RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14240
(106 letters)
>gnl|CDD|99858 cd06105, ScCit1-2_like, Saccharomyces cerevisiae (Sc) citrate
synthases Cit1-2_like. Citrate synthases (CS) catalyzes
the condensation of acetyl coenzyme A (AcCoA) with
oxaloacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the citric acid cycle (TCA or Krebs
cycle). Some CS proteins function as 2-methylcitrate
synthase (2MCS). 2MCS catalyzes the condensation of
propionyl-coenzyme A (PrCoA) and OAA to form
2-methylcitrate and CoA during propionate metabolism.
The overall CS reaction is thought to proceed through
three partial reactions and involves both closed and
open conformational forms of the enzyme: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA. In addition to its CS function, ScCit1 plays
a part in the construction of the TCA cycle metabolon.
Yeast cells deleted for Cit1 are hyper-susceptible to
apoptosis induced by heat and aging stress. ScCit2 is a
peroxisomal CS involved in the glyoxylate cycle; in
addition to having activity with AcCoA, it may have
activity with PrCoA. Chicken and pig heart CS, two
Arabidopsis thaliana (Ath) CSs, CSY4 and -5, and
Aspergillus niger (An) CS also belong to this group. Ath
CSY4 has a mitochondrial targeting sequence; AthCSY5 has
no identifiable targeting sequence. AnCS encoded by the
citA gene has both an N-terminal mitochondrial import
signal and a C-terminal peroxisiomal target sequence; it
is not known if both these signals are functional in
vivo. This group contains proteins which functions
exclusively as either a CS or a 2MCS, as well as those
with relaxed specificity which have dual functions as
both a CS and a 2MCS.
Length = 427
Score = 152 bits (387), Expect = 3e-46
Identities = 62/71 (87%), Positives = 66/71 (92%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
RA LPSHVVTML+NFP +LHPMSQ SAAITALNSESKFAKAY +G+HKSKYWEYVYEDSM
Sbjct: 112 RAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESKFAKAYAEGIHKSKYWEYVYEDSM 171
Query: 72 DLIAKLPVVAA 82
DLIAKLP VAA
Sbjct: 172 DLIAKLPCVAA 182
>gnl|CDD|99857 cd06103, ScCS-like, Saccharomyces cerevisiae (Sc) citrate synthase
(CS)-like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) with oxaloacetate (OAA) to form
citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). Some CS proteins
function as 2-methylcitrate synthase (2MCS). 2MCS
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and OAA to form 2-methylcitrate and CoA during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). This group includes three S.
cerevisiae CS proteins, ScCit1,-2,-3. ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA; in addition to having activity with AcCoA, it
plays a part in the construction of the TCA cycle
metabolon. Yeast cells deleted for Cit1 are
hyper-susceptible to apoptosis induced by heat and aging
stress. ScCit2 is a peroxisomal CS involved in the
glyoxylate cycle; in addition to having activity with
AcCoA, it may have activity with PrCoA. ScCit3 is a
mitochondrial CS and functions in the metabolism of
PrCoA; it is a dual specificity CS and 2MCS, having
similar catalytic efficiency with both AcCoA and PrCoA.
The pattern of expression of the ScCIT3 gene follows
that of the ScCIT1 gene and its expression is increased
in the presence of a ScCIT1 deletion. Included in this
group is the Tetrahymena 14 nm filament protein which
functions as a CS in mitochondria and as a cytoskeletal
component in cytoplasm and Geobacter sulfurreducens
(GSu) CS. GSuCS is dimeric and eukaryotic-like; it lacks
2MCS activity and is inhibited by ATP. In contrast to
eukaryotic and other prokaryotic CSs, GSuCIT is not
stimulated by K+ ions. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS.
