RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6642
(292 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 = 227 bits (581), Expect = 5e-76
Identities = 74/124 (59%), Positives = 93/124 (75%), Gaps = 2/124 (1%)
Query: 71 TIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP--QADSDRVKDP 128
+EVDL+ I EGQ +T +WRGKP+FIR RT +EI + ++S L DP A+ R P
Sbjct: 1 PVEVDLSKIEEGQLITVEWRGKPVFIRRRTPEEIAEAKAVDLSLLDDPDPAANRVRSGKP 60
Query: 129 SWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDE 188
WLV+IGICTHLGCVP AGD+GG++CPCHGSHYDASGRIRKGPAP N+EVPPY+F +
Sbjct: 61 EWLVVIGICTHLGCVPTYRAGDYGGFFCPCHGSHYDASGRIRKGPAPLNLEVPPYKFLSD 120
Query: 189 GILI 192
++
Sbjct: 121 TTIV 124
Score = 58.3 bits (142), Expect = 8e-11
Identities = 18/29 (62%), Positives = 23/29 (79%)
Query: 264 TIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
+EVDL+ I EGQ +T +WRGKP+FIR R
Sbjct: 1 PVEVDLSKIEEGQLITVEWRGKPVFIRRR 29
>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 = 207 bits (529), Expect = 2e-67
Identities = 90/176 (51%), Positives = 112/176 (63%), Gaps = 15/176 (8%)
Query: 29 QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVDLNLIPEGQSVTF 87
R+ F Y + VG V A + FI SM+ SA V A A EVD++ I GQ +T
Sbjct: 1 TRRDFLYA---ATGAVGAVGAAAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTV 57
Query: 88 KWRGKPLFIRHRTQKEIDTEQNTNISQLRDP-----QADSDRVKD---PSWLVIIGICTH 139
+WRGKP+FIR RT+KEID + ++ L+DP Q D RVK P WLV+IGICTH
Sbjct: 58 EWRGKPVFIRRRTKKEIDELKALDLGALKDPNSEAQQPDYARVKRSGKPEWLVVIGICTH 117
Query: 140 LGCVPI--ANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI 192
LGC+P GD GG++CPCHGSHYD +GR+RKGPAP N+ VPPY+F D ILI
Sbjct: 118 LGCIPTYGPEEGDKGGFFCPCHGSHYDTAGRVRKGPAPLNLPVPPYKFLSDTTILI 173
Score = 74.0 bits (182), Expect = 5e-16
Identities = 32/72 (44%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 222 QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVDLNLIPEGQSVTF 280
R+ F Y + VG V A + FI SM+ SA V A A EVD++ I GQ +T
Sbjct: 1 TRRDFLYA---ATGAVGAVGAAAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTV 57
Query: 281 KWRGKPLFIRHR 292
+WRGKP+FIR R
Sbjct: 58 EWRGKPVFIRRR 69
>gnl|CDD|223795 COG0723, QcrA, Rieske Fe-S protein [Energy production and
conversion].
