RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13852
(78 letters)
>gnl|CDD|173789 cd04059, Peptidases_S8_Protein_convertases_Kexins_Furin-like,
Peptidase S8 family domain in Protein convertases.
Protein convertases, whose members include furins and
kexins, are members of the peptidase S8 or Subtilase
clan of proteases. They have an Asp/His/Ser catalytic
triad that is not homologous to trypsin. Kexins are
involved in the activation of peptide hormones, growth
factors, and viral proteins. Furin cleaves cell surface
vasoactive peptides and proteins involved in
cardiovascular tissue remodeling in the TGN, at cell
surface, or in endosomes but rarely in the ER. Furin
also plays a key role in blood pressure regulation
though the activation of transforming growth factor
(TGF)-beta. High specificity is seen for cleavage after
dibasic (Lys-Arg or Arg-Arg) or multiple basic residues
in protein convertases. There is also strong sequence
conservation.
Length = 297
Score = 88.4 bits (220), Expect = 5e-23
Identities = 34/57 (59%), Positives = 40/57 (70%), Gaps = 1/57 (1%)
Query: 19 IRMLDQPYMTDLIEANSMGHEPNLIDIYSASWGPTDDGKTVDGPRNATMRAIVRGVN 75
IRMLD +TD++EA S+G P+ IDIYS SWGP DDGKTVDGP RA+ GV
Sbjct: 116 IRMLDGD-VTDVVEAESLGLNPDYIDIYSNSWGPDDDGKTVDGPGPLAQRALENGVT 171
>gnl|CDD|215701 pfam00082, Peptidase_S8, Subtilase family. Subtilases are a family
of serine proteases. They appear to have independently
and convergently evolved an Asp/Ser/His catalytic triad,
like that found in the trypsin serine proteases (see
pfam00089). Structure is an alpha/beta fold containing a
7-stranded parallel beta sheet, order 2314567.
Length = 277
Score = 33.9 bits (78), Expect = 0.003
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 19 IRMLDQPYMTDLIEANSMG---HEPNLIDIYSASWGPTDDGKTVDGPRNATMRAIVRGV 74
+++L TD A ++ PN I + + S GP D P ++ AI
Sbjct: 77 VKVLPGSGGTDSELAGAIEWAAERPNDIRVINMSLGPVDG------PPSSWSSAIDELA 129
>gnl|CDD|197314 cd09080, TDP2, Phosphodiesterase domain of human TDP2, a 5'-tyrosyl
DNA phosphodiesterase, and related domains. Human TDP2,
also known as TTRAP (TRAF/TNFR-associated factors, and
tumor necrosis factor receptor/TNFR-associated protein),
is a 5'-tyrosyl DNA phosphodiesterase. It is required
for the efficient repair of topoisomerase II-induced DNA
double strand breaks. The topoisomerase is covalently
linked by a phosphotyrosyl bond to the 5'-terminus of
the break. TDP2 cleaves the DNA 5'-phosphodiester bond
and restores 5'-phosphate termini, needed for subsequent
DNA ligation, and hence repair of the break. TDP2 and
3'-tyrosyl DNA phosphodiesterase (TDP1) are
complementary activities; together, they allow cells to
remove trapped topoisomerase from both 3'- and 5'-DNA
termini. TTRAP has been reported as being involved in
apoptosis, embryonic development, and transcriptional
regulation, and it may inhibit the activation of nuclear
factor-kB. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 248
Score = 30.0 bits (68), Expect = 0.078
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 35 SMGHEPNLIDIYSASWGPTDDGKTVDGPRNATMRAIVRG 73
+ G +D + P + G T D +N +R G
Sbjct: 163 TGGLPNGFVDAWEELGPPGEPGYTWDTQKNPMLRKGEAG 201
>gnl|CDD|130895 TIGR01836, PHA_synth_III_C, poly(R)-hydroxyalkanoic acid synthase,
class III, PhaC subunit. This model represents the PhaC
subunit of a heterodimeric form of polyhydroxyalkanoic
acid (PHA) synthase. Excepting the PhaC of Bacillus
megaterium (which needs PhaR), all members require PhaE
(TIGR01834) for activity and are designated class III.
