RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11084
(277 letters)
>gnl|CDD|224316 COG1398, OLE1, Fatty-acid desaturase [Lipid metabolism].
Length = 289
Score = 157 bits (398), Expect = 2e-46
Identities = 72/239 (30%), Positives = 110/239 (46%), Gaps = 9/239 (3%)
Query: 40 AKETPEKEYRIVPVWRNIVLFAYLHLAALYGAYLIFTSAKLQTTIFAILMYQAGATGITA 99
E P + W N++ F + A Y A+ + L IF + Y G GIT
Sbjct: 6 IAEAPWTLPKYPYHWNNVLFFIGPLIVA-YLAFYPDFFSWLAELIFTLAYYLIGGIGITL 64
Query: 100 GAHRLWAHRAYKAKTPLKLILLLFNTLAFQNHVYEWARDHRVHHKYSETNADPH-NAKRG 158
G HRLW+HRA+KA L+ +L + L Q EW HR HH+ ++T+ DPH ++ +G
Sbjct: 65 GLHRLWSHRAFKAHKWLEYVLAFWGALTTQGPAIEWVGIHRKHHRKTDTDQDPHYDSFKG 124
Query: 159 FFFSHVGWLMCRKHPDVIAKGQGIDLSDLKADKLVMFQKKHYMKLMPVICFVLPTVIPMV 218
F++SH+GW++ AK + + L D + +Q ++ + ++ VLP I
Sbjct: 125 FWWSHIGWML---LYSAEAKDR-ETIQKLGKDIPLDWQHRNLYLIALLMQIVLPLFIGYA 180
Query: 219 AWSESFLNAWFVATMFRYTLTLNVTWLVNSAAHMWGQRPYDKFISPAENLGVAIFAMGE 277
L + R L + TW VNS H G RP+D + VA+ GE
Sbjct: 181 LGGWLGL---IWGGVQRLVLVQHATWCVNSLGHYIGYRPFDCRDTARNCWWVALVTFGE 236
>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 = 139 bits (352), Expect = 6e-41
Identities = 47/91 (51%), Positives = 61/91 (67%)
Query: 79 KLQTTIFAILMYQAGATGITAGAHRLWAHRAYKAKTPLKLILLLFNTLAFQNHVYEWARD 138
T +F +L Y GITAG HRLWAHR++KA PL++ L + +LA Q W D
Sbjct: 1 SWATLVFLVLYYLLTGLGITAGYHRLWAHRSFKAPKPLRIFLAILGSLAGQGSPLWWVAD 60
Query: 139 HRVHHKYSETNADPHNAKRGFFFSHVGWLMC 169
HR+HH+YS+T+ DPH+ KRGF+FSHVGWL
Sbjct: 61 HRLHHRYSDTDGDPHSPKRGFWFSHVGWLGG 91
Score = 62.6 bits (153), Expect = 5e-12
Identities = 23/50 (46%), Positives = 29/50 (58%)
Query: 228 WFVATMFRYTLTLNVTWLVNSAAHMWGQRPYDKFISPAENLGVAIFAMGE 277
++ + R L L+ TWLVNS AHMWG RPYD + N VA+ GE
Sbjct: 87 GWLGGLLRIVLVLHATWLVNSLAHMWGYRPYDTRDTSRNNWWVALLTFGE 136
>gnl|CDD|177866 PLN02220, PLN02220, delta-9 acyl-lipid desaturase.
Length = 299
Score = 84.1 bits (208), Expect = 6e-19
Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 15/196 (7%)
Query: 85 FAILMYQAGATGITAGAHRLWAHRAYKAKTPLKLILLLFNTLAFQNHVYEWARDHRVHHK 144
F +++Y IT HR AHR++K L+ A Q +W HR HH+
Sbjct: 60 FGLILYIVTGLSITFSYHRNLAHRSFKLPKWLEYPFAYSALFALQGDPIDWVSTHRFHHQ 119
Query: 145 YSETNADPHNAKRGFFFSHVGWLMCRKHPDVIAK-GQGIDLSDLKADKLVMFQKKH--YM 201
+++++ DPH+ GF+FSHV W+ + + K G ++ DLK F +K
Sbjct: 120 FTDSDRDPHSPIEGFWFSHVLWIFDTSY--IREKCGGRDNVMDLKQQWFYRFLRKTIGLH 177
Query: 202 KLMPVICFVLPTVIPMVAWSESFLNAWFVATMFRYTLTLNVTWLVNSAAHMWGQRPYDKF 261
LM L +P + W A + +VTWL+NSA H+WG R +
Sbjct: 178 ILMFWTLLYLWGGLPYLTWGVGVGGA----------IGYHVTWLINSACHIWGSRTWKTK 227
Query: 262 ISPAENLGVAIFAMGE 277
+ +++F MGE
Sbjct: 228 DTSRNVWWLSLFTMGE 243
>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 = 54.8 bits (132), Expect = 1e-09
Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 84 IFAILMYQAGATGITAGAHRLWAHRAYKAKTPLKLILLLFNTLAFQNHVYEWARDHRVHH 143
+ A+L+ G G+T AH L HR++ L +L LA W R HR HH
Sbjct: 2 LLALLLGLLGGLGLTVLAHEL-GHRSFFRSRWLNRLLGALLGLALGGSYGWWRRSHRRHH 60
Query: 144 KYSET-NADPHNAKRGFFFSHVG 165
+Y+ T DP +A + H G
Sbjct: 61 RYTNTPGKDPDSA--VNYLEHYG 81
>gnl|CDD|215943 pfam00487, FA_desaturase, Fatty acid desaturase.
