RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781042|ref|YP_003065455.1| succinate dehydrogenase
hydrophobic membrane anchor [Candidatus Liberibacter asiaticus str.
psy62]
(130 letters)
>gnl|CDD|32325 COG2142, SdhD, Succinate dehydrogenase, hydrophobic anchor subunit
[Energy production and conversion].
Length = 117
Score = 85.6 bits (212), Expect = 3e-18
Identities = 33/117 (28%), Positives = 61/117 (52%)
Query: 9 LGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVAS 68
L RG GSA+ G+ ++ QR TA+ + +I+ + F + + +A Y V+ L+N
Sbjct: 1 LMVARGSGSARYGSHDWLLQRVTAVILVLLVIWHLYFLLTWLNATYAAWVAFLANPFWKV 60
Query: 69 IMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIA 125
+ L ++ +H G++VIIEDYI L++ + ++L ++ F L +A
Sbjct: 61 FLLLLLVAALIHAWNGLRVIIEDYIKPEKLRLALQILLVLALVLTGVYGTFVLWGVA 117
>gnl|CDD|48056 cd03495, SQR_TypeC_SdhD_like, Succinate:quinone oxidoreductase
(SQR) Type C subfamily, Succinate dehydrogenase D (SdhD)
subunit-like; composed of predominantly uncharacterized
bacterial proteins with similarity to the E. coli SdhD
subunit. One characterized protein is the respiratory
Complex II SdhD subunit of the only eukaryotic member,
Reclinomonas americana. SQR catalyzes the oxidation of
succinate to fumarate coupled to the reduction of
quinone to quinol. It is also called succinate
dehydrogenase or Complex II, and is part of the citric
acid cycle and the aerobic respiratory chain. SQR is
composed of a flavoprotein catalytic subunit, an
iron-sulfur protein and one or two hydrophobic
transmembrane subunits. E. coli SQR is classified as
Type C SQRs because it contains two transmembrane
subunits and one heme group. The SdhD and SdhC subunits
are membrane anchor subunits containing heme and quinone
binding sites. The two-electron oxidation of succinate
in the flavoprotein active site is coupled to the
two-electron reduction of quinone in the membrane anchor
subunits via electron transport through FAD and three
iron-sulfur centers. The reversible reduction of quinone
is an essential feature of respiration, allowing
transfer of electrons between respiratory complexes..
Length = 100
Score = 77.9 bits (192), Expect = 8e-16
Identities = 30/100 (30%), Positives = 55/100 (55%)
Query: 23 GHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQ 82
H+ QR TA+A +P +++F+ A Y ++V+ L++ A ++ L +S H +
Sbjct: 1 HHWWAQRVTAVALVPLVLWFVFSVALLLGASYAEVVAWLAHPFNAILLILTLVSAFYHAR 60
Query: 83 LGMQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLL 122
LGMQV+IEDY+H L++ + F + +F++L
Sbjct: 61 LGMQVVIEDYVHSEGLRLALIIAVKLFAIATAAAGIFAIL 100
>gnl|CDD|144645 pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase
transmembrane subunit. This family includes a
transmembrane protein from both the Succinate
dehydrogenase and Fumarate reductase complexes.
Length = 122
Score = 41.2 bits (97), Expect = 7e-05
Identities = 24/119 (20%), Positives = 45/119 (37%), Gaps = 5/119 (4%)
Query: 3 FDMRSSLGRVRGMGSAKDGTGHFIKQRFTAIAN----IPFIIFFIAFFIKYGDAPYEQI- 57
L G+ A GT I R T +A I +++ + + G Y ++
Sbjct: 1 MRKNRPLSPHLGLYRAHLGTILSILHRITGVALAVLLIHLLLWLLLLALLLGPDSYARVV 60
Query: 58 VSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIF 116
V+ LS+ ++ L +++ H G++ +I D LK L L++
Sbjct: 61 VAWLSSPFKLILLLLLLLALFYHAANGLRHLIWDVGKGLELKTARKTGLLVLALSLVLT 119
>gnl|CDD|48055 cd03494, SQR_TypeC_SdhD, Succinate:quinone oxidoreductase (SQR)
Type C subfamily, Succinate dehydrogenase D (SdhD)
subunit; SQR catalyzes the oxidation of succinate to
fumarate coupled to the reduction of quinone to quinol.
