RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10539
(109 letters)
>gnl|CDD|239582 cd03505, Delta9-FADS-like, The Delta9 Fatty Acid Desaturase
(Delta9-FADS)-like CD includes the delta-9 and delta-11
acyl CoA desaturases found in various eukaryotes
including vertebrates, insects, higher plants, and
fungi. The delta-9 acyl-lipid desaturases are found in a
wide range of bacteria. These enzymes play essential
roles in fatty acid metabolism and the regulation of
cell membrane fluidity. Acyl-CoA desaturases are the
enzymes involved in the CoA-bound desaturation of fatty
acids. Mammalian stearoyl-CoA delta-9 desaturase is a
key enzyme in the biosynthesis of monounsaturated fatty
acids, and in yeast, the delta-9 acyl-CoA desaturase
(OLE1) reaction accounts for all de nova unsaturated
fatty acid production in Saccharomyces cerevisiae. These
non-heme, iron-containing, ER membrane-bound enzymes are
part of a three-component enzyme system involving
cytochrome b5, cytochrome b5 reductase, and the delta-9
fatty acid desaturase. This complex catalyzes the NADH-
and oxygen-dependent insertion of a cis double bond
between carbons 9 and 10 of the saturated fatty acyl
substrates, palmitoyl (16:0)-CoA or stearoyl (18:0)-CoA,
yielding the monoenoic products palmitoleic (16:l) or
oleic (18:l) acids, respectively. In cyanobacteria, the
biosynthesis of unsaturated fatty acids is initiated by
delta 9 acyl-lipid desaturase (DesC) which introduces
the first double bond at the delta-9 position of a
saturated fatty acid that has been esterified to a
glycerolipid. This domain family has extensive
hydrophobic regions that would be capable of spanning
the membrane bilayer at least twice. Comparison of
sequences also reveals the existence of three regions of
conserved histidine cluster motifs that contain the
residues: HXXXXH, HXXHH, and H/QXXHH. These histidine
residues are reported to be catalytically essential and
proposed to be the ligands for the iron atoms contained
within the rat stearoyl CoA delta-9 desaturase. Some
eukaryotic (Fungi, Euglenozoa, Mycetozoa, Rhodophyta)
desaturase domains have an adjacent C-terminal
cytochrome b5-like domain.
Length = 178
Score = 81.1 bits (201), Expect = 1e-20
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 1 MKGKR----RILPSENVWVSIVSLGEGWHNYHHVFPWDYRAAEMGSYSLNLTTFWLDQFA 56
M G R R N WV++++ GEGWHN HH FP D R + Y ++ T + +
Sbjct: 111 MWGYRPYDTRDTSRNNWWVALLTFGEGWHNNHHAFPGDARNG-LKWYQIDPTKWVIRLLE 169
Query: 57 KIGWAYDLK 65
K+G A+DLK
Sbjct: 170 KLGLAWDLK 178
>gnl|CDD|224316 COG1398, OLE1, Fatty-acid desaturase [Lipid metabolism].
Length = 289
Score = 63.2 bits (154), Expect = 3e-13
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 RRILPSENVWVSIVSLGEGWHNYHHVFPWDYRAAEMGSYSLNLTTFWLDQFAKIGWAYDL 64
R WV++V+ GEGWHN HH FP R + + ++T + + + +G A +
Sbjct: 219 CRDTARNCWWVALVTFGEGWHNNHHAFPNSARNG-LKWWEFDVTWWIIKLLSLLGLAKVV 277
Query: 65 KKPSDKMI 72
K I
Sbjct: 278 KLAPKARI 285
>gnl|CDD|177866 PLN02220, PLN02220, delta-9 acyl-lipid desaturase.
Length = 299
Score = 43.6 bits (103), Expect = 3e-06
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 10 SENVW-VSIVSLGEGWHNYHHVFPWDYRAAEMGSYSLNLTTFWLDQFAKIGWAYDLKKPS 68
S NVW +S+ ++GE WHN HH F R + + +++T + + F +G A D+K P+
Sbjct: 230 SRNVWWLSLFTMGESWHNNHHAFESSARQG-LEWWQIDITWYLIRFFEVLGLATDVKLPT 288
Query: 69 DKMIRSHA 76
+ R A
Sbjct: 289 EAQKRKMA 296
>gnl|CDD|238511 cd01060, Membrane-FADS-like, The membrane fatty acid desaturase
(Membrane_FADS)-like CD includes membrane FADSs, alkane
hydroxylases, beta carotene ketolases (CrtW-like),
hydroxylases (CrtR-like), and other related proteins.