Length = 177
Score = 141 bits (356), Expect = 2e-41
Identities = 57/166 (34%), Positives = 76/166 (45%), Gaps = 14/166 (8%)
Query: 30 RKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADV-LAMATIEVDLNLIPEGQSVTFK 88
R+ F ++ G VG A + + S+ A LA A IEVD + I G VT
Sbjct: 11 RRDFLVLLTTGVGAVGAGAA---LYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVP 67
Query: 89 WRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA 148
WRGKP+F+ RT+ T + ICTHLGC N
Sbjct: 68 WRGKPVFLLRRTEYAGPKGGVTRDGDGGVGN--------KEIVAYSAICTHLGCTVPWNN 119
Query: 149 GDW-GGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI 192
GG++CPCHGS YD G + KGPAP + +PP ++ D+ LI
Sbjct: 120 AGAEGGFFCPCHGSRYDPDGGVVKGPAPRPLPIPPLEYDSDKLYLI 165
Score = 49.4 bits (118), Expect = 3e-07
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 223 RKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADV-LAMATIEVDLNLIPEGQSVTFK 281
R+ F ++ G VG A + + S+ A LA A IEVD + I G VT
Sbjct: 11 RRDFLVLLTTGVGAVGAGAA---LYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVP 67
Query: 282 WRGKPLFIRHR 292
WRGKP+F+ R
Sbjct: 68 WRGKPVFLLRR 78
>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 = 85.1 bits (211), Expect = 2e-21
Identities = 33/63 (52%), Positives = 44/63 (69%), Gaps = 1/63 (1%)
Query: 4 HSDIRTPDFSKYRRDRNPDKGQE-ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSA 62
H+D+R PDFS YRR DK +E + R+AF+Y++ GG+ V+ AKS V F+SSMSA
Sbjct: 1 HTDVRVPDFSDYRRKSTKDKSRESDDGRRAFSYLMVGGAGVLSAYAAKSTVTTFLSSMSA 60
Query: 63 SAD 65
SAD
Sbjct: 61 SAD 63
Score = 85.1 bits (211), Expect = 2e-21
Identities = 33/63 (52%), Positives = 44/63 (69%), Gaps = 1/63 (1%)
Query: 197 HSDIRTPDFSKYRRDRNPDKGQE-ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSA 255
H+D+R PDFS YRR DK +E + R+AF+Y++ GG+ V+ AKS V F+SSMSA
Sbjct: 1 HTDVRVPDFSDYRRKSTKDKSRESDDGRRAFSYLMVGGAGVLSAYAAKSTVTTFLSSMSA 60
Query: 256 SAD 258
SAD
Sbjct: 61 SAD 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 = 73.3 bits (180), Expect = 1e-16
Identities = 23/101 (22%), Positives = 37/101 (36%), Gaps = 12/101 (11%)
Query: 95 FIRHRTQKEIDTEQNTNISQLRDPQADSDRV----KDPSWLVIIGICTHLGCVPIANA-- 148
++ + E+ + D + V KD + +CTH G
Sbjct: 2 WVPVCHESELP---EPGDFKTVDLDGEDPVVVRRDKDGEVRALSNVCTHRGAPLSRGGVG 58
Query: 149 GDWGGYYCPCHGSHYDAS-GRIRKGPAP--TNMEVPPYQFG 186
+ GG+ CP HG +D S G++ GPAP + G
Sbjct: 59 NEKGGFECPYHGWRFDLSTGKLVGGPAPRPLKTYPVLEEVG 99
>gnl|CDD|237392 PRK13474, PRK13474, cytochrome b6-f complex iron-sulfur subunit;
Provisional.
Length = 178
Score = 69.3 bits (170), Expect = 2e-14
Identities = 32/87 (36%), Positives = 49/87 (56%), Gaps = 12/87 (13%)
Query: 127 DPSWLVIIG-----------ICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP 175
DP++LV+ +CTHLGCV N+G+ + CPCHGS YDA+G++ +GPAP
Sbjct: 86 DPTYLVVEEDGTIASYGINAVCTHLGCVVPWNSGE-NKFQCPCHGSQYDATGKVVRGPAP 144
Query: 176 TNMEVPPYQFGDEGILIRMLAHSDIRT 202
++ + D+ +L +D RT
Sbjct: 145 LSLALVHVTVEDDKVLFSPWTETDFRT 171
>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 = 67.8 bits (166), Expect = 3e-14
Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 12/87 (13%)
Query: 127 DPSWLVIIG-----------ICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP 175
DP++L++ +CTHLGCV NA + + CPCHGS YDA+G++ +GPAP
Sbjct: 34 DPTYLIVEEDKTIANYGINAVCTHLGCVVPWNAAE-NKFKCPCHGSQYDATGKVVRGPAP 92