E. coli SQR, a member of this subfamily, reduces the
high potential quinine, ubiquinone. SQR is also called
succinate dehydrogenase or Complex II, and is part of
the citric acid cycle and the aerobic respiratory chain.
SQR is composed of a flavoprotein catalytic subunit, an
iron-sulfur protein and one or two hydrophobic
transmembrane subunits. Members of this subfamily are
classified as Type C SQRs because they contain two
transmembrane subunits and one heme group. SdhD and
SdhC are the two transmembrane proteins of bacterial
SQRs. They contain heme and quinone binding sites. The
two-electron oxidation of succinate in the flavoprotein
active site is coupled to the two-electron reduction of
quinone in the membrane anchor subunits via electron
transport through FAD and three iron-sulfur centers. The
reversible reduction of quinone is an essential feature
of respiration, allowing transfer of electrons between
respiratory complexes..
Length = 99
Score = 37.4 bits (87), Expect = 0.001
Identities = 20/100 (20%), Positives = 48/100 (48%), Gaps = 4/100 (4%)
Query: 25 FIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLG 84
++ QR TA+ + IF + F + YE + S++ + L +++ +H +G
Sbjct: 2 WLVQRVTAVIMALYTIFLVGFLLASPPLTYEAWSGLFSSLWMKIFTLLALLALLLHAWIG 61
Query: 85 MQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKI 124
+ I+ DY+ L+++ + ++L++ L ++I
Sbjct: 62 LWDILTDYVKPAGLRLLLQVL----IILVLFGYLIWGIQI 97
>gnl|CDD|36299 KOG1083, KOG1083, KOG1083, Putative transcription factor
ASH1/LIN-59 [Transcription].
Length = 1306
Score = 32.4 bits (73), Expect = 0.034
Identities = 14/45 (31%), Positives = 18/45 (40%)
Query: 17 SAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVL 61
S+K+ H K R T P+ F F Y PY Q +L
Sbjct: 667 SSKNDHKHRQKHRHTFYHEGPYPSIFRINFNHYYTVPYIQYDPLL 711
>gnl|CDD|48054 cd03493, SQR_QFR_TM, Succinate:quinone oxidoreductase (SQR) and
Quinol:fumarate reductase (QFR) family, transmembrane
subunits; SQR catalyzes the oxidation of succinate to
fumarate coupled to the reduction of quinone to quinol,
while QFR catalyzes the reverse reaction. SQR, also
called succinate dehydrogenase or Complex II, is part of
the citric acid cycle and the aerobic respiratory chain,
while QFR is involved in anaerobic respiration with
fumarate as the terminal electron acceptor. SQRs may
reduce either high or low potential quinones while QFRs
oxidize only low potential quinols. SQR and QFR share a
common subunit arrangement, composed of a flavoprotein
catalytic subunit, an iron-sulfur protein and one or two
hydrophobic transmembrane subunits. The structural
arrangement allows efficient electron transfer between
the catalytic subunit, through iron-sulfur centers, and
the transmembrane subunit(s) containing the electron
donor/acceptor (quinol or quinone). The reversible
reduction of quinone is an essential feature of
respiration, allowing the transfer of electrons between
respiratory complexes. SQRs and QFRs can be classified
into five types (A-E) according to the number of their
hydrophobic subunits and heme groups. This
classification is consistent with the characteristics
and phylogeny of the catalytic and iron-sulfur subunits.
Type E proteins, e.g. non-classical archael SQRs,
contain atypical transmembrane subunits and are not
included in this hierarchy. The heme and quinone binding
sites reside in the transmembrane subunits. Although
succinate oxidation and fumarate reduction are carried
out by separate enzymes in most organisms, some
bifunctional enzymes that exhibit both SQR and QFR
activities exist..
