RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14238
(203 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 = 334 bits (859), Expect = e-115
Identities = 133/166 (80%), Positives = 147/166 (88%)
Query: 32 LKAVLAAKIPSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGLVCETSVLDPEEGIR 91
LK LA IP EQ R+K FRK +G T VGEVTVDM+YGGMRGIKGLV ETSVLDPEEGIR
Sbjct: 1 LKDRLAELIPKEQARIKKFRKEHGKTVVGEVTVDMVYGGMRGIKGLVWETSVLDPEEGIR 60
Query: 92 FRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVV 151
FRGLSIPECQK+LPKA GGEEPLPEGLFWLL+TG+VP++ QV ALSK WA+RA LPSHVV
Sbjct: 61 FRGLSIPECQKLLPKAPGGEEPLPEGLFWLLLTGEVPTKEQVSALSKEWAARAALPSHVV 120
Query: 152 TMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYI 197
TML+NFP +LHPMSQ SAAITALNSESKFAKAY +G+HKSKYWEY+
Sbjct: 121 TMLDNFPTNLHPMSQLSAAITALNSESKFAKAYAEGIHKSKYWEYV 166
>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 = 285 bits (730), Expect = 5e-96
Identities = 112/168 (66%), Positives = 131/168 (77%)
Query: 29 STDLKAVLAAKIPSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGLVCETSVLDPEE 88
DLK L KIP +QE+VK R +G +G +TVDM+YGGMRG+KGLV ETSVLDPEE
Sbjct: 1 DLDLKEQLKEKIPEQQEKVKKLRAEHGKVVLGNITVDMVYGGMRGMKGLVWETSVLDPEE 60
Query: 89 GIRFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPS 148
GIRFRGLSIPECQK+LPKAKGGEEPLPEGL WLL+TG VPSE QV ALS W +RA+LP
Sbjct: 61 GIRFRGLSIPECQKLLPKAKGGEEPLPEGLLWLLLTGKVPSEEQVDALSAEWRARADLPE 120
Query: 149 HVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEY 196
HV ++ P LHPM+QF+ A+ AL ES+FAKAY G+HK+KYWEY
Sbjct: 121 HVYKTIDALPVTLHPMAQFATAVMALQVESEFAKAYAKGIHKTKYWEY 168
>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 = 276 bits (707), Expect = 2e-92
Identities = 113/167 (67%), Positives = 138/167 (82%), Gaps = 1/167 (0%)
Query: 32 LKAVLAAKIPSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGLVCETSVLDPEEGIR 91
LK LA IP +Q R+K RK YG+TK+G++TVD + GGMRG+KGLV ETSVLDP+EGIR
Sbjct: 1 LKDKLAELIPKKQARIKELRKKYGNTKLGQITVDQVIGGMRGMKGLVYETSVLDPDEGIR 60
Query: 92 FRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVV 151
FRG +IPECQ++LPKA GG EPLPEGLFWLL+TG+VP+E QV LSK WA RAE+PSHVV
Sbjct: 61 FRGKTIPECQELLPKADGGGEPLPEGLFWLLLTGEVPTEEQVDELSKEWAKRAEVPSHVV 120
Query: 152 TMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDG-VHKSKYWEYI 197
M++N P +LHPM+Q SAAI AL SESKFAKAY +G ++K+ YWEY+
Sbjct: 121 KMIDNLPRNLHPMTQLSAAILALQSESKFAKAYAEGKINKTTYWEYV 167
>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 = 219 bits (559), Expect = 3e-70
Identities = 84/165 (50%), Positives = 112/165 (67%)
Query: 32 LKAVLAAKIPSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGLVCETSVLDPEEGIR 91
LK L IP+++E++K + YG T VG+V V + GGMRG+K ++ E SVLD EEGIR
Sbjct: 1 LKEALKEVIPAKREQLKKLKAEYGETVVGDVKVSNVLGGMRGLKSMLWEGSVLDAEEGIR 60
Query: 92 FRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVV 151
F G +IPECQK LPKA G E LPE + WLL+TG VP+ Q + LSK A R +LP ++
Sbjct: 61 FHGKTIPECQKELPKAPIGGEMLPESMLWLLLTGKVPTFEQARGLSKELAERGKLPHYIE 120
Query: 152 TMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEY 196
+L++ P LHPM+Q S + ALN +SKFA AY G+ K++YWE
Sbjct: 121 KLLDSLPKTLHPMTQLSIGVAALNHDSKFAAAYEKGIKKTEYWEP 165
>gnl|CDD|181961 PRK09569, PRK09569, type I citrate synthase; Reviewed.
