RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12870
(417 letters)
>gnl|CDD|224316 COG1398, OLE1, Fatty-acid desaturase [Lipid metabolism].
Length = 289
Score = 174 bits (442), Expect = 2e-51
Identities = 74/241 (30%), Positives = 114/241 (47%), Gaps = 9/241 (3%)
Query: 46 KLQIVWRNVILFAYLHLAALYGAYLLVTSAKWPTVIWAILLYQASGLGITAGAHRLWAHR 105
K W NV+ F + A Y A+ + +I+ + Y G+GIT G HRLW+HR
Sbjct: 15 KYPYHWNNVLFFIGPLIVA-YLAFYPDFFSWLAELIFTLAYYLIGGIGITLGLHRLWSHR 73
Query: 106 SYKAKWPLRLILVIFNTIAFENHVYEWARDHRVHHKYSETNADPH-NAKRGFFFSHMGWL 164
++KA L +L + + + EW HR HH+ ++T+ DPH ++ +GF++SH+GW+
Sbjct: 74 AFKAHKWLEYVLAFWGALTTQGPAIEWVGIHRKHHRKTDTDQDPHYDSFKGFWWSHIGWM 133
Query: 165 MCKKHPDVIEKGKGIDLADLEQDKLLMFQKKYYMILMPIFCFVLPTIVPALVWGETWRNS 224
+ E + L +D L +Q + ++ + VLP + + G W
Sbjct: 134 LLYS----AEAKDRETIQKLGKDIPLDWQHRNLYLIALLMQIVLPLFIGYALGG--WL-G 186
Query: 225 WFVATMFRYTFTLNMTWLVNSAAHMWGQRPYDQYINPSENLGVAVFALGEGWHNYHHVFP 284
+ R + TW VNS H G RP+D VA+ GEGWHN HH FP
Sbjct: 187 LIWGGVQRLVLVQHATWCVNSLGHYIGYRPFDCRDTARNCWWVALVTFGEGWHNNHHAFP 246
Query: 285 G 285
Sbjct: 247 N 247
>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 = 142 bits (360), Expect = 1e-40
Identities = 49/91 (53%), Positives = 66/91 (72%)
Query: 76 KWPTVIWAILLYQASGLGITAGAHRLWAHRSYKAKWPLRLILVIFNTIAFENHVYEWARD 135
W T+++ +L Y +GLGITAG HRLWAHRS+KA PLR+ L I ++A + W D
Sbjct: 1 SWATLVFLVLYYLLTGLGITAGYHRLWAHRSFKAPKPLRIFLAILGSLAGQGSPLWWVAD 60
Query: 136 HRVHHKYSETNADPHNAKRGFFFSHMGWLMC 166
HR+HH+YS+T+ DPH+ KRGF+FSH+GWL
Sbjct: 61 HRLHHRYSDTDGDPHSPKRGFWFSHVGWLGG 91
Score = 101 bits (253), Expect = 3e-25
Identities = 37/76 (48%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 291 SVNSAAHMWGQRPYDQYINPSENLGVAVFALGEGWHNYHHVFPWDYKTAELGNYRANLTT 350
VNS AHMWG RPYD N VA+ GEGWHN HH FP D + L Y+ + T
Sbjct: 104 LVNSLAHMWGYRPYDTRDTSRNNWWVALLTFGEGWHNNHHAFPGDARNG-LKWYQIDPTK 162
Query: 351 GFIDFFAKLGWAYDLK 366
I KLG A+DLK
Sbjct: 163 WVIRLLEKLGLAWDLK 178
>gnl|CDD|177866 PLN02220, PLN02220, delta-9 acyl-lipid desaturase.
