RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14237
(360 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 = 658 bits (1699), Expect = 0.0
Identities = 252/307 (82%), Positives = 279/307 (90%), Gaps = 1/307 (0%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
ML+NFP +LHPMSQ SAAITALNSESKFAKAY +G+HKSKYWEYVYEDSMDLIAKLP VA
Sbjct: 122 MLDNFPTNLHPMSQLSAAITALNSESKFAKAYAEGIHKSKYWEYVYEDSMDLIAKLPCVA 181
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLYLTIHSDHEGGNVSAH 120
A IYRN ++GGK I AID+N DWSANF +MLG+ + QFTELMRLYLTIHSDHEGGNVSAH
Sbjct: 182 AKIYRNLYRGGK-IIAIDSNLDWSANFANMLGYTDPQFTELMRLYLTIHSDHEGGNVSAH 240
Query: 121 TVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFIW 180
T HLVGSALSDPYLSFAA MNGLAGPLHGLANQEVL+WL KLQ++VG +VS+E+L+E++W
Sbjct: 241 TTHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTKLQKEVGKDVSDEQLREYVW 300
Query: 181 NTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIETGK 240
TL SG+VVPGYGHAVLRKTDPRYTCQREFA KHLP+D LFKLVSQ+YK+VPPVL E GK
Sbjct: 301 KTLNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLPNDPLFKLVSQLYKIVPPVLTEQGK 360
Query: 241 VKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKSLS 300
KNPWPNVDAHSGVLLQYYGL EMNYYTVLFGVSRALGVL+ LIWDRALGLP+ERPKS+S
Sbjct: 361 AKNPWPNVDAHSGVLLQYYGLTEMNYYTVLFGVSRALGVLSQLIWDRALGLPLERPKSVS 420
Query: 301 TNDLVKQ 307
T+ L K
Sbjct: 421 TDGLEKL 427
>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 = 573 bits (1480), Expect = 0.0
Identities = 225/302 (74%), Positives = 266/302 (88%), Gaps = 1/302 (0%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDG-VHKSKYWEYVYEDSMDLIAKLPVV 59
M++N P +LHPM+Q SAAI AL SESKFAKAY +G ++K+ YWEYVYED+MDLIAKLPVV
Sbjct: 122 MIDNLPRNLHPMTQLSAAILALQSESKFAKAYAEGKINKTTYWEYVYEDAMDLIAKLPVV 181
Query: 60 AATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLYLTIHSDHEGGNVSA 119
AA IYR ++ G IGAID+ DWSANF MLG+++ +FT+LMRLYLT+HSDHEGGNVSA
Sbjct: 182 AAKIYRRKYRKGGEIGAIDSKLDWSANFAHMLGYEDEEFTDLMRLYLTLHSDHEGGNVSA 241
Query: 120 HTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFI 179
HT HLVGSALSDPYLSF+A +NGLAGPLHGLANQEVL WL K+Q+++G +VS+E+L+++I
Sbjct: 242 HTSHLVGSALSDPYLSFSAALNGLAGPLHGLANQEVLKWLLKMQKELGKDVSDEELEKYI 301
Query: 180 WNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIETG 239
W+TL SG+VVPGYGHAVLRKTDPR+TCQREFA KHLPDD LFKLV+Q YK++P VL E G
Sbjct: 302 WDTLNSGRVVPGYGHAVLRKTDPRFTCQREFALKHLPDDPLFKLVAQCYKIIPGVLKEHG 361
Query: 240 KVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKSL 299
KVKNP+PNVDAHSGVLLQ+YG+ E YYTVLFGVSRALGVLA L+W RALGLPIERPKS+
Sbjct: 362 KVKNPYPNVDAHSGVLLQHYGMTEPQYYTVLFGVSRALGVLAQLVWSRALGLPIERPKSM 421
Query: 300 ST 301
ST
Sbjct: 422 ST 423
>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 = 544 bits (1403), Expect = 0.0
Identities = 225/304 (74%), Positives = 259/304 (85%), Gaps = 1/304 (0%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
++ P LHPM+QF+ A+ AL ES+FAKAY G+HK+KYWEY YEDSMDLIAKLP VA
Sbjct: 125 TIDALPVTLHPMAQFATAVMALQVESEFAKAYAKGIHKTKYWEYTYEDSMDLIAKLPTVA 184
