RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10521
(66 letters)
>gnl|CDD|204131 pfam09092, Lyase_N, Lyase, N terminal. Members of this family are
predominantly found in chondroitin ABC lyase I, and
adopt a jelly-roll fold topology consisting of a
two-layered bent beta-sheet sandwich with one short
alpha-helix. The convex beta sheet is composed of five
antiparallel strands, whilst the concave beta-sheet
contains five antiparallel beta-strands with a loop
between two consecutive strands folding back onto the
concave surface. This domain is required for binding of
the protein to long glycosaminoglycan chains.
Length = 178
Score = 28.3 bits (63), Expect = 0.17
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 14 LSSGDLYVFNATPNDGYKSYRCRTVNKITGESQASVFQTRLSITGFRAVY 63
S+ L+++N P D Y ++ + +GE A F+ ++ TG+RAV+
Sbjct: 72 RSAISLWIYNEKPVDDYITFEFGSKLGPSGEPDAG-FKVGINFTGWRAVW 120
>gnl|CDD|173895 cd00517, ATPS, ATP-sulfurylase. ATP-sulfurylase (ATPS), also known
as sulfate adenylate transferase, catalyzes the transfer
of an adenylyl group from ATP to sulfate, forming
adenosine 5'-phosphosulfate (APS). This reaction is
generally accompanied by a further reaction, catalyzed
by APS kinase, in which APS is phosphorylated to yield
3'-phospho-APS (PAPS). In some organisms the APS kinase
is a separate protein, while in others it is
incorporated with ATP sulfurylase in a bifunctional
enzyme that catalyzes both reactions. In bifunctional
proteins, the domain that performs the kinase activity
can be attached at the N-terminal end of the sulfurylase
unit or at the C-terminal end, depending on the
organism. While the reaction is ubiquitous among
organisms, the physiological role of the reaction
varies. In some organisms it is used to generate APS
from sulfate and ATP, while in others it proceeds in the
opposite direction to generate ATP from APS and
pyrophosphate. ATP sulfurylase can be a monomer, a
homodimer, or a homo-oligomer, depending on the
organism. ATPS belongs to a large superfamily of
nucleotidyltransferases that includes pantothenate
synthetase (PanC), phosphopantetheine
adenylyltransferase (PPAT), and the amino-acyl tRNA
synthetases. The enzymes of this family are structurally
similar and share a dinucleotide-binding domain.
Length = 353
Score = 26.4 bits (59), Expect = 0.95
Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 11/63 (17%)
Query: 2 TSDDFVGGKYVVLSS------GDLYVFNATPNDGYKSYR-----CRTVNKITGESQASVF 50
T+D G V+ G + V P + YR R + K G + F
Sbjct: 103 TTDPHHPGVKKVMEQGDWLVGGPIEVLELPPFPDFDQYRLTPAELRALFKERGWRRVVAF 162
Query: 51 QTR 53
QTR
Sbjct: 163 QTR 165
>gnl|CDD|215067 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 25.9 bits (57), Expect = 1.3
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 27 NDGYKSYRCRTV 38
+D +K YRC T+
Sbjct: 238 DDEFKLYRCHTI 249
>gnl|CDD|241300 cd01270, PTB_CAPON-like, Carboxyl-terminal PDZ ligand of neuronal
nitric oxide synthase protein (CAPON)
Phosphotyrosine-binding (PTB) domain. CAPON (also known
as Nitric oxide synthase 1 adaptor protein, NOS1AP,
encodes a cytosolic protein that binds to the signaling
molecule, neuronal NOS (nNOS). It contains a N-terminal
PTB domain that binds to the small monomeric G protein,
Dexras1 and a C-terminal PDZ-binding domain that
mediates interactions with nNOS. Included in this cd
are C. elegan proteins dystrobrevin, DYB-1, which
controls neurotransmitter release and muscle Ca(2+)
transients by localizing BK channels and DYstrophin-like
phenotype and CAPON related,DYC-1, which is functionally
related to dystrophin homolog, DYS-1. Mutations in the
dystrophin gene causes Duchenne muscular dystrophy.