Length = 299
Score = 105 bits (263), Expect = 1e-25
Identities = 70/212 (33%), Positives = 104/212 (49%), Gaps = 17/212 (8%)
Query: 76 KWPTVIWAILLYQASGLGITAGAHRLWAHRSYK-AKWPLRLILVIFNTIAFENHVYEWAR 134
KW + + ++LY +GL IT HR AHRS+K KW L A + +W
Sbjct: 54 KWEALRFGLILYIVTGLSITFSYHRNLAHRSFKLPKW-LEYPFAYSALFALQGDPIDWVS 112
Query: 135 DHRVHHKYSETNADPHNAKRGFFFSHMGWLMCKKHPDVIEK-GKGIDLADLEQDKLLMFQ 193
HR HH++++++ DPH+ GF+FSH+ W+ + + EK G ++ DL+Q F
Sbjct: 113 THRFHHQFTDSDRDPHSPIEGFWFSHVLWIFDTSY--IREKCGGRDNVMDLKQQWFYRFL 170
Query: 194 KKY--YMILMPIFCFVLPTIVPALVWGETWRNSWFVATMFRYTFTLNMTWLVNSAAHMWG 251
+K ILM L +P L WG V Y ++TWL+NSA H+WG
Sbjct: 171 RKTIGLHILMFWTLLYLWGGLPYLTWGVG------VGGAIGY----HVTWLINSACHIWG 220
Query: 252 QRPYDQYINPSENLGVAVFALGEGWHNYHHVF 283
R + +++F +GE WHN HH F
Sbjct: 221 SRTWKTKDTSRNVWWLSLFTMGESWHNNHHAF 252
>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 = 54.4 bits (131), Expect = 3e-09
Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 6/85 (7%)
Query: 80 VIWAILLYQASGLGITAGAHRLWAHRSY-KAKWPLRLILVIFNTIAFENHVYEWARDHRV 138
++ A+LL GLG+T AH L HRS+ +++W RL+ + A W R HR
Sbjct: 1 LLLALLLGLLGGLGLTVLAHEL-GHRSFFRSRWLNRLLGALLGL-ALGGSYGWWRRSHRR 58
Query: 139 HHKYSET-NADPHNAKRGFFFSHMG 162
HH+Y+ T DP +A + H G
Sbjct: 59 HHRYTNTPGKDPDSA--VNYLEHYG 81
Score = 46.7 bits (111), Expect = 1e-06
Identities = 20/67 (29%), Positives = 26/67 (38%), Gaps = 10/67 (14%)
Query: 277 HNYHHVFPGLW---PQCSVNSAAHMWGQRPYDQ-------YINPSENLGVAVFALGEGWH 326
H HH + P +VN H G RP+D N + G G+H
Sbjct: 56 HRRHHRYTNTPGKDPDSAVNYLEHYGGDRPFDTDGEWLRTTDNSRNGWLNLLLTGGLGYH 115
Query: 327 NYHHVFP 333
N HH+FP
Sbjct: 116 NEHHLFP 122
Score = 39.4 bits (92), Expect = 6e-04
Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 7/51 (13%)
Query: 241 WLVNSAAHMWGQRPYDQ-------YINPSENLGVAVFALGEGWHNYHHVFP 284
VN H G RP+D N + G G+HN HH+FP
Sbjct: 72 SAVNYLEHYGGDRPFDTDGEWLRTTDNSRNGWLNLLLTGGLGYHNEHHLFP 122
>gnl|CDD|215943 pfam00487, FA_desaturase, Fatty acid desaturase.