Length = 437
Score = 190 bits (485), Expect = 5e-59
Identities = 72/167 (43%), Positives = 97/167 (58%), Gaps = 1/167 (0%)
Query: 32 LKAVLAAKIPSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGLVCETSVLDPEEGIR 91
LK L KI + R K +GS + EVT++ GG R I+ LV + S LDP+EGIR
Sbjct: 3 LKETLKQKIEEHRPRTTRLVKEFGSVVIDEVTIEQCIGGARDIRSLVTDISYLDPQEGIR 62
Query: 92 FRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVV 151
FRG +IPE + LPKA G E P E ++ L+TG+VP++ QVQ + W R +P +V+
Sbjct: 63 FRGKTIPETFEALPKAPGSEYPTVESFWYFLLTGEVPTQEQVQEVVAEWKKRQNVPQYVI 122
Query: 152 TMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDG-VHKSKYWEYI 197
+ P HPM S I A+ ESKFAK YN+G +K WEY+
Sbjct: 123 DAIRALPRDSHPMVMLSVGILAMQRESKFAKFYNEGKFNKMDAWEYM 169
>gnl|CDD|215250 PLN02456, PLN02456, citrate synthase.
Length = 455
Score = 171 bits (436), Expect = 2e-51
Identities = 54/180 (30%), Positives = 87/180 (48%), Gaps = 15/180 (8%)
Query: 18 SNFLRTFATDASTDLKAVLAAKIPSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGL 77
S L D ++ L+ P + ER+K + G +G TVD G R +
Sbjct: 20 SGSLTIVDNRTGKDYESPLSELGPVQAERLKKIKA--GKDDLGLKTVD---PGYRNTAPV 74
Query: 78 VCETSVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQAL 136
+ E S++D +EGI RFRG I E + P E + +LL+ G++P++ Q+
Sbjct: 75 LSEISLIDGDEGILRFRGYPIEELAEKSPF---------EEVAYLLLYGNLPTKEQLADW 125
Query: 137 SKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEY 196
+ +P HV+ +++ P+ HPM+Q + + AL++ S A AY G HK K WE
Sbjct: 126 EAELRQHSAVPEHVLDVIDALPHDAHPMTQLVSGVMALSTFSPDANAYLRGQHKYKSWEV 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 = 109 bits (275), Expect = 1e-28
Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 10/119 (8%)
Query: 69 GGMRGIKGLVCETSVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDV 127
G+ G+K S +D +EGI R+RG I E E+ E + +LL+ G +
Sbjct: 1 PGLEGVKAKETSISYIDGDEGILRYRGYDIEELA---------EKSSFEEVAYLLLYGKL 51
Query: 128 PSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYND 186
P++ ++ K AS LP HVV +L+ P + HPM A++AL S FA+ +
Sbjct: 52 PTKEELAEFKKKLASHRALPEHVVEILDLLPKNAHPMDVLRTAVSALGSFDPFARDKSP 110
>gnl|CDD|215837 pfam00285, Citrate_synt, Citrate synthase.
Length = 352
Score = 88.7 bits (221), Expect = 5e-21
Identities = 33/111 (29%), Positives = 57/111 (51%), Gaps = 10/111 (9%)
Query: 70 GMRGIKGLVCETSVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVP 128
G+ G+ E S +D E+GI R+RG I + + K+ E +LL+ G++P
Sbjct: 1 GLEGVVACETEISYIDGEKGILRYRGYDIEDLAE---KSS-----FEEVA-YLLLYGELP 51
Query: 129 SEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESK 179
+ +++ S A+R ELP V +++ P HPM+ AA++AL +
Sbjct: 52 TAEELEEFSSELAARRELPEDVKEVIDALPKDAHPMAVLRAAVSALAAYDP 102
>gnl|CDD|223449 COG0372, GltA, Citrate synthase [Energy production and conversion].