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLYLTIHSDHEGGNVSAH 120
A IYRN ++ G+ I +ID +KD+SANF MLG+D+ F ELMRLYLTIHSDHEGGNVSAH
Sbjct: 185 AYIYRNMYKDGQSI-SIDDSKDYSANFAHMLGYDSPSFQELMRLYLTIHSDHEGGNVSAH 243
Query: 121 TVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFIW 180
T HLVGSALSDPYLSFAA +NGLAGPLHGLANQEVL+WLK + + G+NV++E+LK++IW
Sbjct: 244 TGHLVGSALSDPYLSFAAALNGLAGPLHGLANQEVLLWLKSVVSECGENVTKEQLKDYIW 303
Query: 181 NTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIETGK 240
TL SG+VVPGYGHAVLRKTDPRY CQREFA KHLPDD LFKLVS +YK+VP +L E GK
Sbjct: 304 KTLNSGKVVPGYGHAVLRKTDPRYICQREFALKHLPDDPLFKLVSNLYKIVPGILTELGK 363
Query: 241 VKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKSLS 300
VKNPWPNVDAHSGVLLQYYGL E YYTVLFGVSRALG+L+ LIWDRALGLP+ERPKS+S
Sbjct: 364 VKNPWPNVDAHSGVLLQYYGLTEARYYTVLFGVSRALGILSQLIWDRALGLPLERPKSVS 423
Query: 301 TNDL 304
T L
Sbjct: 424 TEWL 427
>gnl|CDD|181961 PRK09569, PRK09569, type I citrate synthase; Reviewed.
Length = 437
Score = 463 bits (1192), Expect = e-163
Identities = 176/303 (58%), Positives = 226/303 (74%), Gaps = 4/303 (1%)
Query: 6 PNHLHPMSQFSAAITALNSESKFAKAYNDG-VHKSKYWEYVYEDSMDLIAKLPVVAATIY 64
P HPM S I A+ ESKFAK YN+G +K WEY+YED+ DL+A++PV+AA IY
Sbjct: 129 PRDSHPMVMLSVGILAMQRESKFAKFYNEGKFNKMDAWEYMYEDASDLVARIPVIAAYIY 188
Query: 65 RNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLYLTIHSDHEGGNVSAHTVHL 124
++G K I D D+ ANF M+G + ++ R+Y +HSDHE GNVSAHT HL
Sbjct: 189 NLKYKGDKQI-PSDPELDYGANFAHMIGQPK-PYKDVARMYFILHSDHESGNVSAHTTHL 246
Query: 125 VGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGD-NVSEEKLKEFIWNTL 183
V SALSD Y S++AG+NGLAGPLHGLANQEVL W+++ Q+++G ++E++++ +W+TL
Sbjct: 247 VASALSDAYYSYSAGLNGLAGPLHGLANQEVLGWIQQFQEKLGGEEPTKEQVEQALWDTL 306
Query: 184 KSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIETGKVKN 243
+GQV+PGYGHAVLRKTDPRYT QREF KHLPDD LFKLV+ +++V P VL E GK KN
Sbjct: 307 NAGQVIPGYGHAVLRKTDPRYTAQREFCLKHLPDDPLFKLVAMIFEVAPGVLTEHGKTKN 366
Query: 244 PWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKSLSTND 303
PWPNVDA SGV+ YYG+KE ++YTVLFGV RALGV+A++ WDR LG IERPKS++T
Sbjct: 367 PWPNVDAQSGVIQWYYGVKEWDFYTVLFGVGRALGVMANITWDRGLGYAIERPKSVTTEM 426
Query: 304 LVK 306
L K
Sbjct: 427 LEK 429
>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 = 451 bits (1161), Expect = e-158
Identities = 183/307 (59%), Positives = 234/307 (76%), Gaps = 3/307 (0%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
+L++ P LHPM+Q S + ALN +SKFA AY G+ K++YWE EDS++LIA+LP +A
Sbjct: 122 LLDSLPKTLHPMTQLSIGVAALNHDSKFAAAYEKGIKKTEYWEPTLEDSLNLIARLPALA 181
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGF-DNHQFTELMRLYLTIHSDHEGGNVSA 119
A IYRN + G G+G ID DWS NFTSMLG+ DN F +L+RLY+ +H DHEGGNVSA
Sbjct: 182 ARIYRNVYGEGHGLGKIDPEVDWSYNFTSMLGYGDNLDFVDLLRLYIALHGDHEGGNVSA 241
Query: 120 HTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFI 179
HT HLVGSALSDPYLS++AG+ GLAGPLHGLA QEVL W+ ++Q+ +G +++ +++++
Sbjct: 242 HTTHLVGSALSDPYLSYSAGLMGLAGPLHGLAAQEVLRWILEMQKNIGSKATDQDIRDYL 301
Query: 180 WNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKH--LPDDSLFKLVSQVYKVVPPVLIE 237
