RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17358
(202 letters)
>gnl|CDD|239552 cd03470, Rieske_cytochrome_bc1, Iron-sulfur protein (ISP) component
of the bc(1) complex family, Rieske domain; The Rieske
domain is a [2Fe-2S] cluster binding domain involved in
electron transfer. The bc(1) complex is a multisubunit
enzyme found in many different organisms including uni-
and multi-cellular eukaryotes, plants (in their
mitochondria) and bacteria. The cytochrome bc(1) and b6f
complexes are central components of the respiratory and
photosynthetic electron transport chains, respectively,
which carry out similar core electron and proton
transfer steps. The bc(1) and b6f complexes share a
common core structure of three catalytic subunits: cyt
b, the Rieske ISP, and either a cyt c1 in the bc(1)
complex or cyt f in the b6f complex, which are arranged
in an integral membrane-bound dimeric complex. While the
core of the b6f complex is similar to that of the bc(1)
complex, the domain arrangement outside the core and the
complement of prosthetic groups are strikingly
different.
Length = 126
Score = 217 bits (556), Expect = 1e-73
Identities = 76/126 (60%), Positives = 95/126 (75%), Gaps = 2/126 (1%)
Query: 79 KIEVKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDP--QADSERVKDP 136
+EV L+ I EG+ +T +WRGKP+FIR R EIA+ +AV +S L DP A+ R P
Sbjct: 1 PVEVDLSKIEEGQLITVEWRGKPVFIRRRTPEEIAEAKAVDLSLLDDPDPAANRVRSGKP 60
Query: 137 KWLVLIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEFPEP 196
+WLV+IG+CTHLGCVP AGD+GG++CPCHGSHYDASGRIRKGPAPLNLEVP Y+F
Sbjct: 61 EWLVVIGICTHLGCVPTYRAGDYGGFFCPCHGSHYDASGRIRKGPAPLNLEVPPYKFLSD 120
Query: 197 GLLVVG 202
+V+G
Sbjct: 121 TTIVIG 126
>gnl|CDD|233404 TIGR01416, Rieske_proteo, ubiquinol-cytochrome c reductase,
iron-sulfur subunit. This model represents the
Proteobacterial and mitochondrial type of the Rieske
[2Fe-2S] iron-sulfur as found in ubiquinol-cytochrome c
reductase. The model excludes the Rieske iron-sulfur
protein as found in the cytochrome b6-f complex of the
Cyanobacteria and chloroplasts. Most members of this
family have a recognizable twin-arginine translocation
(tat) signal sequence (DeltaPh-dependent translocation
in chloroplast) for transport across the membrane with
the 2Fe-2S group already bound. These signal sequences
include a motif resembling RRxFLK before the
transmembrane helix [Energy metabolism, Electron
transport].
Length = 174
Score = 186 bits (474), Expect = 2e-60
Identities = 77/159 (48%), Positives = 101/159 (63%), Gaps = 11/159 (6%)
Query: 46 AAGTAIGGAYAAKAVVTQFISSMAASADVLAM-AKIEVKLADIPEGRNVTFKWRGKPLFI 104
A T GA A A FI SM SA V A A EV ++ I G+ +T +WRGKP+FI
Sbjct: 7 YAATGAVGAVGAAAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTVEWRGKPVFI 66
Query: 105 RHRAAAEIAKEQAVAISTLRDPQADSE--------RVKDPKWLVLIGVCTHLGCVPV--A 154
R R EI + +A+ + L+DP ++++ R P+WLV+IG+CTHLGC+P
Sbjct: 67 RRRTKKEIDELKALDLGALKDPNSEAQQPDYARVKRSGKPEWLVVIGICTHLGCIPTYGP 126
Query: 155 NAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEF 193
GD GG++CPCHGSHYD +GR+RKGPAPLNL VP Y+F
Sbjct: 127 EEGDKGGFFCPCHGSHYDTAGRVRKGPAPLNLPVPPYKF 165
>gnl|CDD|223795 COG0723, QcrA, Rieske Fe-S protein [Energy production and
conversion].
