RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7726
(96 letters)
>gnl|CDD|173839 cd01150, AXO, Peroxisomal acyl-CoA oxidase. Peroxisomal acyl-CoA
oxidases (AXO) catalyze the first set in the peroxisomal
fatty acid beta-oxidation, the alpha,beta
dehydrogenation of the corresponding trans-enoyl-CoA by
FAD, which becomes reduced. In a second oxidative
half-reaction, the reduced FAD is reoxidized by
molecular oxygen. AXO is generally a homodimer, but it
has been reported to form a different type of oligomer
in yeast. There are several subtypes of AXO's, based on
substrate specificity. Palmitoyl-CoA oxidase acts on
straight-chain fatty acids and prostanoids; whereas, the
closely related Trihydroxycoprostanoly-CoA oxidase has
the greatest activity for 2-methyl branched side chains
of bile precursors. Pristanoyl-CoA oxidase, acts on
2-methyl branched fatty acids. AXO has an additional
domain, C-terminal to the region with similarity to
acyl-CoA dehydrogenases, which is included in this
alignment.
Length = 610
Score = 95.5 bits (238), Expect = 1e-24
Identities = 36/93 (38%), Positives = 50/93 (53%)
Query: 1 MMFSHYWVPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLIPLFLGRWCVLGCTWGNLL 60
+ F + +PR +LL RF VSP G Y S DP R+ + L GR ++ +L
Sbjct: 242 LQFRNVRIPRENLLNRFGDVSPDGTYVSPFKDPNKRYGAMLGTRSGGRVGLIYDAAMSLK 301
Query: 61 KATLIAVRYSTVRKQFGEDREGRETSVIEYQTQ 93
KA IA+RYS VR+QFG E +++YQ Q
Sbjct: 302 KAATIAIRYSAVRRQFGPKPSDPEVQILDYQLQ 334
>gnl|CDD|215342 PLN02636, PLN02636, acyl-coenzyme A oxidase.
Length = 686
Score = 68.7 bits (168), Expect = 4e-15
Identities = 36/91 (39%), Positives = 54/91 (59%), Gaps = 1/91 (1%)
Query: 3 FSHYWVPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLIPLFLGRWCVLGCTWGNLLKA 62
F +PR +LL RF VS G Y+S +P RFA++L L GR + + G L +
Sbjct: 289 FRSVRIPRDNLLNRFGDVSRDGKYTSSLPTINKRFAATLGELVGGRVGLAYGSVGVLKAS 348
Query: 63 TLIAVRYSTVRKQFGEDREGRETSVIEYQTQ 93
IA+RYS +R+QFG ++ E S+++YQ+Q
Sbjct: 349 NTIAIRYSLLRQQFGPPKQ-PEISILDYQSQ 378
>gnl|CDD|178062 PLN02443, PLN02443, acyl-coenzyme A oxidase.
Length = 664
Score = 60.2 bits (146), Expect = 4e-12
Identities = 34/97 (35%), Positives = 48/97 (49%), Gaps = 6/97 (6%)
Query: 1 MMFSHYWVPRCSLLARFSSVSPQGDY-SSLIPDPGLRFASSLIPLFLGRWCVLGCTWGNL 59
+ F H +PR +L R S V+ +G Y S +P + + R ++ L
Sbjct: 242 LRFDHVRIPRDQMLMRLSKVTREGKYVQSDVPRQLVYGTMVYV-----RQTIVADASTAL 296
Query: 60 LKATLIAVRYSTVRKQFGEDREGRETSVIEYQTQIPR 96
+A IA RYS VR+QFG G ET VI+Y+TQ R
Sbjct: 297 SRAVCIATRYSAVRRQFGSQDGGPETQVIDYKTQQSR 333
>gnl|CDD|185639 PTZ00460, PTZ00460, acyl-CoA dehydrogenase; Provisional.
Length = 646
Score = 56.4 bits (136), Expect = 7e-11
Identities = 34/102 (33%), Positives = 47/102 (46%), Gaps = 24/102 (23%)
Query: 1 MMFSHYWVPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLI---------PLFLGRWCV 51
+ F HY +P SLLAR+ VS G +P + +AS + P F +
Sbjct: 235 LSFDHYRIPLDSLLARYIKVSEDGQVERQ-GNPKVSYASMMYMRNLIIDQYPRFAAQ--- 290
Query: 52 LGCTWGNLLKATLIAVRYSTVRKQFGEDREGRETSVIEYQTQ 93
A +A+RYS R+QF D +E SV+EYQTQ
Sbjct: 291 ----------ALTVAIRYSIYRQQFTNDN-KQENSVLEYQTQ 321
>gnl|CDD|215178 PLN02312, PLN02312, acyl-CoA oxidase.