Length = 251
Score = 36.5 bits (84), Expect = 0.008
Identities = 18/79 (22%), Positives = 24/79 (30%), Gaps = 1/79 (1%)
Query: 85 FAILMYQAGATGITAGAHRLWAHRAYKAKTPLKLILLLFNTLAFQNHVYEWARDHRVHHK 144
L+ GI G AH A L +L L W H HH
Sbjct: 7 LLALLLAGLLLGILGGLAHEAAHGALFRSRRLNDLLGRLLALLLGISYSAWRISHLRHHH 66
Query: 145 YSET-NADPHNAKRGFFFS 162
++ DP +A+R
Sbjct: 67 HTNNPGKDPDSARRRLLRY 85
>gnl|CDD|239589 cd03512, Alkane-hydroxylase, Alkane hydroxylase is a bacterial,
integral-membrane di-iron enzyme that shares a
requirement for iron and oxygen for activity similar to
that of the non-heme integral-membrane acyl coenzyme A
(CoA) desaturases and acyl lipid desaturases. The alk
genes in Pseudomonas oleovorans encode conversion of
alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB)
system is responsible for the initial oxidation of
inactivated alkanes. It is a three-component system
comprising a soluble NADH-rubredoxin reductase (AlkT), a
soluble rubredoxin (AlkG), and the integral membrane
oxygenase (AlkB). AlkB utilizes the oxygen rebound
mechanism to hydroxylate alkanes. This mechanism
involves homolytic cleavage of the C-H bond by an
electrophilic metal-oxo intermediate to generate a
substrate-based radical. As with other members of this
superfamily, this domain family has extensive
hydrophobic regions that would be capable of spanning
the membrane bilayer at least twice. The active site
structure of AlkB is not known, however, spectroscopic
and genetic evidence points 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.
Like all other members of this superfamily, there are
eight conserved histidines seen in the histidine cluster
motifs: HXXXH, HXXXHH, and HXXHH. These histidine
residues are reported to be catalytically essential and
proposed to be the ligands for the iron atoms contained
within the homolog, stearoyl CoA desaturase. Also
included in this CD are terminal alkane hydroxylases
(AlkM), xylene monooxygenase hydroxylases (XylM),
p-cymene monooxygenase hydroxylases (CymAa), and other
related proteins.
Length = 314
Score = 30.3 bits (69), Expect = 1.1
Identities = 29/105 (27%), Positives = 40/105 (38%), Gaps = 11/105 (10%)
Query: 58 VLFAYLHLAALYGAYLIFTSAKLQTTIFAILMYQAGATGITAG---AHRLWAHRAYKAKT 114
L L A L+ ++ L L+ G G AH L HR + +
Sbjct: 45 YLLLPLQFALLFLGVWAVSTGDLSALEKVGLILSLGLLSGVIGINTAHEL-IHRRSRLER 103
Query: 115 PLKLILLLFNTLAFQNHVYEWARDH-RVHHKYSETNADPHNAKRG 158
L +LL L + + E H R HH+Y T DP A+RG
Sbjct: 104 WLGKLLLAS--LLYGHFAIE----HVRGHHRYVATPEDPATARRG 142
>gnl|CDD|240474 cd12894, SPRY_PRY_TRIM36, PRY/SPRY domain in tripartite
motif-containing protein 36 (TRIM36). This domain,
consisting of the distinct N-terminal PRY subdomain
followed by the SPRY subdomain, is found at the
C-terminus of TRIM36, a Class I TRIM protein. TRIM36
(also known as Haprin or RNF98) has a ubiquitin ligase
activity and interacts with centromere protein-H, one of
the kinetochore proteins. It has been shown that TRIM36
is potentially associated with chromosome segregation
and that an excess of TRIM36 may cause chromosomal
instability. In Xenopus laevis, TRIM36 is expressed
during early embryogenesis and plays an important role
in the arrangement of somites during their formation.