Length = 177
Score = 129 bits (326), Expect = 4e-38
Identities = 58/168 (34%), Positives = 77/168 (45%), Gaps = 13/168 (7%)
Query: 28 GVNARETEEARKAFSYVVAAGTAIGGAYAAKAVVTQFISSMAASADV-LAMAKIEVKLAD 86
G+ A T +R+ F ++ G GA AA + + S+ A LA A IEV +
Sbjct: 1 GLAAAATGLSRRDFLVLLTTGVGAVGAGAA---LYPAVESVDPPAGGGLAGAPIEVDDSG 57
Query: 87 IPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVLIGVCT 146
I G VT WRGKP+F+ R K + + +CT
Sbjct: 58 IGPGPLVTVPWRGKPVFLLRRTEYAGPKGGVTRDGDGGVGNKE--------IVAYSAICT 109
Query: 147 HLGCVPVAN-AGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEF 193
HLGC N AG GG++CPCHGS YD G + KGPAP L +P E+
Sbjct: 110 HLGCTVPWNNAGAEGGFFCPCHGSRYDPDGGVVKGPAPRPLPIPPLEY 157
>gnl|CDD|217287 pfam02921, UCR_TM, Ubiquinol cytochrome reductase transmembrane
region. Each subunit of the cytochrome bc1 complex
provides a single helix (this family) to make up the
transmembrane region of the complex.
Length = 63
Score = 95.5 bits (238), Expect = 2e-26
Identities = 37/66 (56%), Positives = 50/66 (75%), Gaps = 3/66 (4%)
Query: 8 HTDIKVPDFSHYRRDSVKDPGVNARETEEARKAFSYVVAAGTAIGGAYAAKAVVTQFISS 67
HTD++VPDFS YRR S KD +RE+++ R+AFSY++ G + AYAAK+ VT F+SS
Sbjct: 1 HTDVRVPDFSDYRRKSTKDK---SRESDDGRRAFSYLMVGGAGVLSAYAAKSTVTTFLSS 57
Query: 68 MAASAD 73
M+ASAD
Sbjct: 58 MSASAD 63
>gnl|CDD|215875 pfam00355, Rieske, Rieske [2Fe-2S] domain. The rieske domain has a
[2Fe-2S] centre. Two conserved cysteines that one Fe ion
while the other Fe ion is coordinated by two conserved
histidines.
Length = 99
Score = 71.0 bits (174), Expect = 2e-16
Identities = 26/101 (25%), Positives = 37/101 (36%), Gaps = 12/101 (11%)
Query: 103 FIRHRAAAEIAKEQAVAISTLRDPQADSERV----KDPKWLVLIGVCTHLGCVPVANAGD 158
++ +E+ + D + V KD + L VCTH G
Sbjct: 2 WVPVCHESELPE---PGDFKTVDLDGEDPVVVRRDKDGEVRALSNVCTHRGAPLSRGGVG 58
Query: 159 F--GGYYCPCHGSHYDAS-GRIRKGPAP--LNLEVPKYEFP 194
GG+ CP HG +D S G++ GPAP L E
Sbjct: 59 NEKGGFECPYHGWRFDLSTGKLVGGPAPRPLKTYPVLEEVG 99
>gnl|CDD|239553 cd03471, Rieske_cytochrome_b6f, Iron-sulfur protein (ISP) component
of the b6f complex family, Rieske domain; The Rieske
domain is a [2Fe-2S] cluster binding domain involved in
electron transfer. The cytochrome b6f complex from
Mastigocladus laminosus, a thermophilic cyanobacterium,
contains four large subunits, including cytochrome f,
cytochrome b6, the Rieske ISP, and subunit IV; as well
as four small hydrophobic subunits, PetG, PetL, PetM,
and PetN. Rieske ISP, one of the large subunits of the
cytochrome bc-type complexes, is involved in respiratory
and photosynthetic electron transfer. The core of the
chloroplast b6f complex is similar to the analogous
respiratory cytochrome bc(1) complex, but the domain
arrangement outside the core and the complement of
prosthetic groups are strikingly different.