Length = 680
Score = 50.2 bits (120), Expect = 1e-08
Identities = 31/88 (35%), Positives = 43/88 (48%)
Query: 3 FSHYWVPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLIPLFLGRWCVLGCTWGNLLKA 62
F + +PR +LL + VSP G Y S I DP RF + L PL GR + +
Sbjct: 294 FDNLRIPRENLLNSVADVSPDGKYVSAIKDPDQRFGAFLAPLTSGRVTIAVSAIYSSKVG 353
Query: 63 TLIAVRYSTVRKQFGEDREGRETSVIEY 90
IA+RYS R+ F G E +++Y
Sbjct: 354 LAIAIRYSLSRRAFSVTPNGPEVLLLDY 381
>gnl|CDD|173838 cd00567, ACAD, Acyl-CoA dehydrogenase. Both mitochondrial acyl-CoA
dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases
(AXO) catalyze the alpha,beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of ACAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. In contrast, AXO catalyzes
a different oxidative half-reaction, in which the
reduced FAD is reoxidized by molecular oxygen. The ACAD
family includes the eukaryotic beta-oxidation enzymes,
short (SCAD), medium (MCAD), long (LCAD) and very-long
(VLCAD) chain acyl-CoA dehydrogenases. These enzymes all
share high sequence similarity, but differ in their
substrate specificities. The ACAD family also includes
amino acid catabolism enzymes such as Isovaleryl-CoA
dehydrogenase (IVD), short/branched chain acyl-CoA
dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase
(IBDH), glutaryl-CoA deydrogenase (GCD) and
Crotonobetainyl-CoA dehydrogenase. The mitochondrial
ACAD's are generally homotetramers, except for VLCAD,
which is a homodimer. Related enzymes include the SOS
adaptive reponse proten aidB, Naphthocyclinone
hydroxylase (NcnH), and and Dibenzothiophene (DBT)
desulfurization enzyme C (DszC).
Length = 327
Score = 28.0 bits (63), Expect = 0.74
Identities = 19/75 (25%), Positives = 24/75 (32%), Gaps = 16/75 (21%)
Query: 3 FSHYWVPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLIPLFLGRWCVLGCTWGNLLKA 62
F VP +LL G A + + GR + G A
Sbjct: 165 FDDVRVPEDNLLGE--------------EGGGFELAMKGLNV--GRLLLAAVALGAARAA 208
Query: 63 TLIAVRYSTVRKQFG 77
AV Y+ RKQFG
Sbjct: 209 LDEAVEYAKQRKQFG 223
>gnl|CDD|188649 cd09817, linoleate_diol_synthase_like, Linoleate (8R)-dioxygenase
and related enzymes. These fungal enzymes, related to
animal heme peroxidases, catalyze the oxygenation of
linoleate and similar targets. Linoleate
(8R)-dioxygenase, also called linoleate:oxygen
7S,8S-oxidoreductase, generates
(9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate as a
product. Other members are 5,8-linoleate dioxygenase
(LDS, ppoA) and linoleate 10R-dioxygenase (ppoC),
involved in the biosynthesis of oxylipins.
Length = 550
Score = 27.7 bits (62), Expect = 0.84
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 19 SVSPQGDYSSLIPDPGLRFASSL 41
SV P+ D ++PDPGL F + L
Sbjct: 58 SVPPKHDQPGVLPDPGLIFDTLL 80
>gnl|CDD|173851 cd01162, IBD, Isobutyryl-CoA dehydrogenase. Isobutyryl-CoA
dehydrogenase (IBD) catalyzes the alpha, beta-
dehydrogenation of short branched chain acyl-CoA
intermediates in valine catabolism. It is predicted to
be a homotetramer.
Length = 375
Score = 27.8 bits (62), Expect = 0.90
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 47 GRWCVLGCTWGNLLKATLIAVRYSTVRKQFGE 78
GR + C+ G A +A Y RKQFG+
Sbjct: 236 GRLNIASCSLGAAQAALDLARAYLEERKQFGK 267
>gnl|CDD|236034 PRK07502, PRK07502, cyclohexadienyl dehydrogenase; Validated.
Length = 307
Score = 26.5 bits (59), Expect = 2.4
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 6/22 (27%)
Query: 31 PDPGLRFASSLIPLFLGRWCVL 52
PD G FA LF RWC+L
Sbjct: 134 PDAG--FAE----LFENRWCIL 149
>gnl|CDD|132863 cd07224, Pat_like, Patatin-like phospholipase. Patatin-like
phospholipase. This family consists of various patatin
glycoproteins from plants. The patatin protein accounts
for up to 40% of the total soluble protein in potato
tubers. Patatin is a storage protein, but it also has
the enzymatic activity of lipid acyl hydrolase,
catalysing the cleavage of fatty acids from membrane
lipids. Members of this family have been found also in
vertebrates.
Length = 233
Score = 26.1 bits (58), Expect = 3.1
Identities = 24/76 (31%), Positives = 30/76 (39%), Gaps = 21/76 (27%)
Query: 7 WVPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLIPLFL---------GRWCVLGCTWG 57
VPR L++ F S S LI AS IP +L G+ CV G +
Sbjct: 109 PVPRGLLVSSFDS------KSDLI---DALLASCNIPGYLAPWPATMFRGKLCVDG-GFA 158
Query: 58 NLLKATLIAVRYSTVR 73
+ T A R TVR
Sbjct: 159 LFIPPTTAADR--TVR 172
>gnl|CDD|179566 PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated.