W TLKSG+VVPGYGHAVLRK DPR+T EFAQ L +D + +LV ++ ++ P VL E
Sbjct: 302 WKTLKSGRVVPGYGHAVLRKPDPRFTALMEFAQTRPELENDPVVQLVQKLSEIAPGVLTE 361
Query: 238 TGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPK 297
GK KNP+PNVDA SGVL +YG++E YYTV+FGVSRALG L L+WDR LGLPIERPK
Sbjct: 362 HGKTKNPFPNVDAASGVLFYHYGIREFLYYTVIFGVSRALGPLTQLVWDRILGLPIERPK 421
Query: 298 SLSTNDL 304
SLS L
Sbjct: 422 SLSLEGL 428
>gnl|CDD|215250 PLN02456, PLN02456, citrate synthase.
Length = 455
Score = 419 bits (1079), Expect = e-145
Identities = 139/328 (42%), Positives = 190/328 (57%), Gaps = 27/328 (8%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
+++ P+ HPM+Q + + AL++ S A AY G HK K WE ED + LI KLP +A
Sbjct: 142 VIDALPHDAHPMTQLVSGVMALSTFSPDANAYLRGQHKYKSWEVRDEDIVRLIGKLPTLA 201
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGF-------DNHQFTELMRLYLTIHSDHE 113
A IYR + G+G D + D++ NF MLG + + L+ LY IH+DHE
Sbjct: 202 AAIYRRMY--GRGPVIPDNSLDYAENFLYMLGSLGDRSYKPDPRLARLLDLYFIIHADHE 259
Query: 114 GGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEE 173
GG +A HLVGS+ DPY S AAG+N LAGPLHG AN+ VL L +++G + E
Sbjct: 260 GGCSTAAARHLVGSSGVDPYTSVAAGVNALAGPLHGGANEAVLKML----KEIG---TVE 312
Query: 174 KLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQ---KHLPDDSLFKLVSQVYKV 230
+ E++ S +V+PG+GH V + DPR C REFA KH+ DD LFK+ S + +V
Sbjct: 313 NIPEYVEGVKNSKKVLPGFGHRVYKNYDPRAKCIREFALEVFKHVGDDPLFKVASALEEV 372
Query: 231 VPPVLIETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALG 290
+L E KV+ +PNVD +SGVLL+ G E ++TVLF VSRA G L+ WD ALG
Sbjct: 373 A--LLDEYFKVRKLYPNVDFYSGVLLRALGFPE-EFFTVLFAVSRAAGYLSQ--WDEALG 427
Query: 291 LPIER---PKSLSTNDLVKQYSKIKSTP 315
LP ER PK + T + ++ Y
Sbjct: 428 LPDERIMRPKQVYTGEWLRHYCPKAERT 455
>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 = 310 bits (797), Expect = e-104
Identities = 109/305 (35%), Positives = 162/305 (53%), Gaps = 28/305 (9%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
+L+ P + HPM A++AL S FA+ K E YE ++ LIAKLP +A
Sbjct: 77 ILDLLPKNAHPMDVLRTAVSALGSFDPFAR--------DKSPEARYEKAIRLIAKLPTIA 128
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFD--NHQFTELMRLYLTIHSDHEGGNVS 118
A IYRN G I A D + ++ NF ML + + + + M L L +H+DHEG N S
Sbjct: 129 ANIYRNR--EGLEIIAPDPDLSYAENFLYMLFGEEPDPEEAKAMDLALILHADHEG-NAS 185
Query: 119 AHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEF 178
T +V S LSD Y + AA + L GPLHG AN+ VL K+ ++G + E ++ +
Sbjct: 186 TFTARVVASTLSDMYSAIAAAIAALKGPLHGGANEAVL----KMLLEIG---TPENVEAY 238
Query: 179 IWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLP---DDSLFKLVSQVYKVVPPVL 235
IW L + + + G+GH V + DPR +E A++ DD LF++ ++ ++ VL
Sbjct: 239 IWKKLANKRRIMGFGHRVYKTYDPRAKILKELAEELAEEKGDDKLFEIAEELEEIALEVL 298
Query: 236 IETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIER 295
E K +PNVD +SGV+ + G +T LF VSRA+G LA +I R + R
Sbjct: 299 GE----KGIYPNVDFYSGVVYKALGF-PTELFTPLFAVSRAVGWLAHIIEYRENNQRLIR 353
Query: 296 PKSLS 300
P++
Sbjct: 354 PRAEY 358
>gnl|CDD|215837 pfam00285, Citrate_synt, Citrate synthase.