Query: 176 TNMEVPPYQFGDEGILIRMLAHSDIRT 202
++ + D+ +++ +D RT
Sbjct: 93 LSLALVHATVDDDKVVLSPWTETDFRT 119
>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 = 61.4 bits (149), Expect = 4e-12
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 124 RVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYD-ASGRIRKGPAPTNMEVPP 182
R + + CTH GC G+ G CPCHGS +D +G + GPAP + P
Sbjct: 29 RREGGEVYALSNRCTHQGCPLSEGEGEDGCIVCPCHGSRFDLRTGEVVSGPAPRPLPKYP 88
Query: 183 YQFGDEGILI 192
+ +G++
Sbjct: 89 VKVEGDGVVW 98
>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 = 45.8 bits (109), Expect = 9e-07
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 136 ICTHLGCVPIANAGD--WGGYYCPCHGSHYDASGRIRKGPAPTNMEV 180
CTHLGC+ N + W CPCHGS + G + +GPA + ++
Sbjct: 39 TCTHLGCIVHWNDAEKSWD---CPCHGSRFSYDGEVIEGPAVSGLKP 82
>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 = 38.9 bits (91), Expect = 5e-04
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 135 GICTHLGCVPIANAGDWGGYYCPCHGSHYDAS 166
+CTH+GC P+ + CPCH S +D +
Sbjct: 53 ALCTHMGC-PLTYDPSNKTFVCPCHFSQFDPA 83
>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 = 37.6 bits (87), Expect = 0.002
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 136 ICTHLGCVPIANAGDWGGYYCPCHGSHYDAS--GRIRKGPAPTNMEVPPYQFGDEG 189
+CTH+GC P++ + D + CPCH S +D G+ G A N+ + D G
Sbjct: 57 LCTHMGC-PVSYSADNKTFNCPCHFSVFDPEKGGQQVWGQATQNLPQIVLRVADNG 111
>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 = 34.2 bits (79), Expect = 0.014
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 6/58 (10%)
Query: 135 GICTHLGCVPIANAGDWGGYY--CPCHGSHYD-ASGRIRKGPAPTNMEVPPYQFGDEG 189
C H G P++ G CP HG+ +D +G + PA + Y EG
Sbjct: 44 NRCPHAGA-PLSRGLVEGDETVVCPLHGARFDLRTGECLEPPAGK--TLKTYPVRVEG 98
>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 = 34.4 bits (79), Expect = 0.031
Identities = 20/57 (35%), Positives = 22/57 (38%), Gaps = 17/57 (29%)
Query: 136 ICTHLGCVP--------------IANAGDWGG-YYCPCHGSHYD--ASGRIRKGPAP 175
IC HLGC P G +C CHGS YD G + GPAP
Sbjct: 83 ICQHLGCQPPPIVSYPSYYPPDKAPGLASKGAVIHCCCHGSTYDPYKGGVVLTGPAP 139
>gnl|CDD|239615 cd03542, Rieske_RO_Alpha_HBDO, Rieske non-heme iron oxygenase (RO)
family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily,
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. HBDO catalyzes the double hydroxylation of
2-halobenzoates with concomitant release of halogenide
and carbon dioxide, yielding catechol.
Length = 123
Score = 31.3 bits (71), Expect = 0.24
Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 8/87 (9%)
Query: 124 RVKDPSWLVIIGICTHLGCVPIA-NAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPP 182
R KD I C+H G + G+ G + CP HG + +G++ K P P
Sbjct: 30 RDKDGELNAFINACSHRGAMLCRRKQGNKGTFTCPFHGWTFSNTGKLLKVKDPKTAGYPE 89
Query: 183 YQFGDEGILIRMLAHSDIRTPDFSKYR 209
F +G +H + F YR
Sbjct: 90 -GFNCDG------SHDLTKVARFESYR 109
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 31.6 bits (72), Expect = 0.39
Identities = 20/45 (44%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 135 GICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPA-PTNM 178
G+ LG P AN GD G + P HGS D +G KG A PT
Sbjct: 235 GLVGGLGLAPSANIGDKYGLFEPVHGSAPDIAG---KGIANPTAT 276
>gnl|CDD|215345 PLN02641, PLN02641, anthranilate phosphoribosyltransferase.