Length = 390
Score = 85.8 bits (213), Expect = 7e-20
Identities = 37/132 (28%), Positives = 62/132 (46%), Gaps = 15/132 (11%)
Query: 60 GEVTVDMMYGGMRGIKGLVCET--SVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPE 116
+V G+ G+ CET S +D + GI R+RG I + E+ E
Sbjct: 9 SDVGRFTYDPGLEGV--AACETAISYIDGDGGILRYRGYDIEDLA---------EKSSFE 57
Query: 117 GLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNS 176
+ +LL+ G++P++A++ A A+R LP V+ +L + P HPM+ A++AL S
Sbjct: 58 EVAYLLLYGELPTKAELAAFFAKLAARRTLPEQVIRLLESLPRDAHPMAVLRTAVSAL-S 116
Query: 177 ESKFAKAYNDGV 188
K +
Sbjct: 117 AFYPDKLDLNDR 128
>gnl|CDD|99855 cd06101, citrate_synt, 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 form
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. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 265
Score = 54.2 bits (131), Expect = 5e-09
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 10/64 (15%)
Query: 69 GGMRGIKGLVCETSVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDV 127
G+RG+ L E SV+D +EG R+RG I E E E + +LL+TG++
Sbjct: 1 PGLRGVAALESEISVIDGDEGGLRYRGYPIEELA---------ENSSFEEVAYLLLTGEL 51
Query: 128 PSEA 131
PS A
Sbjct: 52 PSYA 55
>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 = 52.6 bits (127), Expect = 2e-08
Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 25/129 (19%)
Query: 60 GEVTVDMMYGGMRGIKGLV-----------CETSV--LDPEEGI-RFRGLSIPECQKVLP 105
GE +D+ +R G+ CE+++ +D E+GI R+RG I + L
Sbjct: 9 GEKVIDI--SSLRKKTGVFTYDPGFMNTASCESAITYIDGEKGILRYRGYPIEQ----LA 62
Query: 106 KAKGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMS 165
+ E + +LL+ G++P+ Q+Q + + + N FP HPM+
Sbjct: 63 EKSSFLE-----VCYLLLYGELPTAEQLQEFREEITRHTLVHEQMKRFFNGFPRDAHPMA 117
Query: 166 QFSAAITAL 174
SA + AL
Sbjct: 118 ILSAMVNAL 126
>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 = 48.1 bits (115), Expect = 7e-07
Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 14/108 (12%)
Query: 70 GMRGIKGLVCETSV--LDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGD 126
G+ G+ + ET++ +D GI +RG I + L + EE + +LL+ G
Sbjct: 2 GLEGV--IAGETALSTIDGSGGILTYRGYDIED----LAEHASFEE-----VAYLLLHGK 50
Query: 127 VPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITAL 174
+P+ ++++ A LP V+ ++ P HPM A++ L
Sbjct: 51 LPTRSELRKFKTELAKLRGLPDEVIELIEALPAESHPMDVLRTAVSYL 98
>gnl|CDD|237069 PRK12349, PRK12349, citrate synthase 3; Provisional.
Length = 369
Score = 47.0 bits (112), Expect = 2e-06
Identities = 29/106 (27%), Positives = 45/106 (42%), Gaps = 13/106 (12%)
Query: 73 GIKGLV-CET--SVLDPEEG-IRFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVP 128
G+ G++ ET S LD +G I +G + E L K K + + LL+ +P
Sbjct: 8 GLDGVIAAETKISFLDTVKGEIVIQGYDLIE----LSKTKEYLD-----IVHLLLEEHLP 58
Query: 129 SEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITAL 174
+E + L K +P V +L P HPM ++AL
Sbjct: 59 NEDEKATLEKKLKEEYAVPEGVFNILKALPKETHPMDGLRTGVSAL 104
>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 = 45.1 bits (107), Expect = 8e-06
Identities = 29/106 (27%), Positives = 47/106 (44%), Gaps = 10/106 (9%)
Query: 70 GMRGIKGLVCETSVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVP 128
G+ G+ S +D + GI +RG I E L + EE + LL+ GD+P
Sbjct: 4 GLAGVPAAESSISYIDGKNGILEYRGYDIEE----LAEYSSFEE-----VALLLLDGDLP 54
Query: 129 SEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITAL 174
+ A+++ K + ++ M+ FP HPM A + AL
Sbjct: 55 TAAELEEFDKELRQHRRVKYNIRDMMKCFPETGHPMDMLQATVAAL 100
>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 = 44.2 bits (105), Expect = 1e-05
Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 14/108 (12%)
Query: 70 GMRGIKGLVCETSV--LDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGD 126
G+ G+ + ++ + +D + GI +RG I + L + EE +LL G+