Length = 352
Score = 305 bits (785), Expect = e-102
Identities = 101/301 (33%), Positives = 151/301 (50%), Gaps = 29/301 (9%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
+++ P HPM+ AA++AL + + E V ED++ LIAKLP +
Sbjct: 76 VIDALPKDAHPMAVLRAAVSALAAYDPMLY--------DESPEDVLEDAIRLIAKLPTIV 127
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLG--FDNHQFTELMRLYLTIHSDHEGGNVS 118
A IYR+ G A D + ++ NF ML + + + L L +H+DHE N S
Sbjct: 128 AAIYRHRK--GLPPIAPDPDLSYAENFLYMLFGEEPDPEEARALDLALILHADHEL-NAS 184
Query: 119 AHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEF 178
T +V S LSD Y + +A + L GPLHG AN+ VL L+++ S E ++E+
Sbjct: 185 TFTARVVASTLSDLYSAISAAIGALKGPLHGGANEAVLRMLEEIG-------SPENVEEY 237
Query: 179 IWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQ---KHLPDDSLFKLVSQVYKVVPPVL 235
I L G+ + G+GH V + DPR ++FA+ L DD L ++ ++ +V L
Sbjct: 238 IEKALDKGERLMGFGHRVYKTYDPRAKILKKFARELAAELGDDPLLEIAEKIEEVALEDL 297
Query: 236 IETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIER 295
E K +PNVD +SGVL G+ +T LF VSR +G LA +I R + R
Sbjct: 298 KE----KKLYPNVDFYSGVLYYALGIPT-ELFTPLFAVSRVVGWLAHIIEQRE-NNKLIR 351
Query: 296 P 296
P
Sbjct: 352 P 352
>gnl|CDD|223449 COG0372, GltA, Citrate synthase [Energy production and conversion].
Length = 390
Score = 276 bits (709), Expect = 9e-91
Identities = 96/317 (30%), Positives = 151/317 (47%), Gaps = 23/317 (7%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
+L + P HPM+ A++AL S K + E ++ LIAKLP +A
Sbjct: 94 LLESLPRDAHPMAVLRTAVSAL-SAFYPDKLDLNDR---------REAALRLIAKLPTIA 143
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQ---FTELMRLYLTIHSDHEGGNV 117
A +YR + G+ A D + ++ NF ML + M L +H+DHE N
Sbjct: 144 AAVYRYSR--GEPPIAPDPDLSYAENFLYMLFGEPPSPPVEARAMDRALILHADHEL-NA 200
Query: 118 SAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKE 177
S T +V S SD Y AAG+ L GPLHG AN+ V+ L +++G S E +
Sbjct: 201 STFTARVVASTGSDLYACIAAGIGALKGPLHGGANEAVMKML----EEIGS--SGESAEA 254
Query: 178 FIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIE 237
++ L + + G+GH V + DPR +E A+K + KL ++ L +
Sbjct: 255 YVRKALDRKERIMGFGHRVYKNYDPRAKVLKELAEKLGKELGDLKLYEIAEELEEIALED 314
Query: 238 TGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPK 297
G K +PNVD +SG++ + G+ + +T LF ++R +G +A I + G I RP+
Sbjct: 315 LGFEKKLYPNVDFYSGIVYRALGIPT-DMFTPLFAIARTVGWIAHWIEQKEDGNKIIRPR 373
Query: 298 SLSTNDLVKQYSKIKST 314
+L T + Y I+
Sbjct: 374 ALYTGPEERDYVPIEER 390
>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 = 250 bits (641), Expect = 3e-82
Identities = 92/224 (41%), Positives = 131/224 (58%), Gaps = 16/224 (7%)
Query: 82 DWSANFTSMLGFD--NHQFTELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAG 139
++ NF MLG + + +F + M L L +H+DHEG N S T +VGS LSDPY + AA