This enzyme builds ester polymers for carbon and energy
storage that accumulate in inclusions, and both this
enzyme and the depolymerase associate with the
inclusions. Class III enzymes polymerize
short-chain-length hydroxyalkanoates [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 350
Score = 27.4 bits (61), Expect = 0.65
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 21 MLDQPYMTDLIEANSMGHEPNL----IDIYSASWGPTD 54
++++PYM DL E S+ L D+Y WG D
Sbjct: 71 LVNRPYMLDLQEDRSLVR--GLLERGQDVYLIDWGYPD 106
>gnl|CDD|178238 PLN02631, PLN02631, ferric-chelate reductase.
Length = 699
Score = 26.2 bits (57), Expect = 1.9
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 25 PYMTDLIEANSM--GHEPNLIDIYSASWGPTDDGKTVDGPR 63
PY + +++A S+ G +PNL I + G D G V GPR
Sbjct: 633 PYQS-IVQATSVHFGSKPNLKKILLEAEGSEDVGVMVCGPR 672
>gnl|CDD|220363 pfam09724, DUF2036, Uncharacterized conserved protein (DUF2036).
This family of proteins includes members ranging in size
from approximately 300 to 460 residues. There are a
number of well-conserved domains along the length.
Length = 325
Score = 25.4 bits (56), Expect = 3.1
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 8 HELLQISHDGRIRMLDQPYMTDLI 31
+L I DGR R+L Y T +
Sbjct: 148 KKLGAIEIDGRARVLSPDYETKAL 171
>gnl|CDD|187887 cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
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;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-C subtype; also
known as Csd1 family.
Length = 569
Score = 24.9 bits (55), Expect = 4.8
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 37 GHEPNLIDIYSASWGPTDDGKTVDGPRN---ATMRAIVRG 73
G P+ DI +G DGKT + P N +R+I+ G
Sbjct: 363 GGAPSPPDIARLLYGTARDGKTENIPPNLAGRLLRSILDG 402
>gnl|CDD|173875 cd08510, PBP2_Lactococcal_OppA_like, The substrate binding
component of an ABC-type lactococcal OppA-like transport
system contains. This family represents the substrate
binding domain of an ATP-binding cassette (ABC)-type
oligopeptide import system from Lactococcus lactis and
other gram-positive bacteria, as well as its closet
homologs from gram-negative bacteria.
Oligopeptide-binding protein (OppA) from Lactococcus
lactis can bind peptides of length from 4 to at least 35
residues without sequence preference. The oligopeptide
import system OppABCDEF is consisting of five subunits:
two homologous integral membrane proteins OppB and OppF
that form the translocation pore; two homologous
nucleotide-binding domains OppD and OppF that drive the
transport process through binding and hydrolysis of ATP;
and the substrate-binding protein or receptor OppA that
determines the substrate specificity of the transport
system. The dipeptide (DppA) and oligopeptide (OppA)
binding proteins differ in several ways. The DppA binds
dipeptides and some tripeptides and also is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 residues) and
plays a role in recycling of cell wall peptides, which
precludes any involvement in chemotaxis. Most of other
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the dipeptide/oligopeptide binding proteins. The
structural topology of these domains is most similar to
that of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 516
Score = 24.5 bits (54), Expect = 7.8
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 30 LIEANS----MGHEPNLIDIYSASWG 51
LIE NS + + ID++ +WG
Sbjct: 410 LIEFNSFYDKLQADDPDIDVFQGAWG 435
>gnl|CDD|218669 pfam05638, DUF796, Protein of unknown function (DUF796). This
family consists of several bacterial proteins of
unknown function.
Length = 131
Score = 24.1 bits (53), Expect = 7.9
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 26 YMT-DLIEANSM--GHEPNLIDIYSASWG 51
Y+ D I+ S GHE + I++ S SWG
Sbjct: 1 YLKIDGIKGESTDAGHE-DEIEVLSFSWG 28
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
0.317 0.133 0.396
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,877,108
Number of extensions: 292512
Number of successful extensions: 235
Number of sequences better than 10.0: 1
Number of HSP's gapped: 235
Number of HSP's successfully gapped: 12
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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 (24.2 bits)