Length = 126
Score = 66.2 bits (162), Expect = 2e-14
Identities = 26/43 (60%), Positives = 33/43 (76%), Gaps = 1/43 (2%)
Query: 144 VCTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 186
VCTHLGCV NA + + CPCHGS YDA+G++ +GPAPL+L
Sbjct: 54 VCTHLGCVVPWNAAE-NKFKCPCHGSQYDATGKVVRGPAPLSL 95
>gnl|CDD|237392 PRK13474, PRK13474, cytochrome b6-f complex iron-sulfur subunit;
Provisional.
Length = 178
Score = 66.6 bits (163), Expect = 5e-14
Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 12/64 (18%)
Query: 135 DPKWLV-----------LIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAP 183
DP +LV + VCTHLGCV N+G+ + CPCHGS YDA+G++ +GPAP
Sbjct: 86 DPTYLVVEEDGTIASYGINAVCTHLGCVVPWNSGE-NKFQCPCHGSQYDATGKVVRGPAP 144
Query: 184 LNLE 187
L+L
Sbjct: 145 LSLA 148
>gnl|CDD|239550 cd03467, Rieske, Rieske domain; a [2Fe-2S] cluster binding domain
commonly found in Rieske non-heme iron oxygenase (RO)
systems such as naphthalene and biphenyl dioxygenases,
as well as in plant/cyanobacterial chloroplast b6f and
mitochondrial cytochrome bc(1) complexes. The Rieske
domain can be divided into two subdomains, with an
incomplete six-stranded, antiparallel beta-barrel at one
end, and an iron-sulfur cluster binding subdomain at the
other. The Rieske iron-sulfur center contains a [2Fe-2S]
cluster, which is involved in electron transfer, and is
liganded to two histidine and two cysteine residues
present in conserved sequences called Rieske motifs. In
RO systems, the N-terminal Rieske domain of the alpha
subunit acts as an electron shuttle that accepts
electrons from a reductase or ferredoxin component and
transfers them to the mononuclear iron in the alpha
subunit C-terminal domain to be used for catalysis.
Length = 98
Score = 59.0 bits (143), Expect = 8e-12
Identities = 32/112 (28%), Positives = 43/112 (38%), Gaps = 29/112 (25%)
Query: 82 VKLADIPEGRNVTFKWRGKPLFIRHRAAAEIAKEQAVAISTLRDPQADSERVKDPKWLVL 141
L+++P G G P+ + R E+ A+S
Sbjct: 5 GALSELPPGGGRVVVVGGGPVVVVRREGGEV-----YALS-------------------- 39
Query: 142 IGVCTHLGCVPVANAGDFGGYYCPCHGSHYD-ASGRIRKGPAPLNLEVPKYE 192
CTH GC G+ G CPCHGS +D +G + GPAP L PKY
Sbjct: 40 -NRCTHQGCPLSEGEGEDGCIVCPCHGSRFDLRTGEVVSGPAPRPL--PKYP 88
>gnl|CDD|239559 cd03477, Rieske_YhfW_C, YhfW family, C-terminal Rieske domain; YhfW
is a protein of unknown function with an N-terminal
DadA-like (glycine/D-amino acid dehydrogenase) domain
and a C-terminal Rieske domain. The Rieske domain is a
[2Fe-2S] cluster binding domain involved in electron
transfer. It is commonly found in Rieske non-heme iron
oxygenase (RO) systems such as naphthalene and biphenyl
dioxygenases, as well as in plant/cyanobacterial
chloroplast b6f and mitochondrial cytochrome bc(1)
complexes. YhfW is found in bacteria, some eukaryotes
and archaea.