Length = 343
Score = 31.6 bits (72), Expect = 0.48
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 32 AFTYMIAGGSSVVGMVCAKSVV---NQFISSMSASADVLAMATIEVDLNLIPEG 82
A T I+ GSS++ C V N+ SS SADVL + +DL PEG
Sbjct: 86 ANTVNISTGSSILAAACGAKVAKQGNRSSSSACGSADVLEALGVAIDLG--PEG 137
Score = 31.6 bits (72), Expect = 0.48
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 225 AFTYMIAGGSSVVGMVCAKSVV---NQFISSMSASADVLAMATIEVDLNLIPEG 275
A T I+ GSS++ C V N+ SS SADVL + +DL PEG
Sbjct: 86 ANTVNISTGSSILAAACGAKVAKQGNRSSSSACGSADVLEALGVAIDLG--PEG 137
>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 = 31.3 bits (71), Expect = 0.57
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 123 DRVKDPSWLVIIGICTHLGCVPIANA--GDWGGYYCPCHGSHYDASGRIRKGPAP 175
R KD + +C H G ++ G G CP HG YD GR+R PA
Sbjct: 55 VRDKDGQVHALADVCPHRG-ARLSEGRVGGKGRLTCPYHGWTYDLDGRLRGVPAR 108
>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 = 29.8 bits (67), Expect = 0.84
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 124 RVKDPSWLVIIGICTHLGC-VPIANAGDWGGYYCPCHGSHYDASGRIRKGP 173
R KD S V + C H G + ++AG+ + C HG YD +G + P
Sbjct: 38 RQKDGSIRVFLNQCRHRGMRICRSDAGNAKAFTCTYHGWAYDTAGNLVNVP 88
>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 = 30.6 bits (69), Expect = 0.92
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 124 RVKDPSWLVIIGICTHLGCVPIANA-GDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPP 182
R KD I C+H G + + G+ Y CP HG ++ SG++ K P + P
Sbjct: 68 RNKDGELNAFINACSHRGAMLCRHKRGNKTTYTCPFHGWTFNNSGKLLKVKDPEDAGYPE 127
Query: 183 YQFGDEGILIRMLAHSDIRTPDFSKYR 209
F +G +H + F YR
Sbjct: 128 -CFNKDG------SHDLKKVARFESYR 147
>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 = 30.5 bits (69), Expect = 0.99
Identities = 18/40 (45%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 140 LGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPA-PTNM 178
LG P AN GD + P HGS D +G KG A PT
Sbjct: 235 LGLAPSANIGDRKALFEPVHGSAPDIAG---KGIANPTAA 271
>gnl|CDD|173879 cd08514, PBP2_AppA_like, The substrate-binding component of the
oligopeptide-binding protein, AppA, from Bacillus
subtilis contains the type 2 periplasmic-binding fold.
This family represents the substrate-binding domain of
the oligopeptide-binding protein, AppA, from Bacillus
subtilis and its closest homologs from other bacteria
and archaea. Bacillus subtilis has three ABC-type
peptide transport systems, a dipeptide-binding protein
(DppA) and two oligopeptide-binding proteins (OppA and
AppA) with overlapping specificity. The dipeptide
(DppA) and oligopeptide (OppA) binding proteins differ
in several ways. The DppA binds dipeptides and some
tripeptides and also is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which
precludes any involvement in chemotaxis. Most of other
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the dipeptide/oligopeptide binding proteins. The
structural topology of these domains is most similar to
that of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2
bind their ligand in the cleft between these domains in
a manner resembling a Venus flytrap. After binding
their specific ligand with high affinity, they can
interact with a cognate membrane transport complex
comprised of two integral membrane domains and two
cytoplasmically located ATPase domains. This
interaction triggers the ligand translocation across
the cytoplasmic membrane energized by ATP hydrolysis.
Besides transport proteins, the PBP2 superfamily
includes the ligand-binding domains from ionotropic
glutamate receptors, LysR-type transcriptional
regulators, and unorthodox sensor proteins involved in
signal transduction.