Sbjct: 53 SYAENFLYMLGGEEPDPEFAKAMDLALILHADHEG-NASTFTARVVGSTLSDPYSAIAAA 111
Query: 140 MNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRK 199
+ L GPLHG AN+ VL K+ +++G + E + +I L S +V+ G+GH V +K
Sbjct: 112 IAALKGPLHGGANEAVL----KMLEEIGTPKN-EPAEAYIRKKLNSKRVLMGFGHRVYKK 166
Query: 200 TDPRYTCQREFAQKHLP---DDSLFKLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLL 256
DPR T ++FA+K L D +F+L +++ K+ P VL E K +PNVD +SGVL
Sbjct: 167 YDPRATVLKKFAEKLLKEKGLDPMFELAAELEKIAPEVLYE----KKLYPNVDFYSGVLY 222
Query: 257 QYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKSLS 300
+ G +T LF VSRA+G LA LI R G I RP++
Sbjct: 223 KAMGF-PTELFTPLFAVSRAVGWLAHLIEQREDGQRIIRPRAEY 265
>gnl|CDD|99853 cd06099, CS_ACL-C_CCL, Citrate synthase (CS), citryl-CoA lyase
(CCL), the C-terminal portion of the single-subunit type
ATP-citrate lyase (ACL) and the C-terminal portion of
the large subunit of the two-subunit type ACL. CS
catalyzes the condensation of acetyl coenzyme A (AcCoA)
and oxalacetate (OAA) from 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. Some CS proteins function 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.
CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs
catalyze an ATP- and a CoA- dependant cleavage of
citrate to form AcCoA and OAA; they do this in a
multistep reaction, the final step of which is likely to
involve the cleavage of CiCoA to generate AcCoA and OAA.
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 CiCoA, and c) the
hydrolysis of CiCoA to produce citrate and CoA. 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. 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. In fungi, yeast,
plants, and animals ACL is cytosolic and generates AcCoA
for lipogenesis. In several groups of autotrophic
prokaryotes and archaea, ACL carries out the
citrate-cleavage reaction of the reductive tricarboxylic
acid (rTCA) cycle. In the family Aquificaceae this
latter reaction in the rTCA cycle is carried out via a
two enzyme system the second enzyme of which is CCL.
Length = 213
Score = 241 bits (616), Expect = 4e-79
Identities = 88/224 (39%), Positives = 128/224 (57%), Gaps = 16/224 (7%)
Query: 82 DWSANFTSMLGFD--NHQFTELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAG 139
++ NF MLG + + +F M L L +H+DHEG N S T +VGS SDPY + AA
Sbjct: 1 SYAENFLYMLGGEEPDPEFARAMDLALILHADHEG-NASTFTARVVGSTGSDPYSAIAAA 59
Query: 140 MNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRK 199
+ L GPLHG AN+ VL K+ +++G + E + +I L+S +V+ G+GH V +K
Sbjct: 60 IGALKGPLHGGANEAVL----KMLEEIGTPKN-EPAEAYIRKKLESKRVIMGFGHRVYKK 114
Query: 200 TDPRYTCQREFAQKHLP---DDSLFKLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLL 256