Length = 426
Score = 127 bits (322), Expect = 1e-36
Identities = 53/72 (73%), Positives = 63/72 (87%), Gaps = 1/72 (1%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDG-VHKSKYWEYVYEDS 70
RAE+PSHVV M++N P +LHPM+Q SAAI AL SESKFAKAY +G ++K+ YWEYVYED+
Sbjct: 112 RAEVPSHVVKMIDNLPRNLHPMTQLSAAILALQSESKFAKAYAEGKINKTTYWEYVYEDA 171
Query: 71 MDLIAKLPVVAA 82
MDLIAKLPVVAA
Sbjct: 172 MDLIAKLPVVAA 183
>gnl|CDD|130853 TIGR01793, cit_synth_euk, citrate (Si)-synthase, eukaryotic. This
model includes both mitochondrial and peroxisomal forms
of citrate synthase. Citrate synthase is the entry point
to the TCA cycle from acetyl-CoA. Peroxisomal forms,
such as SP:P08679 from yeast (recognized by the
C-terminal targeting motif SKL) act in the glyoxylate
cycle. Eukaryotic homologs excluded by the high trusted
cutoff of this model include a Tetrahymena thermophila
citrate synthase that doubles as a filament protein, a
putative citrate synthase from Plasmodium falciparum (no
TCA cycle), and a methylcitrate synthase from
Aspergillus nidulans.
Length = 427
Score = 121 bits (306), Expect = 2e-34
Identities = 46/71 (64%), Positives = 55/71 (77%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
RA+LP HV ++ P LHPM+QF+ A+ AL ES+FAKAY G+HK+KYWEY YEDSM
Sbjct: 115 RADLPEHVYKTIDALPVTLHPMAQFATAVMALQVESEFAKAYAKGIHKTKYWEYTYEDSM 174
Query: 72 DLIAKLPVVAA 82
DLIAKLP VAA
Sbjct: 175 DLIAKLPTVAA 185
>gnl|CDD|99859 cd06106, ScCit3_like, Saccharomyces cerevisiae (Sc) 2-methylcitrate
synthase Cit3-like. 2-methylcitrate synthase (2MCS)
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate
and CoA. Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) with OAA to
form citrate and CoA, the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). ScCit3 is mitochondrial and functions
in the metabolism of PrCoA; it is a dual specificity CS
and 2MCS, having similar catalytic efficiency with both
AcCoA and PrCoA. The pattern of expression of the ScCIT3
gene follows that of the major mitochondrial CS gene
(CIT1, not included in this group) and its expression is
increased in the presence of a CIT1 deletion. This group
also contains Aspergillus nidulans 2MCS; a deletion of
the gene encoding this protein results in a strain
unable to grow on propionate. This group contains
proteins which functions exclusively as either a CS or a
2MCS, as well as those with relaxed specificity which
have dual functions as both a CS and a 2MCS.
Length = 428
Score = 106 bits (267), Expect = 9e-29
Identities = 35/71 (49%), Positives = 51/71 (71%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
R +LP ++ +L++ P LHPM+Q S + ALN +SKFA AY G+ K++YWE EDS+
Sbjct: 112 RGKLPHYIEKLLDSLPKTLHPMTQLSIGVAALNHDSKFAAAYEKGIKKTEYWEPTLEDSL 171
Query: 72 DLIAKLPVVAA 82
+LIA+LP +AA
Sbjct: 172 NLIARLPALAA 182
>gnl|CDD|215250 PLN02456, PLN02456, citrate synthase.
Length = 455
Score = 98.2 bits (245), Expect = 1e-25
Identities = 29/71 (40%), Positives = 43/71 (60%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
+ +P HV+ +++ P+ HPM+Q + + AL++ S A AY G HK K WE ED +
Sbjct: 132 HSAVPEHVLDVIDALPHDAHPMTQLVSGVMALSTFSPDANAYLRGQHKYKSWEVRDEDIV 191
Query: 72 DLIAKLPVVAA 82
LI KLP +AA
Sbjct: 192 RLIGKLPTLAA 202
>gnl|CDD|181961 PRK09569, PRK09569, type I citrate synthase; Reviewed.
