RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10541
(152 letters)
>gnl|CDD|224316 COG1398, OLE1, Fatty-acid desaturase [Lipid metabolism].
Length = 289
Score = 99.0 bits (247), Expect = 6e-26
Identities = 43/137 (31%), Positives = 66/137 (48%), Gaps = 10/137 (7%)
Query: 6 WVRDHRVHHKFSDTDADPH-NAQRGFFFSHIGWLMQKKSKAVIEKGRQLDLSDLFEDPLV 64
WV HR HH+ +DTD DPH ++ +GF++SHIGW++ ++A + + L +D +
Sbjct: 100 WVGIHRKHHRKTDTDQDPHYDSFKGFWWSHIGWMLLYSAEA----KDRETIQKLGKDIPL 155
Query: 65 VVFQKYYIYIRFVMCFFLPAYINTVWLGEDWWISFITMDFIRYVANLNFTFLVNSAAHMY 124
+ I +M LP +I G W+ I R V + T+ VNS H
Sbjct: 156 DWQHRNLYLIALLMQIVLPLFIGYALGG---WLGLIWGGVQRLVLVQHATWCVNSLGHYI 212
Query: 125 GYKPYDTCRGRRPRRVW 141
GY+P+D R W
Sbjct: 213 GYRPFD--CRDTARNCW 227
>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 = 77.6 bits (192), Expect = 1e-18
Identities = 24/39 (61%), Positives = 31/39 (79%)
Query: 1 NSLYDWVRDHRVHHKFSDTDADPHNAQRGFFFSHIGWLM 39
S WV DHR+HH++SDTD DPH+ +RGF+FSH+GWL
Sbjct: 52 GSPLWWVADHRLHHRYSDTDGDPHSPKRGFWFSHVGWLG 90
Score = 44.1 bits (105), Expect = 3e-06
Identities = 19/39 (48%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 95 WWISFI--TMDFIRYVANLNFTFLVNSAAHMYGYKPYDT 131
+W S + +R V L+ T+LVNS AHM+GY+PYDT
Sbjct: 81 FWFSHVGWLGGLLRIVLVLHATWLVNSLAHMWGYRPYDT 119
>gnl|CDD|177866 PLN02220, PLN02220, delta-9 acyl-lipid desaturase.
Length = 299
Score = 60.2 bits (146), Expect = 1e-11
Identities = 42/141 (29%), Positives = 71/141 (50%), Gaps = 19/141 (13%)
Query: 5 DWVRDHRVHHKFSDTDADPHNAQRGFFFSHIGWLMQKKSKAVIEK-GRQLDLSDLFEDPL 63
DWV HR HH+F+D+D DPH+ GF+FSH+ W+ + + EK G + ++ DL +
Sbjct: 109 DWVSTHRFHHQFTDSDRDPHSPIEGFWFSHVLWIFD--TSYIREKCGGRDNVMDLKQ--- 163
Query: 64 VVVFQKYYIYIRFVMCFFLPAYINTVWLGEDWW--ISFITMDF-IRYVANLNFTFLVNSA 120
Q +Y ++R + +I W W + ++T + + T+L+NSA
Sbjct: 164 ----QWFYRFLRKTIGL----HILMFWTLLYLWGGLPYLTWGVGVGGAIGYHVTWLINSA 215
Query: 121 AHMYGYKPYDTCRGRRPRRVW 141
H++G + + T R VW
Sbjct: 216 CHIWGSRTWKT--KDTSRNVW 234
>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 = 34.4 bits (79), Expect = 0.006
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 2 SLYDWVRDHRVHHKFSDTD-ADPHNAQRGFFFSHIG 36
S W R HR HH++++T DP +A + H G
Sbjct: 48 SYGWWRRSHRRHHRYTNTPGKDPDSA--VNYLEHYG 81
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 28.3 bits (64), Expect = 0.46
Identities = 14/26 (53%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 57 DLFEDPLVVVFQKY-YIY-IRFVMCF 80
DLFED LV +F+K IY +R +M F
Sbjct: 12 DLFEDELVPLFEKAGPIYELRLMMDF 37
>gnl|CDD|239590 cd03513, CrtW_beta-carotene-ketolase, Beta-carotene
ketolase/oxygenase (CrtW, also known as CrtO), the
carotenoid astaxanthin biosynthetic enzyme, initially
catalyzes the addition of two keto groups to carbons C4
and C4' of beta-carotene. Carotenoids are important
natural pigments produced by many microorganisms and
plants. Astaxanthin is reported to be an antioxidant, an
anti-cancer agent, and an immune system stimulant. A
number of bacteria and green algae can convert
beta-carotene into astaxanthin by using several
ketocarotenoids as intermediates and CrtW and a
beta-carotene hydroxylase (CrtZ). CrtW initially
converts beta-carotene to canthaxanthin via echinenone,
and CrtZ initially mediates the conversion of
beta-carotene to zeaxanthin via beta-cryptoxanthin.