DPR T ++FA++ L DD +F+L +++ K+ VL E K +PNVD +SGVL
Sbjct: 115 YDPRATVLKKFAEELLKEDGDDPMFELAAELEKIAEEVLYE----KKLYPNVDFYSGVLY 170
Query: 257 QYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKSLS 300
+ G +T LF V+RA+G LA LI I RP+S
Sbjct: 171 KAMGF-PTELFTPLFAVARAVGWLAHLIEQLEDNFKIIRPRSEY 213
>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 = 126 bits (319), Expect = 5e-33
Identities = 98/324 (30%), Positives = 152/324 (46%), Gaps = 52/324 (16%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
N FP HPM+ SA + AL++ + ND E ++ LIAK+P +A
Sbjct: 105 FFNGFPRDAHPMAILSAMVNALSAFYPDSLDVNDP-------EQRELAAIRLIAKVPTIA 157
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWS--ANFTSMLGFD--------NHQFTELMRLYLTIHS 110
A YR + G I + D S NF M+ F + + + L +H+
Sbjct: 158 AMAYRYS----IGQPFIYPDNDLSYVENFLHMM-FAVPYEPYEVDPVVVKALDTILILHA 212
Query: 111 DHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNV 170
DHE N S TV +VGS+ ++ + S +AG+ L GPLHG AN+ VL L+++ NV
Sbjct: 213 DHEQ-NASTSTVRMVGSSGANLFASISAGIAALWGPLHGGANEAVLEMLEEIGSV--GNV 269
Query: 171 SE--EKLKEFIWNTLKSGQV-VPGYGHAVLRKTDPRYTCQREFAQKHLP----DDSLFKL 223
+ K K+ K+ + G+GH V + DPR ++ + L DD L ++
Sbjct: 270 DKYIAKAKD------KNDPFRLMGFGHRVYKNYDPRAKILKKTCDEVLAELGKDDPLLEI 323
Query: 224 VSQVYKVV--PPVLIETGKVKNPWPNVDAHSGVLLQYYGL-KEMNYYTVLFGVSRALGVL 280
++ ++ IE + +PNVD +SG++L+ G+ EM +TVLF + R G +
Sbjct: 324 AMELEEIALKDDYFIE----RKLYPNVDFYSGIILRALGIPTEM--FTVLFALGRTPGWI 377
Query: 281 ASLIWDRAL---GLPIERPKSLST 301
A W L I RP+ L T
Sbjct: 378 AQ--WREMHEDPELKIGRPRQLYT 399
>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 = 124 bits (312), Expect = 2e-32
Identities = 87/320 (27%), Positives = 147/320 (45%), Gaps = 34/320 (10%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
M+ FP HPM A + AL + +Y+ ++ LIAK+P +
Sbjct: 79 MMKCFPETGHPMDMLQATVAALGMFYPKPEVLKPNP------DYIDAATVKLIAKMPTLV 132
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWS--ANFTSML-GFDNHQFT-ELMRLYLTIHSDHEGGN 116
A R G I+ D NF ML G + T +++ L +H++H N
Sbjct: 133 AMWARIRN----GDDPIEPRPDLDYAENFLYMLFGEEPDPATAKILDACLILHAEHTM-N 187
Query: 117 VSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLK 176
S + + GS L+DPY ++ + L+GPLHG AN++VL L+++ S E +K
Sbjct: 188 ASTFSALVTGSTLADPYAVISSAIGTLSGPLHGGANEDVLEMLEEIG-------SPENVK 240
Query: 177 EFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQR----EFAQKHLPDDSLFKLVSQVYKVVP 232
++ L + Q + G+GH V + DPR T + + K L+++ +V ++
Sbjct: 241 AYLDKKLANKQKIWGFGHRVYKTKDPRATILQKLAEDLFAKMGELSKLYEIALEVERLC- 299
Query: 233 PVLIETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRALGL- 291
E K +PNVD +SG++ + G+ + +T +F V+R G LA W LG
Sbjct: 300 ---EELLGHKGVYPNVDFYSGIVYKELGIPA-DLFTPIFAVARVAGWLAH--WKEQLGDN 353
Query: 292 PIERPKSLSTNDLVKQYSKI 311