Length = 437
Score = 90.6 bits (225), Expect = 9e-23
Identities = 33/72 (45%), Positives = 46/72 (63%), Gaps = 1/72 (1%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDG-VHKSKYWEYVYEDS 70
R +P +V+ + P HPM S I A+ ESKFAK YN+G +K WEY+YED+
Sbjct: 114 RQNVPQYVIDAIRALPRDSHPMVMLSVGILAMQRESKFAKFYNEGKFNKMDAWEYMYEDA 173
Query: 71 MDLIAKLPVVAA 82
DL+A++PV+AA
Sbjct: 174 SDLVARIPVIAA 185
>gnl|CDD|99871 cd06118, citrate_synt_like_1, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism.
Length = 358
Score = 75.7 bits (187), Expect = 1e-17
Identities = 28/71 (39%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
LP HVV +L+ P + HPM A++AL S FA + K E YE ++
Sbjct: 67 HRALPEHVVEILDLLPKNAHPMDVLRTAVSALGSFDPFA--------RDKSPEARYEKAI 118
Query: 72 DLIAKLPVVAA 82
LIAKLP +AA
Sbjct: 119 RLIAKLPTIAA 129
>gnl|CDD|215837 pfam00285, Citrate_synt, Citrate synthase.
Length = 352
Score = 66.4 bits (163), Expect = 3e-14
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
R ELP V +++ P HPM+ AA++AL + + E V ED++
Sbjct: 66 RRELPEDVKEVIDALPKDAHPMAVLRAAVSALAAYDPML--------YDESPEDVLEDAI 117
Query: 72 DLIAKLPVVAA 82
LIAKLP + A
Sbjct: 118 RLIAKLPTIVA 128
>gnl|CDD|223449 COG0372, GltA, Citrate synthase [Energy production and conversion].
Length = 390
Score = 54.2 bits (131), Expect = 6e-10
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 11 MRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDS 70
R LP V+ +L + P HPM+ A++AL S K + E +
Sbjct: 83 ARRTLPEQVIRLLESLPRDAHPMAVLRTAVSAL-SAFYPDKLDLND---------RREAA 132
Query: 71 MDLIAKLPVVAA 82
+ LIAKLP +AA
Sbjct: 133 LRLIAKLPTIAA 144
>gnl|CDD|99867 cd06114, EcCS_like, Escherichia coli (Ec) citrate synthase (CS)
GltA_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). Some type II CSs including EcCS are
strongly and specifically inhibited by NADH through an
allosteric mechanism. Included in this group is an
NADH-insensitive type II Acetobacter acetii CS which has
retained many of the residues used by EcCS for NADH
binding.
Length = 400
Score = 39.1 bits (92), Expect = 1e-04
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 15 LPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLI 74
+ + N FP HPM+ SA + AL++ + ND E ++ LI
Sbjct: 98 VHEQMKRFFNGFPRDAHPMAILSAMVNALSAFYPDSLDVNDP-------EQRELAAIRLI 150
Query: 75 AKLPVVAA 82
AK+P +AA
Sbjct: 151 AKVPTIAA 158
>gnl|CDD|237069 PRK12349, PRK12349, citrate synthase 3; Provisional.
Length = 369
Score = 35.9 bits (83), Expect = 0.002
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 14 ELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYND---GVHKSKYWEYVYEDS 70
+P V +L P HPM ++AL + + D V+KS+ +
Sbjct: 75 AVPEGVFNILKALPKETHPMDGLRTGVSAL---AGYDNDIEDRSLEVNKSR--------A 123
Query: 71 MDLIAKLPVVAAPS 84
L++K+P + A S
Sbjct: 124 YKLLSKVPNIVANS 137
>gnl|CDD|99865 cd06112, citrate_synt_like_1_1, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism.
Length = 373
Score = 34.3 bits (79), Expect = 0.006
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 18 HVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKL 77
++ M+ FP HPM A + AL + +Y+ ++ LIAK+
Sbjct: 75 NIRDMMKCFPETGHPMDMLQATVAALGMFYPKPEVLKPNP------DYIDAATVKLIAKM 128
Query: 78 PVVAA 82
P + A
Sbjct: 129 PTLVA 133
>gnl|CDD|180164 PRK05614, gltA, type II citrate synthase; Reviewed.