Sbjct: 2 GLEGV--IAADSKISYIDGDAGILIYRGYDIHD----LAENSTFEEVA-----YLLWNGE 50
Query: 127 VPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITAL 174
+P+ ++ A A+ ELP+ ++ +L P HPM A++AL
Sbjct: 51 LPTAEELDAFKAQLAAERELPAEIIDLLKLLPKDAHPMDVLRTAVSAL 98
>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 = 41.3 bits (97), Expect = 2e-04
Identities = 28/100 (28%), Positives = 53/100 (53%), Gaps = 18/100 (18%)
Query: 82 SVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLF----WLLVTGDVPSEAQVQAL 136
S +D ++GI R+RG I EE + F +LL+ G++P+++Q+
Sbjct: 40 SYIDGDKGILRYRGYPI-------------EELAEKSTFLEVAYLLIYGNLPTKSQLSDW 86
Query: 137 SKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNS 176
+ + +P+ V+ M+ +FP+ HPM +AI+AL++
Sbjct: 87 EFAVSQHTAVPTGVLDMIKSFPHDAHPMGMLVSAISALSA 126
>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 = 40.1 bits (94), Expect = 3e-04
Identities = 28/102 (27%), Positives = 52/102 (50%), Gaps = 12/102 (11%)
Query: 78 VCETSV--LDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVPSEAQVQ 134
VCE+S+ +D ++GI +RG I + L ++ EE +LL+ G++P++ Q
Sbjct: 14 VCESSITYIDGDKGILLYRGYPIEQ----LAESSTYEEVA-----YLLLWGELPTQEQYD 64
Query: 135 ALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNS 176
+ + +P V ++ FP HPM A ++AL++
Sbjct: 65 EFQRRLSEHMMVPESVHRLIQTFPRDAHPMGILCAGLSALSA 106
>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 = 37.4 bits (87), Expect = 0.003
Identities = 17/62 (27%), Positives = 35/62 (56%)
Query: 116 EGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALN 175
E + +LL G++P+ AQ+ S+ S L ++++++ + P + HPM A++ L
Sbjct: 40 EEVAYLLWNGELPNAAQLAEFSQRERSYRRLDRNLLSLIASLPKNCHPMDVLRTAVSVLG 99
Query: 176 SE 177
+E
Sbjct: 100 AE 101
>gnl|CDD|184467 PRK14034, PRK14034, citrate synthase; Provisional.
Length = 372
Score = 37.1 bits (86), Expect = 0.004
Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 116 EGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFP-NHLHPMSQFSAAITAL 174
E + +LL +P++ ++ + + A++P ++ L + +HPMS AI+ L
Sbjct: 42 EEVVYLLWHRKLPNKQELAEFKEQLSENAKVPGEIIEHLKQYDLKKVHPMSVLRTAISML 101
>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 = 34.1 bits (78), Expect = 0.037
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 116 EGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALN 175
E + LLV G +P+++++ A S LP++V T L P HPM ++ L
Sbjct: 40 EEVAHLLVHGKLPTKSELAAYKTKLKSLRGLPANVKTALEQLPAAAHPMDVMRTGVSVLG 99
Query: 176 S 176
Sbjct: 100 C 100
>gnl|CDD|237591 PRK14036, PRK14036, citrate synthase; Provisional.
Length = 377
Score = 33.8 bits (78), Expect = 0.041
Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 10/106 (9%)
Query: 70 GMRGIKGLVCETSVLDPEEGI-RFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDVP 128
G+ G+ S +D ++GI +RG I E L + E +LL+ G++P
Sbjct: 7 GLEGVPATQSSISYVDGQKGILEYRGYPIEE----LAEKSSFLETA-----YLLIWGELP 57
Query: 129 SEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITAL 174
+ +++ + + + M+ FP HPM A+ AL
Sbjct: 58 TAEELEEFEQEVRMHRRVKYRIRDMMKCFPETGHPMDALQASAAAL 103
>gnl|CDD|180164 PRK05614, gltA, type II citrate synthase; Reviewed.
Length = 419
Score = 32.2 bits (74), Expect = 0.16
Identities = 33/142 (23%), Positives = 52/142 (36%), Gaps = 29/142 (20%)
Query: 41 PSEQERVKNFRKNYGSTKVGEVTVDMMYGGMRGIKGLVCETSV--LDPEEGI-RFRGLSI 97
+ V + RK YGST G T D + CE+ + +D ++GI +RG I
Sbjct: 24 GTLGPDVIDIRKLYGST--GYFTYDPGFTSTAS-----CESKITYIDGDKGILLYRGYPI 76
Query: 98 PECQKVLPKAKGGEEPLPE-GLF----WLLVTGDVPSEAQVQALSKSWASRAELPSHVVT 152
E L E F +LL+ G++P+ Q + + +
Sbjct: 77 --------------EQLAEKSDFLEVCYLLLYGELPTAEQKAEFDTTVTRHTMVHEQLKR 122
Query: 153 MLNNFPNHLHPMSQFSAAITAL 174
F HPM+ + AL
Sbjct: 123 FFRGFRRDAHPMAVLCGVVGAL 144
>gnl|CDD|237590 PRK14033, PRK14033, citrate synthase; Provisional.