They are present in all groups of organisms with the
exception of archaea. Membrane FADSs are non-heme,
iron-containing, oxygen-dependent enzymes involved in
regioselective introduction of double bonds in fatty
acyl aliphatic chains. They play an important role in
the maintenance of the proper structure and functioning
of biological membranes. Alkane hydroxylases are
bacterial, integral-membrane di-iron enzymes that share
a requirement for iron and oxygen for activity similar
to that of membrane FADSs, and are involved in the
initial oxidation of inactivated alkanes. Beta-carotene
ketolase and beta-carotene hydroxylase are carotenoid
biosynthetic enzymes for astaxanthin and zeaxanthin,
respectively. This superfamily domain has extensive
hydrophobic regions that would be capable of spanning
the membrane bilayer at least twice. Comparison of these
sequences also reveals three regions of conserved
histidine cluster motifs that contain eight histidine
residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional
conserved histidine residue is seen between clusters 2
and 3). Spectroscopic and genetic evidence point to a
nitrogen-rich coordination environment located in the
cytoplasm with as many as eight histidines coordinating
the two iron ions and a carboxylate residue bridging the
two metals in the Pseudomonas oleovorans alkane
hydroxylase (AlkB). In addition, the eight histidine
residues are reported to be catalytically essential and
proposed to be the ligands for the iron atoms contained
within the rat stearoyl CoA delta-9 desaturase.
Length = 122
Score = 34.8 bits (80), Expect = 0.002
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 5 RRILPSENVWVSIVSLGEGWHNYHHVFP 32
+++ G G+HN HH+FP
Sbjct: 95 TTDNSRNGWLNLLLTGGLGYHNEHHLFP 122
>gnl|CDD|215943 pfam00487, FA_desaturase, Fatty acid desaturase.
Length = 251
Score = 31.5 bits (71), Expect = 0.060
Identities = 6/29 (20%), Positives = 16/29 (55%)
Query: 4 KRRILPSENVWVSIVSLGEGWHNYHHVFP 32
++ + S + ++ ++ +H HH+FP
Sbjct: 194 RQLVTTSNSWVLNWLTGNLNYHIEHHLFP 222
>gnl|CDD|72494 pfam09076, Sklp_toxin, Streptomyces killer toxin-like. Members
of this family assume a beta-gamma-crystallin fold,
wherein nine beta-strands are connected by loop, and
are separated into two sheets, each sheet forming the
Greek key motif. The two Greek key motifs face each
other in the global topology. The three-dimensional
structure of the molecule is a 'sandwich'-shaped
beta-barrel structure: hydrophobic side-chains are
packed in the large interface area of the beta-sheets.
This domain confers a cytocidal effect to the toxin,
causing cell death in both budding and fission yeasts,
and morphological changes in yeasts and filamentous
fungi.
Length = 64
Score = 26.6 bits (58), Expect = 0.93
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 9 PSENVWVSIVSLGEGWHNYH 28
P VWV +S G W NYH
Sbjct: 15 PGTTVWVDKISTGNNWVNYH 34
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 27.6 bits (62), Expect = 1.3
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 62 YDLKKPSDKMIRSHAE--KYA-GHDHPVEVTEEDASTMDLE 99
Y LKK ++++ + E +YA H VE++ EDAS DL+
Sbjct: 103 YKLKKTREEVLETAVEAVEYAKDHGLIVELSGEDASRADLD 143
>gnl|CDD|133235 cd05104, PTKc_Kit, Catalytic domain of the Protein Tyrosine Kinase,
Kit. Protein Tyrosine Kinase (PTK) family; Kit (or
c-Kit); catalytic (c) domain. The PTKc family is part of
a larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Kit is a member of the
Platelet Derived Growth Factor Receptor (PDGFR)
subfamily of proteins, which are receptor tyr kinases
(RTKs) containing an extracellular ligand-binding region
with five immunoglobulin-like domains, a transmembrane
segment, and an intracellular catalytic domain. The
binding of Kit to its ligand, the stem-cell factor
(SCF), leads to receptor dimerization, trans
phosphorylation and activation, and intracellular
signaling. Kit is important in the development of
melanocytes, germ cells, mast cells, hematopoietic stem
cells, the interstitial cells of Cajal, and the
pacemaker cells of the GI tract. Kit signaling is
involved in major cellular functions including cell
survival, proliferation, differentiation, adhesion, and
chemotaxis. Mutations in Kit, which result in
constitutive ligand-independent activation, are found in
human cancers such as gastrointestinal stromal tumor
(GIST) and testicular germ cell tumor (TGCT). The
aberrant expression of Kit and/or SCF is associated with
other tumor types such as systemic mastocytosis and
cancers of the breast, neurons, lung, prostate, colon,
and rectum. Although the structure of the human Kit
catalytic domain is known, it is excluded from this
specific alignment model because it contains a deletion
in its sequence.