Length = 419
Score = 33.7 bits (78), Expect = 0.010
Identities = 19/74 (25%), Positives = 24/74 (32%), Gaps = 33/74 (44%)
Query: 22 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMD--------- 72
F HPM+ + AL S F Y DS+D
Sbjct: 123 FFRGFRRDAHPMAVLCGVVGAL---SAF-----------------YHDSLDINDPEHREI 162
Query: 73 ----LIAKLPVVAA 82
LIAK+P +AA
Sbjct: 163 AAIRLIAKMPTLAA 176
>gnl|CDD|130859 TIGR01800, cit_synth_II, 2-methylcitrate synthase/citrate synthase
II. Members of this family are dimeric enzymes with
activity as 2-methylcitrate synthase, citrate synthase,
or both. Many Gram-negative species have a hexameric
citrate synthase, termed citrate synthase I (TIGR01798).
Members of this family (TIGR01800) appear as a second
citrate synthase isozyme but typically are associated
with propionate metabolism and synthesize
2-methylcitrate from propionyl-CoA; citrate synthase
activity may be incidental. A number of species,
including Thermoplasma acidophilum, Pyrococcus furiosus,
and the Antarctic bacterium DS2-3R have a bifunctional
member of this family as the only citrate synthase
isozyme.
Length = 368
Score = 32.7 bits (75), Expect = 0.022
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 10/72 (13%)
Query: 12 RAELPSHVVTMLNNFPNHLHPMSQFSAAITAL-NSESKFAKAYNDGVHKSKYWEYVYEDS 70
LP V+ ++ P HPM A++ L + + + + +
Sbjct: 67 LRGLPDEVIELIEALPAESHPMDVLRTAVSYLGALDPEKFGHTPEE---------ARDIA 117
Query: 71 MDLIAKLPVVAA 82
+ L+AKLP + A
Sbjct: 118 IRLLAKLPTIVA 129
>gnl|CDD|99868 cd06115, AthCS_per_like, Arabidopsis thaliana (Ath) peroxisomal
(Per) CS_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. This group contains three
Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3
which are involved in the glyoxylate cycle. AthCYS1, in
addition to a peroxisomal targeting sequence, has a
predicted secretory signal peptide; it may be targeted
to both the secretory pathway and the peroxisomes and is
thought to be located in the extracellular matrix.
AthCSY1 is expressed only in siliques and specifically
in developing seeds. AthCSY2 and 3 are active during
seed germination and seedling development and are
thought to participate in the beta-oxidation of fatty
acids.
Length = 410
Score = 31.6 bits (72), Expect = 0.043
Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 6/71 (8%)
Query: 15 LPSHVVTMLNNFPNHLHPMSQFSAAITALNS---ESKFAKAYNDGVHKSKYWEYVYEDSM 71
+P+ V+ M+ +FP+ HPM +AI+AL++ E+ A A D ++K+K + + +
Sbjct: 96 VPTGVLDMIKSFPHDAHPMGMLVSAISALSAFHPEANPALAGQD-IYKNK--QVRDKQIV 152
Query: 72 DLIAKLPVVAA 82
++ K P +AA
Sbjct: 153 RILGKAPTIAA 163
>gnl|CDD|99863 cd06110, BSuCS-II_like, Bacillus subtilis (Bs) citrate synthase
(CS)-II_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and CoA during propionate
metabolism. The overall CS reaction is thought to
proceed through three partial reactions: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
This group contains proteins similar to BsCS-II, the
major CS of the gram-positive bacterium Bacillus
subtilis. A mutation in the gene which encodes BsCS-II
(citZ gene) has been described which resulted in a
significant loss of CS activity, partial glutamate
auxotrophy, and a sporulation deficiency, all of which
are characteristic of strains defective in the Krebs
cycle. Streptococcus mutans CS, found in this group, may
participate in a pathway for the anaerobic biosynthesis
of glutamate. This group also contains functionally
uncharacterized CSs of various gram-negative bacteria.
Some of the gram-negative species represented in this
group have a second CS isozyme found in another group.
This group contains proteins which functions exclusively
as either a CS or a 2MCS, as well as those with relaxed
specificity which have dual functions as both a CS and a
2MCS.