I RP + ++ ++Y +
Sbjct: 354 RIFRPTQIYIGEIDRKYVPL 373
>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 = 121 bits (305), Expect = 3e-31
Identities = 84/319 (26%), Positives = 140/319 (43%), Gaps = 38/319 (11%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNS---ESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLP 57
++ FP HPM A ++AL++ E+ A + + E + + +AK+P
Sbjct: 83 LIQTFPRDAHPMGILCAGLSALSAFYPEAIPAHTGDLYQNNP---EVRDKQIIRTLAKMP 139
Query: 58 VVAATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGF-------DNHQFTELMRLYLTIHS 110
+AA Y + G+ N + NF M+G+ N + + +H+
Sbjct: 140 TIAAAAYCHRI--GRPFVYPRANLSYIENFLYMMGYVDQEPYEPNPRLARALDRLWILHA 197
Query: 111 DHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNV 170
DHE N S GS+L+DP AA + L GPLHG AN+ L K+ +++G
Sbjct: 198 DHEM-NCSTSAARHTGSSLADPISCMAAAIAALYGPLHGGANEAAL----KMLREIG--- 249
Query: 171 SEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQ---KHLPDDSLFKLVSQV 227
+ E + FI + + G+GH V + DPR RE + D L K+ ++
Sbjct: 250 TPENVPAFIERVKNGKRRLMGFGHRVYKNYDPRAKVIREILHEVLTEVEKDPLLKVAMEL 309
Query: 228 YKVV--PPVLIETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIW 285
++ + + +PNVD +SG + + G ++TVLF V+R G +A W
Sbjct: 310 ERIALEDEYFVS----RKLYPNVDFYSGFIYKALGF-PPEFFTVLFAVARTSGWMAH--W 362
Query: 286 DRALGLP---IERPKSLST 301
+ P I RP+ + T
Sbjct: 363 REMMEDPLQRIWRPRQVYT 381
>gnl|CDD|180164 PRK05614, gltA, type II citrate synthase; Reviewed.
Length = 419
Score = 118 bits (299), Expect = 4e-30
Identities = 93/339 (27%), Positives = 145/339 (42%), Gaps = 82/339 (24%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMD--------- 51
F HPM+ + AL S F Y DS+D
Sbjct: 123 FFRGFRRDAHPMAVLCGVVGAL---SAF-----------------YHDSLDINDPEHREI 162
Query: 52 ----LIAKLPVVAATIYRNTFQGGKGIGAI----DTNKDWSANFTSMLGFD--------N 95
LIAK+P +AA Y+ IG + ++ NF M+ F N
Sbjct: 163 AAIRLIAKMPTLAAMAYK------YSIGQPFVYPRNDLSYAENFLRMM-FATPCEEYEVN 215
Query: 96 HQFTELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEV 155
+ +H+DHE N S TV L GS+ ++P+ AAG+ L GP HG AN+ V
Sbjct: 216 PVLVRALDRIFILHADHEQ-NASTSTVRLAGSSGANPFACIAAGIAALWGPAHGGANEAV 274
Query: 156 LIWLKKLQQQVGDNVSE--EKLKEFIWNTLKSGQV-VPGYGHAVLRKTDPRYTCQREFAQ 212
L L+++ DN+ E + K+ K+ + G+GH V + DPR RE
Sbjct: 275 LKMLEEIGS--VDNIPEFIARAKD------KNDGFRLMGFGHRVYKNYDPRAKIMRETCH 326
Query: 213 KHLP----DDSLFKLVSQVYKVV--PPVLIETGKVKNPWPNVDAHSGVLLQYYGL-KEMN 265
+ L +D L ++ ++ ++ IE + +PNVD +SG++L+ G+ M
Sbjct: 327 EVLKELGLNDPLLEVAMELEEIALNDEYFIE----RKLYPNVDFYSGIILKALGIPTSM- 381
Query: 266 YYTVLFGVSRALGVLASLIWDRALGLP---IERPKSLST 301
+TV+F ++R +G +A W+ P I RP+ L T
Sbjct: 382 -FTVIFALARTVGWIAH--WNEMHSDPEQKIGRPRQLYT 417
>gnl|CDD|184465 PRK14032, PRK14032, citrate synthase; Provisional.