Length = 98
Score = 29.9 bits (67), Expect = 0.22
Identities = 18/94 (19%), Positives = 40/94 (42%), Gaps = 2/94 (2%)
Query: 28 QRFTAIANIPFIIFFIAFFI--KYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGM 85
R T +A + F+ + + G + ++V+ LS+ + L +++ H G+
Sbjct: 3 HRITGVALLLFLPLHLLGLLALLGGPYAFAEVVAFLSSPLGKLLYLLLLLALLYHALNGI 62
Query: 86 QVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLF 119
+ +I DY LK+ + L +++ L
Sbjct: 63 RHLIWDYGKGLELKLRKALGYAVLALSVLLTVLL 96
>gnl|CDD|146346 pfam03661, UPF0121, Uncharacterized protein family (UPF0121).
Uncharacterized integral membrane protein family.
Length = 248
Score = 27.0 bits (60), Expect = 1.6
Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 86 QVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLL 122
Q+I+ED HY L ++FL + LL +F LFSLL
Sbjct: 87 QLILEDSCHYLLYSLIFLNSYPVTMSLLPVF-LFSLL 122
>gnl|CDD|143966 pfam00209, SNF, Sodium:neurotransmitter symporter family.
Length = 506
Score = 26.5 bits (59), Expect = 2.5
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 7/77 (9%)
Query: 40 IFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLK 99
I+ F Y + V +A+A + GL + LG + K
Sbjct: 392 IYVFTLFDYYAASFGLLFVVFFECIAIAWVYGLDRFYDDIKEMLGFRP-------GLFWK 444
Query: 100 IMFLFMNSCFVLLLIIF 116
+ + F++ +L L IF
Sbjct: 445 LCWKFVSPLILLFLFIF 461
>gnl|CDD|36764 KOG1551, KOG1551, KOG1551, Uncharacterized conserved protein
[Function unknown].
Length = 371
Score = 25.8 bits (56), Expect = 3.4
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 49 YGD-APYEQIVSVLSNVAVASIMGLGTISISVHM 81
YG P EQI+ +L V MG TI V +
Sbjct: 152 YGQRVPEEQIIHMLEYVTDLFKMGRATIQEFVKL 185
>gnl|CDD|147489 pfam05328, CybS, CybS. This family consists of several eukaryotic
succinate dehydrogenase [ubiquinone] cytochrome B small
subunit, mitochondrial precursor (CybS) proteins. SDHD
encodes the small subunit (cybS) of cytochrome b in
succinate-ubiquinone oxidoreductase (mitochondrial
complex II). Mitochondrial complex II is involved in the
Krebs cycle and in the aerobic electron transport chain.
It contains four proteins. The catalytic core consists
of a flavoprotein and an iron-sulfur protein; these
proteins are anchored to the mitochondrial inner
membrane by the large subunit of cytochrome b (cybL) and
cybS, which together comprise the heme-protein
cytochrome b. Mutations in the SDHD gene can lead to
hereditary paraganglioma, characterized by the
development of benign, vascularized tumours in the head
and neck.
Length = 107
Score = 25.6 bits (57), Expect = 3.5
Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 17/84 (20%)
Query: 17 SAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTIS 76
+ G+ H+ +R A+ +P F +P + ++L+ +
Sbjct: 2 NKSHGSYHWTFERILAVGLLPLTP--APFL---AGSPSPVMDAILA------------AA 44
Query: 77 ISVHMQLGMQVIIEDYIHYRLLKI 100
+ +H G Q I DYI R+
Sbjct: 45 LLLHCHWGFQSCIIDYIPKRVYGK 68
>gnl|CDD|38872 KOG3668, KOG3668, KOG3668, Phosphatidylinositol transfer protein
[Lipid transport and metabolism, Signal transduction
mechanisms].