Length = 356
Score = 30.7 bits (70), Expect = 0.089
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 14 ELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDL 73
ELP+ ++ +L P HPM A++AL A + E ++ L
Sbjct: 69 ELPAEIIDLLKLLPKDAHPMDVLRTAVSALALYDPEADDMSR--------EANLRKAIRL 120
Query: 74 IAKLP-VVAA 82
IAK+P +VAA
Sbjct: 121 IAKMPTIVAA 130
>gnl|CDD|237591 PRK14036, PRK14036, citrate synthase; Provisional.
Length = 377
Score = 30.7 bits (70), Expect = 0.10
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 13/75 (17%)
Query: 11 MRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKF--AKAYNDGVHKSKYWEYVYE 68
M + + M+ FP HPM A+ AL F +A +D EY+ +
Sbjct: 71 MHRRVKYRIRDMMKCFPETGHPMDALQASAAALGL---FYSRRALDDP-------EYIRD 120
Query: 69 DSMDLIAKLP-VVAA 82
+ LIAK+P +VAA
Sbjct: 121 AVVRLIAKIPTMVAA 135
>gnl|CDD|99860 cd06107, EcCS_AthCS-per_like, Escherichia coli (Ec) citrate
synthase (CS) gltA and Arabidopsis thaliana (Ath)
peroxisomal (Per) CS_like. CS catalyzes the condensation
of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to
form citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs,
including EcCS, are strongly and specifically inhibited
by NADH through an allosteric mechanism. Included in
this group is an NADH-insensitive type II Acetobacter
acetii CS which has retained many of the residues used
by EcCS for NADH binding. C. aurantiacus is a
gram-negative thermophilic green gliding bacterium; its
CS belonging to this group may be a type I CS. It is
not inhibited by NADH or 2-oxoglutarate and is inhibited
by ATP. Both gram-positive and gram-negative bacteria
are found in this group. This group also contains three
Arabidopsis peroxisomal CS proteins, CYS-1, -2, and -3
which participate in the glyoxylate cycle. AthCYS1, in
addition to a peroxisomal targeting sequence, has a
predicted secretory signal peptide; it may be targeted
to both the secretory pathway and the peroxisomes and
perhaps is located in the extracellular matrix. AthCSY1
is expressed only in siliques and specifically in
developing seeds. AthCSY2 and 3 are active during seed
germination and seedling development and are thought to
participate in the beta-oxidation of fatty acids.
Length = 382
Score = 30.5 bits (69), Expect = 0.13
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 15 LPSHVVTMLNNFPNHLHPMSQFSAAITALNS---ESKFAKAYNDGVHKSKYWEYVYEDSM 71
+P V ++ FP HPM A ++AL++ E+ A + + E + +
Sbjct: 76 VPESVHRLIQTFPRDAHPMGILCAGLSALSAFYPEAIPAHTGDLYQNNP---EVRDKQII 132
Query: 72 DLIAKLPVVAA 82
+AK+P +AA
Sbjct: 133 RTLAKMPTIAA 143
>gnl|CDD|99864 cd06111, DsCS_like, Cold-active citrate synthase (CS) from an
Antarctic bacterial strain DS2-3R (Ds)-like. CS
catalyzes the condensation of acetyl coenzyme A (AcCoA)
and oxalacetate (OAA) to form citrate and coenzyme A
(CoA), the first step in the citric acid cycle (TCA or
Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes
the condensation of propionyl-coenzyme A (PrCoA) and OAA
to form 2-methylcitrate and coenzyme A (CoA) during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions: a)
the carbanion or equivalent is generated from AcCoA by
base abstraction of a proton, b) the nucleophilic attack
of this carbanion on OAA to generate citryl-CoA, and c)
the hydrolysis of citryl-CoA to produce citrate and CoA.
DsCS, compared with CS from the hyperthermophile
Pyrococcus furiosus (not included in this group), has an
increase in the size of surface loops, a higher proline
content in the loop regions, a more accessible active
site, and a higher number of intramolecular ion pairs.