Length = 91
Score = 43.8 bits (104), Expect = 2e-06
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 144 VCTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYE 192
CTHLGC+ N + + CPCHGS + G + +GPA L+
Sbjct: 39 TCTHLGCIVHWNDAE-KSWDCPCHGSRFSYDGEVIEGPAVSGLKPADDA 86
>gnl|CDD|239558 cd03476, Rieske_ArOX_small, Small subunit of Arsenite oxidase
(ArOX) family, Rieske domain; ArOX is a molybdenum/iron
protein involved in the detoxification of arsenic,
oxidizing it to arsenate. It consists of two subunits, a
large subunit similar to members of the DMSO reductase
family of molybdenum enzymes and a small subunit with a
Rieske-type [2Fe-2S] cluster. The large subunit of ArOX
contains the molybdenum site at which the oxidation of
arsenite occurs. The small subunit contains a domain
homologous to the Rieske domains of the cytochrome bc(1)
and cytochrome b6f complexes as well as naphthalene
1,2-dioxygenase. The Rieske domain is a [2Fe-2S] cluster
binding domain involved in electron transfer.
Length = 126
Score = 39.3 bits (92), Expect = 2e-04
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 143 GVCTHLGCVPVANAGDFGGYYCPCHGSHYDAS--GRIRKGPAPLNL 186
+CTH+GC P+ + CPCH S +D + G++ G A NL
Sbjct: 53 ALCTHMGC-PLTYDPSNKTFVCPCHFSQFDPARGGQMVSGQATQNL 97
>gnl|CDD|131741 TIGR02694, arsenite_ox_S, arsenite oxidase, small subunit. This
model represents the small subunit of an arsenite
oxidase complex. It is a Rieske protein and appears to
rely on the Tat (twin-arginine translocation) system to
cross the membrane. Although this enzyme could run in
the direction of arsenate reduction to arsenite in
principle, the relevant biological function is arsenite
oxidation for energy metabolism, not arsenic resistance.
Homologs to both large (TIGR02693) and small subunits
that score in the gray zone between the set trusted and
noise bit score cutoffs for the respective models are
found in Aeropyrum pernix K1 and in Sulfolobus tokodaii
str. 7 [Energy metabolism, Electron transport].
Length = 129
Score = 35.2 bits (81), Expect = 0.007
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 144 VCTHLGCVPVANAGDFGGYYCPCHGSHYDAS--GRIRKGPAPLNLEVPKY 191
+CTH+GC PV+ + D + CPCH S +D G+ G A NL P+
Sbjct: 57 LCTHMGC-PVSYSADNKTFNCPCHFSVFDPEKGGQQVWGQATQNL--PQI 103
>gnl|CDD|239557 cd03475, Rieske_SoxF_SoxL, SoxF and SoxL family, Rieske domain; The
Rieske domain is a [2Fe-2S] cluster binding domain
involved in electron transfer. SoxF is a subunit of the
terminal oxidase supercomplex SoxM in the plasma
membrane of Sulfolobus acidocaldarius that combines
features of a cytochrome bc(1) complex and a cytochrome.
The Rieske domain of SoxF has a 12 residue insertion
which is not found in eukaryotic and bacterial Rieske
proteins and is thought to influence the redox
properties of the iron-sulfur cluster. SoxL is a Rieske
protein which may be part of an archaeal bc-complex
homologue whose physiological function is still unknown.
SoxL has two features not seen in other Rieske proteins;
(i) a significantly greater distance between the two
cluster-binding sites and (ii) an unexpected Pro -> Asp
substitution at one of the cluster binding sites. SoxF
and SoxL are found in archaea and in bacteria.
Length = 171
Score = 33.2 bits (76), Expect = 0.040
Identities = 24/78 (30%), Positives = 30/78 (38%), Gaps = 19/78 (24%)
Query: 144 VCTHLGCVP--------------VANAGDFGG-YYCPCHGSHYD--ASGRIRKGPA--PL 184
+C HLGC P G +C CHGS YD G + GPA PL
Sbjct: 83 ICQHLGCQPPPIVSYPSYYPPDKAPGLASKGAVIHCCCHGSTYDPYKGGVVLTGPAPRPL 142
Query: 185 NLEVPKYEFPEPGLLVVG 202
+ +Y+ L VG
Sbjct: 143 PAVILEYDSSTDDLYAVG 160
>gnl|CDD|226985 COG4638, HcaE, Phenylpropionate dioxygenase and related
ring-hydroxylating dioxygenases, large terminal subunit
[Inorganic ion transport and metabolism / General
function prediction only].