Length = 375
Score = 31.8 bits (73), Expect = 0.20
Identities = 16/62 (25%), Positives = 34/62 (54%)
Query: 116 EGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALN 175
E + +LL G++P++A++ S+ + L V+++++ P HPM A++ L
Sbjct: 50 EEVAYLLWNGELPTDAELALFSQRERAYRRLDRSVLSLIDKLPTTCHPMDVVRTAVSYLG 109
Query: 176 SE 177
+E
Sbjct: 110 AE 111
>gnl|CDD|193129 pfam12652, CotJB, CotJB protein. CotJ is a sigma E-controlled
operon involved in the spore coat of Bacillus subtilis.
This protein has been identified as a spore coat
protein.
Length = 78
Score = 29.4 bits (67), Expect = 0.31
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 154 LNNFPNHLHPMSQFSAAITALN-SESKFAKAY----NDGVHKSKY-WEYIQQPLP 202
L+ P+ + ++ + ++ K Y N GV S Y W +I+ P P
Sbjct: 22 LDTHPDDQEALEYYNEYSAKRKQLKKEYEKQYGPLTNFGVSPSTYPWAWIEGPWP 76
>gnl|CDD|99862 cd06109, BsCS-I_like, Bacillus subtilis (Bs) citrate synthase
CS-I_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 coenzyme A (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. This group contains proteins
similar to BsCS-I, one of two CS isozymes in the
gram-positive B. subtilis. The majority of CS activity
in B. subtilis is provided by the other isozyme, BsCS-II
(not included in this group). BsCS-I has a lower
catalytic activity than BsCS-II, and has a Glu in place
of a key catalytic Asp residue. This change is conserved
in other members of this group. For E. coli CS (not
included in this group), site directed mutagenesis of
the key Asp residue to a Glu converts the enzyme into
citryl-CoA lyase which cleaves citryl-CoA to AcCoA and
OAA. A null mutation in the gene encoding BsCS-I (citA)
had little effect on B. subtilis CS activity or on
sporulation. However, disruption of the citA gene in a
strain null for the gene encoding BsCS-II resulted in a
sporulation deficiency, a characteristic of strains
defective in the Krebs cycle. 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. Many of the
gram-negative species represented in this group have a
second CS isozyme which is in another group.
Length = 349
Score = 31.1 bits (71), Expect = 0.36
Identities = 29/116 (25%), Positives = 45/116 (38%), Gaps = 14/116 (12%)
Query: 72 RGIKGLVCETSVL---DPEEG-IRFRGLSIPECQKVLPKAKGGEEPLPEGLFWLLVTGDV 127
G++G+V +VL D E G + RG S+ + L + E+ LL G
Sbjct: 1 PGLEGVVAAETVLSDVDGEAGRLIIRGYSVED----LAGSASFEDVA-----ALLWNGFF 51
Query: 128 PSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKA 183
P +++ + A+ LP V +L L PM A + L A A
Sbjct: 52 PDLPELEEFRAALAAARALPDVVAALLPAL-AGLDPMDALRALLALLPDSPDLATA 106
>gnl|CDD|133434 cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA-
and pagL-like glycosidases. Bacillus subtilis GlvA and
Clostridium acetobutylicum pagL are
6-phospho-alpha-glucosidase, catalyzing the hydrolysis
of alpha-glucopyranoside bonds to release glucose from
oligosaccharides. The substrate specificities of other
members of this subgroup are unknown. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP_PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases, which
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. Members of this
subfamily are part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 437
Score = 30.3 bits (69), Expect = 0.57
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 108 KGGEEPLPEGLFWLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHL 161
K GE+ LP+ + G +P ++ + SW + M+ +FP++L
Sbjct: 206 KQGEDLLPKLREHVKENGYLPPDSDEEHRDPSWNDTFA---NAKDMMADFPDYL 256
>gnl|CDD|183463 PRK12351, PRK12351, methylcitrate synthase; Provisional.