This group contains proteins which functions exclusively
as either a CS or a 2MCS, as well as those with relaxed
specificity which have dual functions as both a CS and a
2MCS. For example, included in this group are
Corynebacterium glutamicum (Cg) PrpC1 and -2, which are
only synthesized during growth on propionate-containing
medium, can use PrCoA, AcCoA and butyryl-CoA as
substrates, and have comparable catalytic activity with
AcCoA as the major CgCS (GltA, not included in this
group).
Length = 362
Score = 29.3 bits (66), Expect = 0.33
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 14 ELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDL 73
L ++++++ + P + HPM A++ L +E D + ++ L
Sbjct: 69 RLDRNLLSLIASLPKNCHPMDVLRTAVSVLGAE--------DSETDDSSPDANLAKAIRL 120
Query: 74 IAKLPVVAA 82
+A+LP V A
Sbjct: 121 LAQLPTVVA 129
>gnl|CDD|184468 PRK14035, PRK14035, citrate synthase; Provisional.
Length = 371
Score = 27.0 bits (60), Expect = 1.7
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 28 NHLHPMSQFSAAITALNSESKFAKAYNDGVH-KSKYWEYVYEDSMDLIAKLPVVAA 82
+H+HPM TAL + + ++ + + E YE ++ + AK+ +
Sbjct: 86 DHVHPM-------TALRTSVSYLAHFD--PDAEEESDEARYERAIRIQAKVASLVT 132
>gnl|CDD|184467 PRK14034, PRK14034, citrate synthase; Provisional.
Length = 372
Score = 26.7 bits (59), Expect = 2.3
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 13 AELPSHVVTMLNNFP-NHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSM 71
A++P ++ L + +HPMS AI+ L + A+ ++ E Y ++
Sbjct: 70 AKVPGEIIEHLKQYDLKKVHPMSVLRTAISMLGLYDEEAEIMDE--------EANYRKAV 121
Query: 72 DLIAKLP-VVAA 82
L AK+P +VAA
Sbjct: 122 RLQAKVPTIVAA 133
>gnl|CDD|131074 TIGR02019, BchJ, bacteriochlorophyll 4-vinyl reductase. This
model represents the component of bacteriochlorophyll
synthetase responsible for reduction of the B-ring
pendant ethylene (4-vinyl) group. It appears that this
step must precede the reduction of ring D, at least by
the "dark" protochlorophyllide reductase enzymes BchN,
BchB and BchL. This family appears to be present in
photosynthetic bacteria except for the cyanobacterial
clade. Cyanobacteria must use a non-orthologous gene to
carry out this required step for the biosynthesis of
both bacteriochlorophyll and chlorophyll [Biosynthesis
of cofactors, prosthetic groups, and carriers,
Chlorophyll and bacteriochlorphyll].
Length = 188
Score = 26.4 bits (58), Expect = 3.2
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 22 MLNNFPNHLHPMSQFSAAITALNSE 46
+ P+ + P SQFS L
Sbjct: 35 LRPGPPSGMLPESQFSTLHRWLRDT 59
>gnl|CDD|234016 TIGR02791, VirB5, P-type DNA transfer protein VirB5. The VirB5
protein is involved in the type IV DNA secretion
systems typified by the Agrobacterium Ti plasmid vir
system where it interacts with several other proteins
essential for proper pilus formation. VirB5 is
homologous to the IncN (N-type) conjugation system
protein TraC as well as the P-type protein TrbJ and the
F-type protein TraE.
Length = 220
Score = 26.0 bits (57), Expect = 3.5
Identities = 4/39 (10%), Positives = 12/39 (30%)
Query: 21 TMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHK 59
++ N + M+ L+ + + K +
Sbjct: 31 SIANALAQAIEQMAALKTQYEQLSEQIEQYKQQYGSLTG 69
>gnl|CDD|118685 pfam10157, DUF2365, Uncharacterized conserved protein (DUF2365).
This is a family of conserved proteins found from
nematodes to humans. The function is unknown.