Length = 380
Score = 25.6 bits (56), Expect = 4.5
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 48 RWCVLGCTWGNLLKATLIAVRYSTVRKQFGE 78
R+ V +G + A A RY+ R QFGE
Sbjct: 241 RFLVALTNYGTAMCAFEDAARYANQRVQFGE 271
>gnl|CDD|220850 pfam10693, DUF2499, Protein of unknown function (DUF2499).
Members of this family are found in plants, lower
eukaryotes, and bacteria and the chloroplast where it
is annotated as Ycf49 or Ycf49-like. The function is
not known though several members are annotated as
putative membrane proteins.
Length = 90
Score = 24.5 bits (54), Expect = 6.0
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 3/32 (9%)
Query: 26 YSSLIPDPGLR-FASSLIPLFLGRWCVLGCTW 56
Y R A +++P + C CTW
Sbjct: 27 YGERTGRRSWRWLALAMLPALISAMCA--CTW 56
>gnl|CDD|236627 PRK09824, PRK09824, PTS system beta-glucoside-specific transporter
subunits IIABC; Provisional.
Length = 627
Score = 25.4 bits (56), Expect = 6.3
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 12 SLLARFSSVSPQGDYSSL----IPDPGLRFASSLIPLFLGRW 49
++A F + + D L IP L ++SS+IP+ W
Sbjct: 187 LMIAAFEA-GQKADALGLDFLGIPVTLLNYSSSVIPIIFSAW 227
>gnl|CDD|216914 pfam02170, PAZ, PAZ domain. This domain is named PAZ after the
proteins Piwi Argonaut and Zwille. This domain is found
in two families of proteins that are involved in
post-transcriptional gene silencing. These are the Piwi
family and the Dicer family, that includes the Carpel
factory protein. The function of the domains is unknown
but has been suggested to mediate complex formation
between proteins of the Piwi and Dicer families by
hetero-dimerisation. The three-dimensional structure of
this domain has been solved. The PAZ domain is composed
of two subdomains. One subdomain is similar to the OB
fold, albeit with a different topology. The OB-fold is
well known as a single-stranded nucleic acid binding
fold. The second subdomain is composed of a
beta-hairpin followed by an alpha-helix. The PAZ
domains shows low-affinity nucleic acid binding and
appears to interact with the 3' ends of single-stranded
regions of RNA in the cleft between the two subdomains.
PAZ can bind the characteristic two-base 3' overhangs
of siRNAs, indicating that although PAZ may not be a
primary nucleic acid binding site in Dicer or RISC, it
may contribute to the specific and productive
incorporation of siRNAs and miRNAs into the RNAi
pathway.
Length = 114
Score = 24.2 bits (53), Expect = 9.1
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 73 RKQFGEDREGRETSVIEY 90
++G E SV EY
Sbjct: 54 PNSTFPLKDGGEISVAEY 71
>gnl|CDD|237070 PRK12350, PRK12350, citrate synthase 2; Provisional.
Length = 353
Score = 24.5 bits (54), Expect = 9.3
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 14 LARFSSV-------SPQGDYSSLIPDPGLRFASSLIPLFLGRW 49
LAR S + S +G +P + A++++ F+GRW
Sbjct: 104 LARASVMALSAVAQSARGIGQPAVPQREIDHAATILERFMGRW 146
>gnl|CDD|233988 TIGR02734, crtI_fam, phytoene desaturase. Phytoene is converted to
lycopene by desaturation at four (two symmetrical pairs
of) sites. This is achieved by two enzymes (crtP and
crtQ) in cyanobacteria (Gloeobacter being an exception)
and plants, but by a single enzyme in most other
bacteria and in fungi. This single enzyme is called the
bacterial-type phytoene desaturase, or CrtI. Most
members of this family, part of the larger Pfam family
pfam01593, which also contains amino oxidases, are CrtI
itself; it is likely that all members act on either
phytoene or on related compounds such as
dehydrosqualene, for carotenoid biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 502
Score = 24.9 bits (55), Expect = 9.5
Identities = 14/49 (28%), Positives = 16/49 (32%), Gaps = 4/49 (8%)
Query: 3 FSHYW----VPRCSLLARFSSVSPQGDYSSLIPDPGLRFASSLIPLFLG 47
F LLA + S + D LR A S LFLG
Sbjct: 141 FLSPRDLLRADLPQLLALLAWRSLYSKVARFFSDERLRQAFSFHALFLG 189
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 0.139 0.452
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,726,407
Number of extensions: 373468
Number of successful extensions: 365
Number of sequences better than 10.0: 1
Number of HSP's gapped: 360
Number of HSP's successfully gapped: 19
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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: 53 (24.1 bits)