Length = 483
Score = 28.7 bits (65), Expect = 4.0
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 22/74 (29%)
Query: 43 VVGMVCAKSVVNQFISSMSASADVLAM-----ATIEVDLNLIPE----------GQSVTF 87
V+ S +N +S+ SAS++V + + DLN P+ G++ TF
Sbjct: 3 VLATGGDPSNLNPILSTDSASSEVAGLIYEGLLKYDKDLNFEPDLAESWEVSDDGKTYTF 62
Query: 88 KWR-------GKPL 94
K R G+PL
Sbjct: 63 KLRKDVKWHDGEPL 76
Score = 28.7 bits (65), Expect = 4.0
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 22/74 (29%)
Query: 236 VVGMVCAKSVVNQFISSMSASADVLAM-----ATIEVDLNLIPE----------GQSVTF 280
V+ S +N +S+ SAS++V + + DLN P+ G++ TF
Sbjct: 3 VLATGGDPSNLNPILSTDSASSEVAGLIYEGLLKYDKDLNFEPDLAESWEVSDDGKTYTF 62
Query: 281 KWR-------GKPL 287
K R G+PL
Sbjct: 63 KLRKDVKWHDGEPL 76
>gnl|CDD|216013 pfam00591, Glycos_transf_3, Glycosyl transferase family, a/b
domain. This family includes anthranilate
phosphoribosyltransferase (TrpD), thymidine
phosphorylase. All these proteins can transfer a
phosphorylated ribose substrate.
Length = 254
Score = 28.4 bits (64), Expect = 4.1
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 32 AFTYMIAGGSSVVGMVCAKSVV---NQFISSMSASADVLAMATIEVDLNLIPE 81
T+ I+ ++ V C V N+ +SS S SADVL + ++L L PE
Sbjct: 15 DNTFNISTAAAFVAAACGVKVAKHGNRSVSSKSGSADVL--EALGINLELTPE 65
Score = 28.4 bits (64), Expect = 4.1
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 225 AFTYMIAGGSSVVGMVCAKSVV---NQFISSMSASADVLAMATIEVDLNLIPE 274
T+ I+ ++ V C V N+ +SS S SADVL + ++L L PE
Sbjct: 15 DNTFNISTAAAFVAAACGVKVAKHGNRSVSSKSGSADVL--EALGINLELTPE 65
>gnl|CDD|181927 PRK09522, PRK09522, bifunctional glutamine
amidotransferase/anthranilate phosphoribosyltransferase;
Provisional.
Length = 531
Score = 28.1 bits (62), Expect = 6.4
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 37 IAGGSSVVGMVCAKSVV---NQFISSMSASADVLAMATIEVDLN 77
I+ S+ V C V N+ +SS S S+D+LA I +D+N
Sbjct: 289 ISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLLAAFGINLDMN 332
Score = 28.1 bits (62), Expect = 6.4
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 230 IAGGSSVVGMVCAKSVV---NQFISSMSASADVLAMATIEVDLN 270
I+ S+ V C V N+ +SS S S+D+LA I +D+N
Sbjct: 289 ISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLLAAFGINLDMN 332
>gnl|CDD|233329 TIGR01245, trpD, anthranilate phosphoribosyltransferase. In many
widely different species, including E. coli, Thermotoga
maritima, and Archaeoglobus fulgidus, this enzymatic
domain (anthranilate phosphoribosyltransferase) is found
C-terminal to glutamine amidotransferase; the fusion
protein is designated anthranilate synthase component II
(EC 4.1.3.27) [Amino acid biosynthesis, Aromatic amino
acid family].
Length = 330
Score = 28.0 bits (63), Expect = 6.9
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 54 NQFISSMSASADVLAMATIEVDLN 77
N+ +SS S SADVL + +DL
Sbjct: 107 NRSVSSKSGSADVLEALGVNLDLG 130
Score = 28.0 bits (63), Expect = 6.9
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 247 NQFISSMSASADVLAMATIEVDLN 270
N+ +SS S SADVL + +DL
Sbjct: 107 NRSVSSKSGSADVLEALGVNLDLG 130
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
0.320 0.134 0.408
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,803,250
Number of extensions: 1358402
Number of successful extensions: 1172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1155
Number of HSP's successfully gapped: 40
Length of query: 292
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 196
Effective length of database: 6,679,618
Effective search space: 1309205128
Effective search space used: 1309205128
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: 59 (26.6 bits)