Length = 149
Score = 25.9 bits (57), Expect = 4.1
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 14 ELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHK 59
EL + V +L N LH +S ++TA N ++ Y + V K
Sbjct: 63 ELANSVDNLLENLGGLLHSIS----SLTADNVQT-----YRNAVDK 99
>gnl|CDD|99870 cd06117, Ec2MCS_like_1, Subgroup of Escherichia coli (Ec)
2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and
oxalacetate (OAA) to form 2-methylcitrate and coenzyme A
(CoA) during propionate metabolism. Citrate synthase
(CS) catalyzes the condensation of acetyl coenzyme A
(AcCoA) and OAA to form citrate and coenzyme A (CoA),
the first step in the citric acid cycle (TCA or Krebs
cycle). This group contains proteins similar to the E.
coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in
the gram-negative E. coli. EcPrpC is a dimeric (type I )
CS; it is induced during growth on propionate and
prefers PrCoA as a substrate, but has a partial CS
activity with AcCoA. This group also includes Salmonella
typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1
which are also induced during growth on propionate,
prefer PrCoA as substrate, but can also can use AcCoA.
Re 2-MCS1 at a low rate can use butyryl-CoA and
valeryl-CoA. A second Ralstonia eutropha 2MCS is also
found in this group, Re 2-MCS2, which is induced on
propionate. This group contains proteins which functions
exclusively as either a CS or a 2MCS, as well as those
with relaxed specificity which have dual functions as
both a CS and a 2MCS.
Length = 366
Score = 26.0 bits (57), Expect = 4.2
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 10 SMRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNS 45
S+R LP++V T L P HPM ++ L
Sbjct: 66 SLRG-LPANVKTALEQLPAAAHPMDVMRTGVSVLGC 100
>gnl|CDD|202483 pfam02952, Fucose_iso_C, L-fucose isomerase, C-terminal domain.
Length = 140
Score = 25.4 bits (56), Expect = 6.1
Identities = 6/31 (19%), Positives = 8/31 (25%)
Query: 1 MVFTSPNTGSMRAELPSHVVTMLNNFPNHLH 31
V T P + + N NH
Sbjct: 86 AVRTIPEWPQTWFKPDLTGDVLENGGANHGA 116
>gnl|CDD|237590 PRK14033, PRK14033, citrate synthase; Provisional.
Length = 375
Score = 25.3 bits (56), Expect = 7.4
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 18 HVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKL 77
V+++++ P HPM A++ L +E D E ++ L A L
Sbjct: 83 SVLSLIDKLPTTCHPMDVVRTAVSYLGAE--------DPEADDSSPEANLAKALRLFAVL 134
Query: 78 P-VVAA 82
P +VAA
Sbjct: 135 PTIVAA 140
>gnl|CDD|177899 PLN02257, PLN02257, phosphoribosylamine--glycine ligase.
Length = 434
Score = 25.1 bits (55), Expect = 8.4
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 4 TSPNTGSMRAELPSHVVT 21
T PNTG M A P+ V+T
Sbjct: 221 TGPNTGGMGAYSPAPVLT 238
>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases. Small GTP-binding proteins of the Ras
superfamily function as molecular switches in
fundamental events such as signal transduction,
cytoskeleton dynamics and intracellular trafficking.
Guanine-nucleotide-exchange factors (GEFs) positively
regulate these GTP-binding proteins in response to a
variety of signals. GEFs catalyze the dissociation of
GDP from the inactive GTP-binding proteins. GTP can then
bind and induce structural changes that allow
interaction with effectors.
Length = 237
Score = 24.9 bits (55), Expect = 9.7
Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 23/78 (29%)
Query: 7 NTGSMRAELPSHVVTM------LNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKS 60
RA L S + + LNNF + A ++AL+S + +
Sbjct: 69 TNPKKRARLLSKFIQVAKHCRELNNF-------NSLMAIVSALSSSP---------ISRL 112
Query: 61 KY-WEYVYEDSMDLIAKL 77
K WE + L +L
Sbjct: 113 KKTWEVLSSKLKKLFEEL 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
0.319 0.129 0.408
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,208,545
Number of extensions: 403076
Number of successful extensions: 347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 336
Number of HSP's successfully gapped: 37
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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: 53 (24.1 bits)