Length = 367
Score = 33.2 bits (76), Expect = 0.066
Identities = 24/65 (36%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 132 RVKDPKWLVLIGVCTHLGCVPVANA--GDFGGYYCPCHGSHYDASGRIRKGPAP-LNLEV 188
R KD + L VC H G ++ G G CP HG YD GR+R PA L+
Sbjct: 56 RDKDGQVHALADVCPHRG-ARLSEGRVGGKGRLTCPYHGWTYDLDGRLRGVPARGYPLDF 114
Query: 189 PKYEF 193
K E
Sbjct: 115 DKSEH 119
>gnl|CDD|225057 COG2146, {NirD}, Ferredoxin subunits of nitrite reductase and
ring-hydroxylating dioxygenases [Inorganic ion transport
and metabolism / General function prediction only].
Length = 106
Score = 29.6 bits (67), Expect = 0.40
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 6/45 (13%)
Query: 143 GVCTHLGCVPVANAGDFGGYY---CPCHGSHYD-ASGRIRKGPAP 183
C H G + G G CP HG+ +D +G + PA
Sbjct: 44 NRCPHAGAP--LSRGLVEGDETVVCPLHGARFDLRTGECLEPPAG 86
>gnl|CDD|239554 cd03472, Rieske_RO_Alpha_BPDO_like, Rieske non-heme iron oxygenase
(RO) family, Biphenyl dioxygenase (BPDO)-like subfamily,
N-terminal Rieske domain of the oxygenase alpha subunit;
composed of the oxygenase alpha subunits of BPDO and
similar proteins including cumene dioxygenase (CumDO),
nitrobenzene dioxygenase (NBDO), alkylbenzene
dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase
(DFDO). ROs comprise a large class of aromatic
ring-hydroxylating dioxygenases that enable
microorganisms to tolerate and utilize aromatic
compounds for growth. The oxygenase alpha subunit
contains an N-terminal Rieske domain with an [2Fe-2S]
cluster and a C-terminal catalytic domain with a
mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
cluster accepts electrons from a reductase or ferredoxin
component and transfers them to the mononuclear iron for
catalysis. BPDO degrades biphenyls and polychlorinated
biphenyls (PCB's) while CumDO degrades cumene
(isopropylbenzene), an aromatic hydrocarbon that is
intermediate in size between ethylbenzene and biphenyl.
NBDO catalyzes the initial reaction in nitrobenzene
degradation, oxidizing the aromatic rings of mono- and
dinitrotoluenes to form catechol and nitrite. NBDO
belongs to the naphthalene subfamily of ROs. AkbDO is
involved in alkylbenzene catabolism, converting o-xylene
to 2,3- and 3,4-dimethylphenol and ethylbenzene to
cis-dihydrodiol. DFDO is involved in dibenzofuran
degradation.
Length = 128
Score = 29.0 bits (65), Expect = 0.83
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 132 RVKDPKWLVLIGVCTHLGC-VPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPK 190
R KD V + C H G + ++AG+ + C HG YD +G + +N+ K
Sbjct: 38 RQKDGSIRVFLNQCRHRGMRICRSDAGNAKAFTCTYHGWAYDTAGNL------VNVPFEK 91
Query: 191 YEFPEP 196
F +
Sbjct: 92 EAFCDG 97
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 30.1 bits (68), Expect = 1.0
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 71 SADVLAMAKIEVKLADIPEGRNV--TFKWRGKPLFIRHRAAAEIAKEQAV 118
SA LAM+ + V GR+ F RGK L +R + +I K +
Sbjct: 435 SAKALAMSGLSVV------GRDHYGVFPLRGKLLNVREASHKQIMKNAEI 478
>gnl|CDD|233717 TIGR02088, LEU3_arch, isopropylmalate/isohomocitrate
dehydrogenases. This model represents a group of
archaeal decarboxylating dehydrogenases which include
the leucine biosynthesis enzyme 3-isopropylmalate
dehydrogenase (LeuB, LEU3) and the methanogenic cofactor
CoB biosynthesis enzyme isohomocitrate dehydrogenase
(AksF). Both of these have been characterized in
Methanococcus janaschii. Non-methanogenic archaea have
only one hit to this model and presumably this is LeuB,
although phylogenetic trees cannot establish which gene
is which in the methanogens. The AksF gene is capable of
acting on isohomocitrate, iso(homo)2-citrate and
iso(homo)3-citrate in the successive elongation cycles
of coenzyme B (7-mercaptoheptanoyl-threonine phosphate).