Length = 375
Score = 27.2 bits (60), Expect = 2.0
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 57 KIGWAYDLKKPSDKMIRSHAEKYAGHDHPVEVTEEDASTMDLEEI 101
K G +Y + +DK + Y D E+ EED +D E++
Sbjct: 172 KPGVSYVVPTKADKRRSVRSGSYIDQDVTSEILEEDELALDTEDL 216
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 26.9 bits (60), Expect = 2.2
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 75 HAEKYAGHDHPVEVTEEDASTMDLEEIND 103
HAE+ AG + +V ++ +L E++D
Sbjct: 222 HAEELAGKEATFKVKVKEVKKRELPELDD 250
>gnl|CDD|214982 smart01026, Beach, Beige/BEACH domain. The BEACH domain was
described in the BEIGE protein (D1035670) and in the
highly homologous CHS protein. The BEACH domain is
usually followed by a series of WD repeats. The
function of the BEACH domain is unknown.
Length = 280
Score = 26.8 bits (60), Expect = 2.2
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 26/74 (35%)
Query: 25 HNYHHVFPW---DYRAAEMGSYSLNLT---TFWLDQFAKIGWAYDLKKP----SDKMIRS 74
+ VFPW DY S +L+L+ TF DL KP + + +
Sbjct: 29 LTQYPVFPWVLADYT-----SETLDLSNPSTF-----------RDLSKPIGALNPERLEF 72
Query: 75 HAEKYAGHDHPVEV 88
E+Y + P
Sbjct: 73 FYERYEELEDPDIP 86
>gnl|CDD|233121 TIGR00768, rimK_fam, alpha-L-glutamate ligases, RimK family. This
family, related to bacterial glutathione synthetases,
contains at least two different alpha-L-glutamate
ligases. One is RimK, as in E. coli, which adds
additional Glu residues to the native Glu-Glu C-terminus
of ribosomal protein S6, but not to Lys-Glu mutants.
Most species with a member of this subfamily lack an S6
homolog ending in Glu-Glu, however. Members in
Methanococcus jannaschii act instead as a
tetrahydromethanopterin:alpha-l-glutamate ligase
(MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase
(MJ1001).
Length = 277
Score = 26.5 bits (59), Expect = 3.1
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 57 KIGWAYDLKKPSDKMIRSHAEKYAGHDHPVEVTEEDASTMDLEE 100
K+ YD + +KM++ AE+ +V A + E
Sbjct: 1 KLAILYDRIRLDEKMLKEAAEEL---GIDYKVVTPPAIPLTFNE 41
>gnl|CDD|178541 PLN02955, PLN02955, 8-amino-7-oxononanoate synthase.
Length = 476
Score = 26.6 bits (58), Expect = 3.4
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 6 RILPSENVWVSIVSLGEGWHNYHHVFPWDYRAAEMGSYSLNLTTF--WLDQ 54
R E V S + G+ + + + WD + E+ S+++ TF WL
Sbjct: 33 RQNEEEIV-KSRANGGDDYEVFDGLCQWDRTSVEV---SVSIPTFQKWLHD 79
>gnl|CDD|132759 cd07074, NR_LBD_PR, Ligand binding domain of the progesterone
receptor, a member of the nuclear hormone receptor. The
ligand binding domain of the progesterone receptor (PR):
PR is a member of the nuclear receptor superfamily of
ligand dependent transcription factors, mediating the
biological actions of progesterone. PR functions in a
variety of biological processes including development of
the mammary gland, regulating cell cycle progression,
protein processing, and metabolism. When no binding
hormone is present the carboxyl terminal inhibits
transcription. Binding to a hormone induces a structural
change that removes the inhibitory action. After
progesterone binds to the receptor, PR forms a dimer and
the complex enters the nucleus where it interacts with
the hormone response element (HRE) in the promoters of
progesterone responsive genes and alters their
transcription. In addition, rapid actions of PR that
occur independent of transcription, have also been
observed in several tissues like brain, liver, mammary
gland and spermatozoa. There are two natural PR isoforms
called PR-A and PR-B. PR-B has an additional stretc h of
164 amino acids at the N terminus. The extra domain in
PR-B performs activation functions by recruiting
coactivators that could not be recruited by PR-A. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, PR has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD). The LBD is not
only involved in binding to progesterone, but also
involved in coactivator binding and dimerization.
