca++ chelating serine protease. The Ca++-chelating
function would fit with various signaling processes
that members of this family, such as the CRISPs, are
involved in, and is supported by sequence and
structural evidence of a conserved pocket containing
two histidines and a glutamate. It also may explain how
helothermine, a toxic peptide secreted by the beaded
lizard, blocks Ca++ transporting ryanodine receptors.
Little is known about the biological roles of the
bacterial and archaeal SCP domains.
Length = 122
Score = 25.9 bits (57), Expect = 2.2
Identities = 3/28 (10%), Positives = 9/28 (32%)
Query: 60 SDEQKKQDVLKKFMEQHPEMDFSNCKFG 87
S + ++ + + +F F
Sbjct: 59 SYDMTGPAAVQAWYNEIKNYNFGQPGFS 86
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 26.4 bits (59), Expect = 2.2
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 31 KLSDLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFMEQ 75
K +LD ETR L+E+++ D R+ + LP + ++ +K ++
Sbjct: 95 KNEELDPETRRLLERLLRDFRRNGLDLP----EATRERVKALKKE 135
>gnl|CDD|225329 COG2609, AceE, Pyruvate dehydrogenase complex, dehydrogenase (E1)
component [Energy production and conversion].
Length = 887
Score = 25.4 bits (56), Expect = 5.0
Identities = 8/44 (18%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 43 VEKMMYDQRQKEMGLPTSDEQKKQDVLKKFMEQHPEMDFSNCKF 86
V K+++ +R E+ + L++ M + + D+ K
Sbjct: 289 VIKVIWGRRWDELL-----AKDTGGKLRQLMNETVDGDYQTFKA 327
>gnl|CDD|147514 pfam05367, Phage_endo_I, Phage endonuclease I. The bacteriophage
endonuclease I is a nuclease that is selective for the
structure of the four-way Holliday DNA junction.
Length = 149
Score = 24.8 bits (54), Expect = 5.8
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 7/34 (20%)
Query: 56 GLPTSDEQKKQDVLKKFMEQHPEMD----FSNCK 85
GL S+++KK +++ EQHPE+D FS+ +
Sbjct: 68 GLFESEDRKKHLLIR---EQHPELDIRFVFSSSR 98
>gnl|CDD|176471 cd03302, Adenylsuccinate_lyase_2, Adenylsuccinate lyase
(ASL)_subgroup 2. This subgroup contains mainly
eukaryotic proteins similar to ASL, a member of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions
in which a C-N or C-O bond is cleaved with the release
of fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. ASL catalyzes two steps in
the de novo purine biosynthesis: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and, the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP). ASL deficiency has
been linked to several pathologies including
psychomotor retardation with autistic features,
epilepsy and muscle wasting.
Length = 436
Score = 25.0 bits (55), Expect = 6.9
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 52 QKEMGLPTSDEQKKQDVLKKFME 74
+KE+GL SDEQ ++ +K +E
Sbjct: 34 EKELGLDISDEQIEE--MKANVE 54
>gnl|CDD|236070 PRK07636, ligB, ATP-dependent DNA ligase; Reviewed.
Length = 275
Score = 24.7 bits (54), Expect = 8.0
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 32 LSDLDGETRGLVEKMMYDQRQK 53
LS LDG + G++E M YD R+K
Sbjct: 206 LSYLDGRSAGIMEFMPYDARKK 227
>gnl|CDD|219903 pfam08559, Cut8, Cut8. In Schizosaccharomyces pombe, Cut8 is a
nuclear envelope protein that physically interacts with
and tethers 26S proteasome in the nucleus resulting in
the nuclear accumulation of proteasome. Cut8 is a
proteasome substrate and amino terminal residues 1-72
are polyubiquitinated and function as a degron tag.
Ubiquitination of the amino terminal is essential to
the function of Cut8. Lysine residues in the amino
terminal 72 amino acids of Cut8 are required for
physical interaction with proteasome. In fission yeast
the function of Cut8 has been demonstrated to be
regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and
ligating enzymes Ubr1. Cut8 homologs have been
identified in Drosophila melanogaster, Anopheles
gambiae and Dictyostelium discoideum.
Length = 200
Score = 24.5 bits (54), Expect = 8.7
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 57 LPTSDEQKKQDVLKKFMEQHPE 78
L T D+Q+ Q +L +E+HPE
Sbjct: 30 LETLDKQQLQSLLLSLIERHPE 51
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
0.311 0.129 0.378
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,332,689
Number of extensions: 335230
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 20
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 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.1 bits)