After a few more intermediates are formed, CrtW and CrtZ
act in combination to produce astaxanthin. Sequences of
this domain family appear to be structurally related to
membrane fatty acid desaturases and alkane hydroxylases.
They all share in common extensive hydrophobic regions
that are 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: HXXXH, HXXHH, and
HXXHH. These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within homologs, stearoyl
CoA desaturase and alkane hydroxylase.
Length = 225
Score = 27.3 bits (61), Expect = 2.8
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 10/42 (23%)
Query: 8 RDHRVHHKFSDTDADP--HNAQR--------GFFFSHIGWLM 39
R H +HH+ T DP H F ++ GW
Sbjct: 87 RKHHLHHRHPGTAKDPDFHKGNPSGFLPWYLHFMSNYFGWRQ 128
>gnl|CDD|214670 smart00452, STI, Soybean trypsin inhibitor (Kunitz) family of
protease inhibitors.
Length = 172
Score = 26.5 bits (59), Expect = 4.3
Identities = 13/21 (61%), Positives = 17/21 (80%), Gaps = 2/21 (9%)
Query: 50 GRQLDLSDLFEDPLVVVFQKY 70
GR+L LS+ E+PLVVVF+K
Sbjct: 153 GRRLVLSN--ENPLVVVFKKA 171
>gnl|CDD|225500 COG2949, SanA, Uncharacterized membrane protein [Function unknown].
Length = 235
Score = 26.2 bits (58), Expect = 6.5
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 58 LFEDPLVVVFQKYYIYIRFVMCFFLPAYINTVWLGEDWWISFITMDFI 105
LF L+++ + + ++ + A + TV L D WIS+ T I
Sbjct: 1 LFASALLLLRSCMFRRLFRILLVLVGALLATV-LIADRWISWATAGLI 47
>gnl|CDD|130320 TIGR01253, thiP, thiamine ABC transporter, permease protein. The
model describes thiamine ABC transporter, permease
protein in bacteria. The protein belongs to the larger
ABC transport system. It consists of atleast three
components: the inner mebrane permease; thiamine binding
protein; an ATP-binding subunit. It has been
experimentally demonstrated that the mutants in the
various steps in the de novo synthesis of the thiamine
and the biologically active form, namely thiamine
pyrophosphate can be exogenously supplemented with
thiamine, thiamine monophosphate (TMP) or thiamine
pyrophosphate (TPP) [Transport and binding proteins,
Other].
Length = 519
Score = 26.4 bits (58), Expect = 6.9
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 74 IRFVMCFFLPAYINTVWLG-EDWWISFITMDFIRYVANLNF 113
I F++ F A++ L ED W + D+++++ +F
Sbjct: 13 ISFIIAFAGAAFLAIFALAGEDDWRAVFQDDYLQHLILFSF 53
>gnl|CDD|238104 cd00178, STI, Soybean trypsin inhibitor (Kunitz) family of protease
inhibitors. Inhibit proteases by binding with high
affinity to their active sites. Trefoil fold, common to
interleukins and fibroblast growth factors.
Length = 172
Score = 26.2 bits (58), Expect = 7.3
Identities = 12/20 (60%), Positives = 16/20 (80%), Gaps = 2/20 (10%)
Query: 50 GRQLDLSDLFEDPLVVVFQK 69
R+L LSD ++PLVVVF+K
Sbjct: 155 VRRLVLSD--DNPLVVVFKK 172
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
0.329 0.140 0.475
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,034,908
Number of extensions: 724085
Number of successful extensions: 821
Number of sequences better than 10.0: 1
Number of HSP's gapped: 813
Number of HSP's successfully gapped: 30
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 55 (25.0 bits)