This family is closely related to both the LeuB genes
found in TIGR00169 and the mitochondrial eukaryotic
isocitrate dehydratases found in TIGR00175. All of these
are included within the broader subfamily model,
pfam00180.
Length = 322
Score = 29.7 bits (67), Expect = 1.0
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 148 LGCVPVANAGDFGGYYCPCHGSHYDASGR 176
LG P AN GD + P HGS D +G+
Sbjct: 235 LGLAPSANIGDRKALFEPVHGSAPDIAGK 263
>gnl|CDD|132927 cd07016, S14_ClpP_1, Caseinolytic protease (ClpP) is an
ATP-dependent, highly conserved serine protease. Clp
protease (caseinolytic protease; ClpP; Peptidase S14)
is a highly conserved serine protease present
throughout in bacteria and eukaryota, but seems to be
absent in archaea, mollicutes and some fungi. This
subfamily only contains bacterial sequences. Clp
proteases are involved in a number of cellular
processes such as degradation of misfolded proteins,
regulation of short-lived proteins and housekeeping
removal of dysfunctional proteins. They are also
implicated in the control of cell growth, targeting
DNA-binding protein from starved cells. ClpP has also
been linked to the tight regulation of virulence genes
in the pathogens Listeria monocytogenes and Salmonella
typhimurium. This enzyme belong to the family of
ATP-dependent proteases; the functional Clp protease is
comprised of two components: a proteolytic component
and one of several regulatory ATPase components, both
of which are required for effective levels of protease
activity in the presence of ATP, although the
proteolytic subunit alone does possess some catalytic
activity. Active site consists of the triad Ser, His
and Asp; some members have lost all of these active
site residues and are therefore inactive, while others
may have one or two large insertions. ClpP seems to
prefer hydrophobic or non-polar residues at P1 or P1'
positions in its substrate. The protease exists as a
tetradecamer made up of two heptameric rings stacked
back-to-back such that the catalytic triad of each
subunit is located at the interface between three
monomers, thus making oligomerization essential for
function.
Length = 160
Score = 29.0 bits (66), Expect = 1.1
Identities = 20/45 (44%), Positives = 25/45 (55%), Gaps = 10/45 (22%)
Query: 45 VAAGTAIGGAYAA----KAVVTQFISSMAAS-ADVLAMA--KIEV 82
V AG AI Y A K VT I +AAS A V+AMA ++E+
Sbjct: 44 VFAGLAI---YNALKRHKGKVTVKIDGLAASAASVIAMAGDEVEM 85
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 28.9 bits (65), Expect = 1.9
Identities = 14/29 (48%), Positives = 17/29 (58%)
Query: 148 LGCVPVANAGDFGGYYCPCHGSHYDASGR 176
LG P AN GD G + P HGS D +G+
Sbjct: 240 LGLAPSANIGDKYGLFEPVHGSAPDIAGK 268
>gnl|CDD|132273 TIGR03229, benzo_1_2_benA, benzoate 1,2-dioxygenase, large subunit.
Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the
larger family of aromatic ring-hydroxylating
dioxygenases. Members of this family all act on
benzoate, but may have additional activities on various
benozate analogs. This model describes the large
subunit. Between the trusted and noise cutoffs are
similar enzymes, likely to act on benzoate but perhaps
best identified according to some other activity, such
as 2-chlorobenzoate 1,2-dioxygenase (1.14.12.13) [Energy
metabolism, Other].