Length = 251
Score = 51.5 bits (123), Expect = 2e-07
Identities = 35/223 (15%), Positives = 67/223 (30%), Gaps = 13/223 (5%)
Query: 77 WPTVIWAILLYQASGLGITAGAHRLWAHRSYKAKWPLRLILVIFNTIAFENHVYEWARDH 136
++ LL LGI G AH + L +L + W H
Sbjct: 2 SWLLLLLALLLAGLLLGILGGLAHEAAHGALFRSRRLNDLLGRLLALLLGISYSAWRISH 61
Query: 137 RVHHKYSET-NADPHNAKRGFFFSHMGWLMCK------KHPDVIEKGKGIDLADLEQDKL 189
HH ++ DP +A+R + + + + G + L + +L
Sbjct: 62 LRHHHHTNNPGKDPDSARRRLLRYALRRRLLGLGRLLYRFLLGVLLGLLVFLFRFRRRRL 121
Query: 190 LMFQKKYYM--ILMPIFCFVLPTIVPALVWGETWRNSW----FVATMFRYTFTLNMTWLV 243
++++ + +L+ L ++ L T+ L L
Sbjct: 122 RKRRRRFRIRLLLLLALLLALALLLAGLGGWGALLLFLLPLLLALTLLLLVNYLEHYGLD 181
Query: 244 NSAAHMWGQRPYDQYINPSENLGVAVFALGEGWHNYHHVFPGL 286
Q + S + + +H HH+FPG+
Sbjct: 182 TEPERAARTWYERQLVTTSNSWVLNWLTGNLNYHIEHHLFPGV 224
>gnl|CDD|235665 PRK05996, motB, flagellar motor protein MotB; Validated.
Length = 423
Score = 32.7 bits (75), Expect = 0.30
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 3/25 (12%)
Query: 370 HQMIVNRIKRTGDGTHEHHHDGGVW 394
+++I+ ++R GD HE HH GGVW
Sbjct: 11 NEIII--VRRGGDDDHEGHH-GGVW 32
>gnl|CDD|176355 cd01611, GABARAP, Ubiquitin domain of GABA-receptor-associated
protein. GABARAP (GABA-receptor-associated protein)
belongs ot a large family of proteins that mediate
intracellular membrane trafficking and/or fusion.
GABARAP binds not only to GABA, type A but also to
tubulin, gephrin, and ULK1. Orthologues of GABARAP
include Gate-16 (golgi-associated ATPase enhancer), LC3
(microtubule-associated protein light chain 3), and ATG8
(autophagy protein 8). ATG8 is a ubiquitin-like protein
that is conjugated to the membrane phospholipid,
phosphatidylethanolamine as part of a ubiquitin-like
conjugation system essential for
autophagosome-formation.
Length = 112
Score = 28.4 bits (64), Expect = 2.5
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 17/64 (26%)
Query: 167 KKHPD----VIEKGKGIDLADLEQDKLLMFQ-----KKYYMI-----LMP---IFCFVLP 209
K+PD ++E+ DL DL++ K L+ + Y+I L P +F FV
Sbjct: 19 AKYPDRIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNN 78
Query: 210 TIVP 213
++ P
Sbjct: 79 SLPP 82
>gnl|CDD|111837 pfam02991, Atg8, Autophagy protein Atg8 ubiquitin like. Light
chain 3 is proposed to function primarily as a subunit
of microtubule associated proteins 1A and 1B and that
its expression may regulate microtubule binding
activity. Autophagy is generally known as a process
involved in the degradation of bulk cytoplasmic
components that are non-specifically sequestered into an
autophagosome, where they are sequestered into
double-membrane vesicles and delivered to the
degradative organelle, the lysosome/vacuole, for
breakdown and eventual recycling of the resulting
macromolecules. The yeast proteins are involved in the
autophagosome, and Atg8 binds Atg19, via its N-terminus
and the C-terminus of Atg19.
Length = 104
Score = 28.5 bits (64), Expect = 2.5
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 17/63 (26%)
Query: 168 KHPD----VIEKGKGIDLADLEQDKLLM-----FQKKYYMI-----LMP---IFCFVLPT 210
K+PD +IEK G DL D+++ K L+ + Y+I L P IF FV T
Sbjct: 12 KYPDRIPVIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNNT 71
Query: 211 IVP 213
+ P
Sbjct: 72 LPP 74
>gnl|CDD|214387 CHL00177, ccs1, c-type cytochrome biogenensis protein; Validated.