Length = 248
Score = 26.1 bits (57), Expect = 4.0
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 12/57 (21%)
Query: 14 WVSIVSLGEGWHNYHHVFPW-----------DYRAAEMGSYSLNLTTFWLDQ-FAKI 58
W+S++ G GW +Y HV + R E YSL LT + + Q F K+
Sbjct: 70 WMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKL 126
>gnl|CDD|128814 smart00541, FYRN, FY-rich domain, N-terminal region. is
sometimes closely juxtaposed with the C-terminal region
(FYRC), but sometimes is far distant. Unknown function,
but occurs frequently in chromatin-associated proteins.
Length = 44
Score = 24.6 bits (54), Expect = 4.0
Identities = 5/21 (23%), Positives = 12/21 (57%)
Query: 17 IVSLGEGWHNYHHVFPWDYRA 37
+ G+ +H+ +FP Y++
Sbjct: 2 LPIQGKLFHSESAIFPVGYKS 22
>gnl|CDD|238562 cd01142, TroA_e, Periplasmic binding protein TroA_e. These
proteins are predicted to function as initial receptors
in the ABC metal ion uptake in eubacteria and archaea.
They belong to the TroA superfamily of helical backbone
metal receptor proteins that share a distinct fold and
ligand binding mechanism. A typical TroA protein is
comprised of two globular subdomains connected by a
single helix and can bind their ligands in the cleft
between these domains.
Length = 289
Score = 26.2 bits (58), Expect = 4.5
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 3 GKRRILPSENVWVSIVSLGEG--WHNYHHVFPWDYRAAEMGSYSLNLTTFWL 52
+ + ++ W ++ ++ G + N F WD +AE L WL
Sbjct: 229 DTKAAILADPRWQNLRAVKNGRVYVNPEGAFWWDRPSAEEA-----LLGLWL 275
>gnl|CDD|184573 PRK14218, PRK14218, camphor resistance protein CrcB; Provisional.
Length = 133
Score = 25.2 bits (55), Expect = 6.0
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 30 VFPWDYRAAEM-GSYSLNLTTFWLDQFAKIGWAY 62
FPW A + GS+ WLD+ GW +
Sbjct: 38 GFPWGTLAVNLIGSFVAGFLLIWLDKRGSAGWPW 71
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 25.5 bits (57), Expect = 6.5
Identities = 13/70 (18%), Positives = 20/70 (28%), Gaps = 7/70 (10%)
Query: 45 LNLTTFWLDQFAKIGWAYDLKKPS-------DKMIRSHAEKYAGHDHPVEVTEEDASTMD 97
LNL D + + + K DK I + E A+ +
Sbjct: 501 LNLEELTWDDAQQPLAGHPINKFKILFTRIEDKQIEALIEASKEAAAAKAAAAAAAAPLA 560
Query: 98 LEEINDNIEI 107
E I + I
Sbjct: 561 EEPIAETISF 570
>gnl|CDD|232845 TIGR00145, TIGR00145, FTR1 family protein. A characterized member
from yeast acts as oxidase-coupled high affinity iron
transporter. Note that the apparent member from E. coli
K12-MG1655 has a frameshift by homology with member
sequences from other species [Unknown function,
General].
Length = 283
Score = 25.5 bits (56), Expect = 7.1
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 3/46 (6%)
Query: 20 LGEGWHNYHHVFPWD---YRAAEMGSYSLNLTTFWLDQFAKIGWAY 62
LG G H ++ D + N WL +GW Y
Sbjct: 199 LGGGNHRFNLAGGGDGFGSYNFDKAVSCCNPELDWLLFNGLLGWIY 244
>gnl|CDD|232831 TIGR00115, tig, trigger factor. Trigger factor is a
ribosome-associated molecular chaperone and is the first
chaperone to interact with nascent polypeptide. Trigger
factor can bind at the same time as the signal
recognition particle (SRP), but is excluded by the SRP
receptor (FtsY). The central domain of trigger factor
has peptidyl-prolyl cis/trans isomerase activity. This
protein is found in a single copy in virtually every
bacterial genome [Protein fate, Protein folding and
stabilization].
Length = 408
Score = 25.2 bits (56), Expect = 9.7
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 63 DLKKPSDKMIRSHAEKYAGHDHPVEVTEEDASTMDLEEIND 103
+ P D HAE+ AG + +VT ++ +L E++D
Sbjct: 203 KVTFPEDY----HAEELAGKEATFKVTVKEVKEKELPELDD 239
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 0.134 0.435
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,644,901
Number of extensions: 465696
Number of successful extensions: 438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 28
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
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 (24.1 bits)