Length = 433
Score = 28.7 bits (64), Expect = 2.3
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 132 RVKDPKWLVLIGVCTHLGCVPVANA-GDFGGYYCPCHGSHYDASGRIRK 179
R KD + I C+H G + + G+ Y CP HG ++ SG++ K
Sbjct: 68 RNKDGELNAFINACSHRGAMLCRHKRGNKTTYTCPFHGWTFNNSGKLLK 116
>gnl|CDD|177920 PLN02281, PLN02281, chlorophyllide a oxygenase.
Length = 536
Score = 27.8 bits (61), Expect = 4.1
Identities = 18/63 (28%), Positives = 24/63 (38%)
Query: 132 RVKDPKWLVLIGVCTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKY 191
R +D K + C H C + G CP HG Y G +K P+ L+V
Sbjct: 249 RGEDGKPGCVRNTCAHRACPLDLGTVNEGRIQCPYHGWEYSTDGECKKMPSTKLLKVKIK 308
Query: 192 EFP 194
P
Sbjct: 309 SLP 311
>gnl|CDD|223608 COG0534, NorM, Na+-driven multidrug efflux pump [Defense
mechanisms].
Length = 455
Score = 27.6 bits (62), Expect = 5.3
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 31 ARETEEARKAFSYVVAAGTAIGGAYAAKAVV--TQFISSMAASADVLAMAKI 80
A + AR+A + I A ++ IS +V+A+A I
Sbjct: 310 AGNYKRARRAARLALKLSLLIALLIALLLLLFREPIISLFTTDPEVIALAVI 361
>gnl|CDD|239551 cd03469, Rieske_RO_Alpha_N, Rieske non-heme iron oxygenase (RO)
family, N-terminal Rieske domain of the oxygenase alpha
subunit; The RO family comprise a large class of
aromatic ring-hydroxylating dioxygenases found
predominantly in microorganisms. These enzymes enable
microorganisms to tolerate and even exclusively utilize
aromatic compounds for growth. ROs consist of two or
three components: reductase, oxygenase, and ferredoxin
(in some cases) components. The oxygenase component may
contain alpha and beta subunits, with the beta subunit
having a purely structural function. Some oxygenase
components contain only an alpha subunit. The oxygenase
alpha subunit has two domains, an N-terminal Rieske
domain with an [2Fe-2S] cluster and a C-terminal
catalytic domain with a mononuclear Fe(II) binding site.
The Rieske [2Fe-2S] cluster accepts electrons from the
reductase or ferredoxin component and transfers them to
the mononuclear iron for catalysis. Reduced pyridine
nucleotide is used as the initial source of two
electrons for dioxygen activation.
Length = 118
Score = 26.4 bits (59), Expect = 6.1
Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 7/43 (16%)
Query: 144 VCTHLG----CVPVANAGDFGGYYCPCHGSHYDASGRIRKGPA 182
VC H G NAG CP HG YD G++ P
Sbjct: 42 VCPHRGARLCEGRGGNAGRL---VCPYHGWTYDLDGKLVGVPR 81
>gnl|CDD|239829 cd04337, Rieske_RO_Alpha_Cao, Cao (chlorophyll a oxygenase) is a
rieske non-heme iron-sulfur protein located within the
plastid-envelope inner and thylakoid membranes, that
catalyzes the conversion of chlorophyllide a to
chlorophyllide b. CAO is found not only in plants but
also in chlorophytes and prochlorophytes. This domain
represents the N-terminal rieske domain of the oxygenase
alpha subunit. ROs comprise a large class of aromatic
ring-hydroxylating dioxygenases that enable
microorganisms to tolerate and utilize aromatic
compounds for growth. The oxygenase alpha subunit
contains an N-terminal Rieske domain with an [2Fe-2S]
cluster and a C-terminal catalytic domain with a
mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
cluster accepts electrons from a reductase or ferredoxin
component and transfers them to the mononuclear iron for
catalysis. Cao is closely related to several other plant
RO's including Tic 55, a 55 kDa protein associated with
protein transport through the inner chloroplast
membrane; Ptc 52, a novel 52 kDa protein isolated from
chloroplasts; and LLS1/Pao (Lethal-leaf spot
1/pheophorbide a oxygenase).