Length = 378
Score = 29.5 bits (67), Expect = 1.2
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 121 LLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPM 164
LLV G +P++A++ A + LP+ V T+L P HPM
Sbjct: 54 LLVHGKLPTQAELAAYKTKLKALRGLPAAVKTVLEAIPAAAHPM 97
>gnl|CDD|213231 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
system, ATPase component. The biological function of
this family is not well characterized, but display ABC
domains similar to members of ABCA subfamily. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 211
Score = 28.7 bits (65), Expect = 1.8
Identities = 19/40 (47%), Positives = 22/40 (55%), Gaps = 13/40 (32%)
Query: 69 GGMR---GI-KGLVCETSV---------LDPEEGIRFRGL 95
GGMR GI + LV + S+ LDPEE IRFR L
Sbjct: 133 GGMRRRVGIAQALVGDPSILIVDEPTAGLDPEERIRFRNL 172
>gnl|CDD|99861 cd06108, Ec2MCS_like, 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 though it has 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 and prefer PrCoA as
substrate, but can also use AcCoA. Re 2-MCS1 can use
butyryl-CoA and valeryl-CoA at a lower rate. A second
Ralstonia eutropha 2MCS, Re 2-MCS2, which is induced on
propionate is also found in this group. This group may
include proteins which may function exclusively as a CS,
those which may function exclusively as a 2MCS, or those
with dual specificity which functions as both a CS and a
2MCS.
Length = 363
Score = 28.4 bits (64), Expect = 2.8
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 120 WLLVTGDVPSEAQVQALSKSWASRAELPSHVVTMLNNFPNHLHPMSQF---SAAITALNS 176
+LL+ G +P+ Q+ A + LP+ + T+L P HPM + + L
Sbjct: 44 YLLLYGKLPTRKQLDAYKTKLVALRRLPAALKTVLELIPKDSHPMDVMRTGCSMLGCLEP 103
Query: 177 ESKFAKAYN 185
E++F++ Y
Sbjct: 104 ENEFSQQYE 112
>gnl|CDD|183964 PRK13307, PRK13307, bifunctional formaldehyde-activating
enzyme/3-hexulose-6-phosphate synthase; Provisional.
Length = 391
Score = 27.3 bits (61), Expect = 7.1
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 8 ARSVADLHQISNFLRTFATDASTDLKAVLAAKI-PSEQERVKNFRKNYGSTK 58
A++VAD + D + DL V + I P+ ++ K ++ NYG+TK
Sbjct: 87 AKAVADAVEEG----IIPKDKAEDLVIVASVFIHPTAKDYNKIYQYNYGATK 134
>gnl|CDD|221157 pfam11651, P22_CoatProtein, P22 coat protein - gene protein 5.
This family of proteins represents gene product 5 from
bacteriophage P22. This protein is involved in the
formation of the pro-capsid shells in the bacteriophage.
In total, there are 415 molecules of the coat protein
which are arranged in an icosahedral shell.
Length = 413
Score = 27.1 bits (60), Expect = 8.3
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 11/40 (27%)
Query: 55 GSTKVGEVTVDMMYGGMRGIKGLVCETSVLDPEEGIRFRG 94
G T V + +D++YG L PE G+R G
Sbjct: 385 GKTDVDKTRIDILYG-----------VKALRPELGVRLAG 413
>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 = 26.8 bits (59), Expect = 8.4
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 131 AQVQALSKSWASRAELP-SHVVTMLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVH 189
A AL+ + A+ A +P + ++ N + M+ L+ + + K +
Sbjct: 9 ALTAALAAASAAVAGIPVTDPASIANALAQAIEQMAALKTQYEQLSEQIEQYKQQYGSLT 68
Query: 190 K 190
Sbjct: 69 G 69
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 26.8 bits (59), Expect = 9.6
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 167 FSAAITALNSESKFAKAYNDGVHKSK-YWEYIQQPL 201
FS + L+S KF ++D +H S W +Q+ L
Sbjct: 1258 FSDLLPILSSSQKFVSIFHDIMHGSDISWRILQKKL 1293
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
0.316 0.131 0.386
Gapped
Lambda K H
0.267 0.0821 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,088,836
Number of extensions: 901327
Number of successful extensions: 848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 836
Number of HSP's successfully gapped: 42
Length of query: 203
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 111
Effective length of database: 6,857,034
Effective search space: 761130774
Effective search space used: 761130774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.6 bits)