DYS-1 shares sequence similarity, including key motifs,
with their mammalian counterparts. These CAPON-like
proteins all have a single PTB domain. PTB domains have
a common PH-like fold and are found in various
eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 179
Score = 25.7 bits (57), Expect = 1.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 11 YVVLSSGDLYVFNATPNDGYKS-YRCRTVNKITGESQA 47
YV S DL +F+ DG + ++C V K +SQA
Sbjct: 112 YVSHDSQDLKIFSYIARDGSSNVFKC-NVFKSKKKSQA 148
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 25.4 bits (56), Expect = 2.2
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 8 GGKYVVLSSGDL-YVFNATPNDGYKSYR 34
G K +V GDL +VFN P + Y YR
Sbjct: 643 GDKVIVFERGDLVFVFNFHPTNSYSDYR 670
>gnl|CDD|143178 cd04977, Ig1_NCAM-1_like, First immunoglobulin (Ig)-like domain
of neural cell adhesion molecule NCAM-1 and similar
proteins. Ig1_NCAM-1 like: first immunoglobulin
(Ig)-like domain of neural cell adhesion molecule
NCAM-1. NCAM-1 plays important roles in the development
and regeneration of the central nervous system, in
synaptogenesis and neural migration. NCAM mediates
cell-cell and cell-substratum recognition and adhesion
via homophilic (NCAM-NCAM), and heterophilic
(NCAM-nonNCAM), interactions. NCAM is expressed as
three major isoforms having different intracellular
extensions. The extracellular portion of NCAM has five
N-terminal Ig-like domains and two fibronectin type III
domains. The double zipper adhesion complex model for
NCAM homophilic binding involves the Ig1, Ig2, and Ig3
domains. By this model, Ig1 and Ig2 mediate
dimerization of NCAM molecules situated on the same
cell surface (cis interactions), and Ig3 domains
mediate interactions between NCAM molecules expressed
on the surface of opposing cells (trans interactions),
through binding to the Ig1 and Ig2 domains. The
adhesive ability of NCAM is modulated by the addition
of polysialic acid chains to the fifth Ig-like domain.
Also included in this group is NCAM-2 (also known as
OCAM/mamFas II and RNCAM). NCAM-2 is differentially
expressed in the developing and mature olfactory
epithelium (OE).
Length = 92
Score = 24.4 bits (53), Expect = 3.7
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 9 GKYVVLSSGD----LYVFNATPNDGYKSYRCRTVNKITGESQASV 49
+ V+ + D L ++NA D Y+C + ES+A+V
Sbjct: 45 QQISVVQNDDVRSTLTIYNANIEDA-GIYKCVATDAKGTESEATV 88
>gnl|CDD|213240 cd03273, ABC_SMC2_euk, ATP-binding cassette domain of eukaryotic
SMC2 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five
recognizable domains. Amino-acid sequence homology of
SMC proteins between species is largely confined to the
amino- and carboxy-terminal globular domains. The
amino-terminal domain contains a 'Walker A'
nucleotide-binding domain (GxxGxGKS/T, in the
single-letter amino-acid code), which by mutational
studies has been shown to be essential in several
proteins. The carboxy-terminal domain contains a
sequence (the DA-box) that resembles a 'Walker B'
motif, and a motif with homology to the signature
sequence of the ATP-binding cassette (ABC) family of
ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 251
Score = 24.6 bits (54), Expect = 4.0
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 8/24 (33%)
Query: 28 DGYKSYRCRTV--------NKITG 43
DG+KSY RTV N ITG
Sbjct: 9 DGFKSYATRTVISGFDPQFNAITG 32
>gnl|CDD|198067 smart00999, Aerolysin, Aerolysin toxin. This family represents
the pore forming lobe of aerolysin.
Length = 368
Score = 23.7 bits (51), Expect = 8.8
Identities = 13/41 (31%), Positives = 16/41 (39%)
Query: 2 TSDDFVGGKYVVLSSGDLYVFNATPNDGYKSYRCRTVNKIT 42
+ +VG V GD +V N YRC KIT
Sbjct: 36 NASQYVGEDMDVTRVGDGWVIQGNYNGSCSGYRCGEKTKIT 76
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 0.384
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,145,658
Number of extensions: 210227
Number of successful extensions: 183
Number of sequences better than 10.0: 1
Number of HSP's gapped: 183
Number of HSP's successfully gapped: 10
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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 (24.5 bits)