Length = 129
Score = 26.7 bits (59), Expect = 6.1
Identities = 16/50 (32%), Positives = 17/50 (34%)
Query: 145 CTHLGCVPVANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPKYEFP 194
C H C G CP HG YD G K P+ L V P
Sbjct: 59 CAHRACPLSLGKVIEGRIQCPYHGWEYDGDGECTKMPSTKCLNVGIAALP 108
>gnl|CDD|173278 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provisional.
Length = 181
Score = 26.8 bits (59), Expect = 6.4
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 131 ERVKDPKWLVLIGVCTHLG 149
E++ DPKW++ GVC G
Sbjct: 98 EQMADPKWVMAFGVCASSG 116
>gnl|CDD|238896 cd01915, CODH, Carbon monoxide dehydrogenase (CODH) is found in
acetogenic and methanogenic organisms and is responsible
for the synthesis and breakdown of acetyl-CoA,
respectively. CODH has two types of metal clusters, a
cubane [Fe4-S4] center (B-cluster) similar to that of
hybrid cluster protein (HCP) and a Ni-Fe-S center
(C-cluster) where carbon monoxide oxidation occurs.
Bifunctional CODH forms a heterotetramer with acetyl-CoA
synthase (ACS) consisting of two CODH and two ACS
subunits while monofunctional CODH forms a homodimer.
Bifunctional CODH reduces carbon dioxide to carbon
monoxide and ACS then synthesizes acetyl-CoA from carbon
monoxide, CoA, and a methyl group donated by another
protein (CoFeSP), while monofunctional CODH oxidizes
carbon monoxide to carbon dioxide. CODH and ACS each
have a metal cluster referred to as the C- and
A-clusters, respectively.
Length = 613
Score = 27.2 bits (61), Expect = 6.6
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 109 AAEIAKEQAVAISTL----RDPQADSER-VKDPKWLVLIGVCTHLGCVP 152
A +A E V I L P+ E+ V W V +G+ TH+G VP
Sbjct: 515 ATALANELGVDIPDLPLVASAPEWMEEKAVAIGTWAVALGLPTHVGPVP 563
>gnl|CDD|218970 pfam06278, DUF1032, Protein of unknown function (DUF1032). This
family consists of several conserved eukaryotic proteins
of unknown function.
Length = 565
Score = 27.2 bits (60), Expect = 7.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 158 DFGGYYCPCHGSHYDASGRIRKGPAPLNLEV 188
DF ++ + H DA RKGP ++EV
Sbjct: 309 DFHKWFLKAYADHEDARRSRRKGPTFADMEV 339
>gnl|CDD|132272 TIGR03228, anthran_1_2_A, anthranilate 1,2-dioxygenase, large
subunit. Anthranilate (2-aminobenzoate) is an
intermediate of tryptophan (Trp) biosynthesis and
degradation. Members of this family are the large
subunit of anthranilate 1,2-dioxygenase, which acts in
Trp degradation by converting anthranilate to catechol.
Closely related paralogs typically are the benzoate
1,2-dioxygenase large subunit, among the larger set of
ring-hydroxylating dioxygenases [Energy metabolism,
Amino acids and amines].
Length = 438
Score = 26.9 bits (59), Expect = 8.7
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 141 LIGVCTHLGCVPV-ANAGDFGGYYCPCHGSHYDASGRIRKGPAP 183
L+ C H G G+ + CP H Y + GR+ K AP
Sbjct: 77 LVNACQHRGATLTRVGKGNQSTFTCPFHAWCYKSDGRLVKVKAP 120
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
0.319 0.135 0.410
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,503,357
Number of extensions: 973313
Number of successful extensions: 992
Number of sequences better than 10.0: 1
Number of HSP's gapped: 976
Number of HSP's successfully gapped: 46
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)