Length = 202
Score = 29.9 bits (67), Expect = 1.2
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 70 GAYLIFTSAKLQTTIFAILMYQAGATGITAGAHRLWAHR 108
G L+ + ++Q + L Y G TGIT G H WA R
Sbjct: 28 GMSLLLAAERVQVGCYTCLDYIIGDTGITKGRH-FWAFR 65
>gnl|CDD|213673 TIGR02009, PGMB-YQAB-SF, beta-phosphoglucomutase family
hydrolase. This subfamily model groups together three
clades: the characterized beta-phosphoglucomutases
(including those from E.coli, B.subtilus and L.lactis,
TIGR01990), a clade of putative bPGM's from
mycobacteria and a clade including the uncharacterized
E.coli and H.influenzae yqaB genes which may prove to
be beta-mutases of a related 1-phosphosugar. All of
these are members of the larger Haloacid dehalogenase
(HAD) subfamily IA and include the "variant 3" glu-asp
version of the third conserved HAD domain (TIGR01509).
Length = 185
Score = 28.8 bits (65), Expect = 2.4
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 9 PTGVLFEGDSTHTDTMGPIHQQASEDLAEA 38
V+F+ D TDT P+H QA + +A
Sbjct: 1 YKAVIFDMDGVITDTA-PLHAQAWKHIAAK 29
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 29.3 bits (66), Expect = 3.1
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 106 AHRAYKAKTPLKLILLLFNT----LAFQNHVYEWARDHRVHHKYSETNADPHNAKRGF 159
A R + K + IL+LFN+ LA + + +W V H E N +N K+ F
Sbjct: 637 AKRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQ----VSHLAQEKNGTAYNIKKRF 690
>gnl|CDD|129977 TIGR00899, 2A0120, sugar efflux transporter. This family of
proteins is an efflux system for lactose, glucose,
aromatic glucosides and galactosides, cellobiose,
maltose, a-methyl glucoside and other sugar compounds.
They are found in both gram-negative and gram-postitive
bacteria [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 375
Score = 28.6 bits (64), Expect = 3.6
Identities = 13/68 (19%), Positives = 28/68 (41%)
Query: 74 IFTSAKLQTTIFAILMYQAGATGITAGAHRLWAHRAYKAKTPLKLILLLFNTLAFQNHVY 133
+F S +++ I ++ G+ + +L A R+ LIL A ++
Sbjct: 22 LFLSEEVRARPAMIGLFYTGSAIVGIAVSQLLATRSDYQGDRKGLILFCCLLAALACLLF 81
Query: 134 EWARDHRV 141
W R++ +
Sbjct: 82 AWNRNYFL 89
>gnl|CDD|235923 PRK07059, PRK07059, Long-chain-fatty-acid--CoA ligase; Validated.
Length = 557
Score = 28.4 bits (64), Expect = 4.1
Identities = 25/84 (29%), Positives = 31/84 (36%), Gaps = 18/84 (21%)
Query: 49 RIVPVWR--NIVLFAYLHLAALYGAYLIFTSAKLQTTIFAILMYQAGATGITAGA---HR 103
++VP W V F LA GA F KL A L Y G TG++ GA HR
Sbjct: 171 KMVPAWSLPGHVRFNDA-LAE--GARQTFKPVKLGPDDVAFLQYTGGTTGVSKGATLLHR 227
Query: 104 ----------LWAHRAYKAKTPLK 117
W A++ K
Sbjct: 228 NIVANVLQMEAWLQPAFEKKPRPD 251
>gnl|CDD|185120 PRK15198, PRK15198, outer membrane usher protein FimD; Provisional.
Length = 860
Score = 28.0 bits (62), Expect = 6.3
Identities = 8/35 (22%), Positives = 19/35 (54%)
Query: 197 KKHYMKLMPVICFVLPTVIPMVAWSESFLNAWFVA 231
+++ L V L + P ++++ES+ N F++
Sbjct: 2 QRYTWCLAGVALSSLAILPPFLSYAESYFNPAFLS 36
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
0.325 0.135 0.433
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,291,571
Number of extensions: 1342579
Number of successful extensions: 1582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1574
Number of HSP's successfully gapped: 29
Length of query: 277
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 181
Effective length of database: 6,679,618
Effective search space: 1209010858
Effective search space used: 1209010858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (25.9 bits)