Length = 269
Score = 25.6 bits (56), Expect = 3.8
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 84 GMQVIIEDYIHYRLLKIMFLFMNSCFVLL 112
GMQ +E++IH ++ F
Sbjct: 203 GMQTKVENFIHKVERRVFTRAHRQAFCWQ 231
>gnl|CDD|177187 MTH00129, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 230
Score = 24.7 bits (54), Expect = 7.0
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 82 QLGMQ----VIIEDYIHYRLLKIMFLFMNSCFVLLLII 115
QLG Q ++E+ +H+ +M +F+ S VL +I+
Sbjct: 6 QLGFQDAASPVMEELLHFHDHALMIVFLISTLVLYIIV 43
>gnl|CDD|143424 cd07106, ALDH_AldA-AAD23400, Streptomyces aureofaciens putative
aldehyde dehydrogenase AldA (AAD23400)-like. Putative
aldehyde dehydrogenase, AldA, from Streptomyces
aureofaciens (locus AAD23400) and other similar
sequences are present in this CD.
Length = 446
Score = 24.8 bits (55), Expect = 7.5
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 4 DMRSSLGRVRGMGSAKDGTGHFIKQRFTAIANIP 37
D ++ +V G DG G+FI T + + P
Sbjct: 312 DAKAKGAKVLAGGEPLDGPGYFI--PPTIVDDPP 343
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes,
Class 1. Superfamily of trans-isoprenyl diphosphate
synthases (IPPS) and class I terpene cyclases which
either synthesis geranyl/farnesyl diphosphates (GPP/FPP)
or longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids, and
diterpenes; and are widely distributed among archaea,
bacteria, and eukaryota.The enzymes in this superfamily
share the same 'isoprenoid synthase fold' and include
several subgroups. The head-to-tail (HT) IPPS catalyze
the successive 1'-4 condensation of the 5-carbon IPP to
the growing isoprene chain to form linear, all-trans,
C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or
C50-isoprenoid diphosphates. Cyclic monoterpenes,
diterpenes, and sesquiterpenes, are formed from their
respective linear isoprenoid diphosphates by class I
terpene cyclases. The head-to-head (HH) IPPS catalyze
the successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Cyclization of
these 30- and 40-carbon linear forms are catalyzed by
class II cyclases. Both the isoprenoid chain elongation
reactions and the class I terpene cyclization reactions
proceed via electrophilic alkylations in which a new
carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
phosphates via bridging Mg2+ ions, inducing proposed
conformational changes that close the active site to
solvent, stabilizing reactive carbocation intermediates.
Generally, the enzymes in this family exhibit an
all-trans reaction pathway, an exception, is the
cis-trans terpene cyclase, trichodiene synthase.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD.
Length = 243
Score = 24.8 bits (54), Expect = 7.7
Identities = 8/38 (21%), Positives = 14/38 (36%)
Query: 89 IEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIAI 126
+E+Y+ Y K L C + + LL+
Sbjct: 109 LEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALR 146
>gnl|CDD|30131 cd01515, Arch_FBPase_1, Archaeal fructose-1,6-bisphosphatase and
related enzymes of inositol monophosphatase family
(FBPase class IV). These are Mg++ dependent
phosphatases. Members in this family may have both
fructose-1,6-bisphosphatase and inositol-monophosphatase
activity. In hyperthermophilic archaea, inositol
monophosphatase is thought to play a role in the
biosynthesis of di-myo-inositol-1,1'-phosphate, an
osmolyte unique to hyperthermophiles..
Length = 257
Score = 24.4 bits (53), Expect = 9.6
Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 7/44 (15%)
Query: 20 DGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSN 63
DGT + AI IPF +A F PY V L+
Sbjct: 85 DGT-------YNAINGIPFYSVSVAVFKIDKSDPYYGYVYNLAT 121
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.337 0.149 0.436
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,588,489
Number of extensions: 82958
Number of successful extensions: 789
Number of sequences better than 10.0: 1
Number of HSP's gapped: 767
Number of HSP's successfully gapped: 120
Length of query: 130
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,470,190
Effective search space: 210098930
Effective search space used: 210098930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 52 (23.8 bits)