Length = 426
Score = 29.2 bits (66), Expect = 4.2
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 185 EQDKLLMFQKKYYMILMPIFCFVLPTIVPALVWGETWRNSWFVATMFRYTFTL 237
EQD+ + F K Y + PIF F+ I+ L ++ WF++ + + +L
Sbjct: 35 EQDQSIEFYKNNYPLSNPIFGFLSWKIILKLGLDHIYKTWWFLSLLLLFGLSL 87
>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 = 28.4 bits (64), Expect = 6.5
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 27/114 (23%)
Query: 54 VILFAYLHLAALYGAYLLVTSAKWPTVIWAILLYQASGLGITAG----------AHRLWA 103
+ L L A L+ V++ + + GL ++ G AH L
Sbjct: 44 LYLLLPLQFALLFLGVWAVSTG-------DLSALEKVGLILSLGLLSGVIGINTAHEL-I 95
Query: 104 HRSYK-AKWPLRLIL-VIFNTIAFENHVYEWARDHRVHHKYSETNADPHNAKRG 155
HR + +W +L+L + HV R HH+Y T DP A+RG
Sbjct: 96 HRRSRLERWLGKLLLASLLYGHFAIEHV-------RGHHRYVATPEDPATARRG 142
>gnl|CDD|225546 COG3000, ERG3, Sterol desaturase [Lipid metabolism].
Length = 271
Score = 28.2 bits (63), Expect = 7.6
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 19/88 (21%)
Query: 76 KWPTVIWAILL-YQASG---LGITAGAHRLWAHRSYKAKWPLRLILVIFNTIAFENHVYE 131
+ ++ +LL L I + H + PL + +FNT
Sbjct: 153 AFLGLLPLLLLGLSPVAVALLFIFLLFWAVLIHSNLDLPLPLGWLRYVFNT--------- 203
Query: 132 WARDHRVHHKYSETNADPHNAKRGFFFS 159
R HR+HH DP++ G +
Sbjct: 204 -PRHHRLHHSK-----DPYDKNYGVTLT 225
>gnl|CDD|185039 PRK15081, PRK15081, glutathione ABC transporter permease GsiC;
Provisional.
Length = 306
Score = 28.1 bits (63), Expect = 8.1
Identities = 25/97 (25%), Positives = 36/97 (37%), Gaps = 30/97 (30%)
Query: 201 MPIFCFVLPTIVPALVWGET-------WRNSW--------------FVA----TMFRYTF 235
MP + ++V A+++G WRN W F A + F
Sbjct: 96 MPTLWLTITSMVWAVIFGMAIGIASAVWRNRWPDRLGMTLAVSGISFPAFALGMLLMQVF 155
Query: 236 TLNMTWLVNSAAHMWGQRPYDQYINPSENLGVAVFAL 272
++ + WL A W YI PS LG AV A+
Sbjct: 156 SVELGWLPTVGADSW-----QHYILPSLTLGAAVAAV 187
>gnl|CDD|222319 pfam13687, DUF4153, Domain of unknown function (DUF4153). Members
of this family are annotated as putative inner membrane
proteins.
Length = 216
Score = 27.9 bits (63), Expect = 8.3
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 12/89 (13%)
Query: 42 TREYKLQIVWRNVILFAYLHLAALYGAYLLVTSAK------WPT--VIWAILLYQASGLG 93
RE ++ +I + L L +Y L + +AK P V W +L Y A L
Sbjct: 50 DREIDYPKRFKTLIKYILLPLLLIYTLILYLYAAKILITWELPVGWVSWLVLFYIALLLL 109
Query: 94 ITAGAHRL---WAHRSYKAKWPLRLILVI 119
I + W + +PL LI ++
Sbjct: 110 IYFLLYLSEDKWLRLFLRY-FPLLLIPLL 137
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 28.1 bits (64), Expect = 8.9
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 44 EYKLQIVWRNVILFAYLHLAAL 65
EY L + ILF YLHLAA
Sbjct: 81 EYDL--LREGQILFTYLHLAAD 100
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
0.323 0.137 0.463
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: 21,763,754
Number of extensions: 2110813
Number of successful extensions: 1745
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1725
Number of HSP's successfully gapped: 46
Length of query: 417
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 318
Effective length of database: 6,546,556
Effective search space: 2081804808
Effective search space used: 2081804808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (26.8 bits)