Length = 447
Score = 118 bits (298), Expect = 8e-30
Identities = 79/258 (30%), Positives = 128/258 (49%), Gaps = 27/258 (10%)
Query: 45 VYEDSMDLIAKLPVVAATIYR----NTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTE 100
V S+ LIA+ P +A Y+ I + N ML DN ++TE
Sbjct: 164 VLRQSISLIARFPTLAVYAYQAYRHYHDGKSLYIHPPKPELSTAENILYMLRPDN-KYTE 222
Query: 101 L----MRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVL 156
L + L L +H++H GGN S T +V S+ +D Y + AA + L GP HG AN +V+
Sbjct: 223 LEARLLDLALVLHAEHGGGNNSTFTTRVVSSSGTDTYSAIAAAIGSLKGPKHGGANIKVM 282
Query: 157 IWLKKLQQQVGDNVSEEKLKEFIWNTL------KSGQVVPGYGHAVLRKTDPRYTCQREF 210
+ +++ V D E+++ +++ L KSG ++ G GHAV +DPR ++F
Sbjct: 283 EMFEDIKENVKDWEDEDEIADYLTKILNKEAFDKSG-LIYGMGHAVYTISDPRAVILKKF 341
Query: 211 A-----QKHLPDDSLFKLVSQVYKVVPPVLIE-TGKVKNPWPNVDAHSGVLLQYYGL-KE 263
A +K ++ F L ++ K+ P ++ E G K NVD +SG + G+ +E
Sbjct: 342 AEKLAKEKGREEE--FNLYEKIEKLAPELIAEERGIYKGVSANVDFYSGFVYDMLGIPEE 399
Query: 264 MNYYTVLFGVSRALGVLA 281
+ YT LF ++R +G A
Sbjct: 400 L--YTPLFAIARIVGWSA 415
>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 = 114 bits (287), Expect = 7e-29
Identities = 77/289 (26%), Positives = 128/289 (44%), Gaps = 33/289 (11%)
Query: 2 LNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVAA 61
L P HPM A++AL A + E ++ LIAK+P + A
Sbjct: 78 LKLLPKDAHPMDVLRTAVSALALYDPEADDMSR--------EANLRKAIRLIAKMPTIVA 129
Query: 62 TIYRNTFQGGKGIGAIDTNKDWS--ANFTSMLGFD--NHQFTELMRLYLTIHSDHEGGNV 117
+R G+ + + D S ANF ML + + + + L +H+DHE N
Sbjct: 130 AFHRIR----NGLEPVAPDPDLSHAANFLYMLTGEKPSEEAARAFDVALILHADHEL-NA 184
Query: 118 SAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKE 177
S +V S LSD Y + A + L GPLHG AN+ V+ L ++G S + +
Sbjct: 185 STFAARVVASTLSDMYSAVTAAIGALKGPLHGGANERVMKML----LEIG---SVDNVAA 237
Query: 178 FIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQV--YKVVPPVL 235
++ + L + + + G+GH V + DPR RE +++ L K + Y++ +
Sbjct: 238 YVKDKLANKEKIMGFGHRVYKTGDPRAKHLREMSRR------LGKETGEPKWYEMSEAIE 291
Query: 236 IETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLI 284
K PNVD +S + G+ ++ +T +F +SR G A ++
Sbjct: 292 QAMRDEKGLNPNVDFYSASVYYMLGI-PVDLFTPIFAISRVSGWCAHIL 339
>gnl|CDD|99869 cd06116, CaCS_like, Chloroflexus aurantiacus (Ca) citrate synthase
(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). This group is similar to
gram-negative Escherichia coli (Ec) CS (type II, gltA)
and Arabidopsis thaliana (Ath) peroxisomal (Per) CS.
However EcCS and AthPerCS are not found in this group.
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. 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.
Length = 384
Score = 112 bits (282), Expect = 4e-28
Identities = 97/345 (28%), Positives = 146/345 (42%), Gaps = 77/345 (22%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
++ F HPM +++ AL++ AK D ++K + LI K+P +A
Sbjct: 83 FMDGFRYDAHPMGILISSVAALSTFYPEAKNIGDEEQRNK-------QIIRLIGKMPTIA 135
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGF-------DNHQFTELMRLYLTIHSDHE 113
A YR+ G D + ++ NF SML N + + + +H+DHE
Sbjct: 136 AFAYRHRL--GLPYVLPDNDLSYTGNFLSMLFKMTEPKYEPNPVLAKALDVLFILHADHE 193
Query: 114 GGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEE 173
N S + VGS+ +DPY + AA + L GPLHG AN+ VL ++ QQ+G S +
Sbjct: 194 Q-NCSTSAMRSVGSSRADPYTAVAAAVAALYGPLHGGANEAVL----RMLQQIG---SPK 245
Query: 174 KLKEFIWNTLKSGQV-VPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVP 232
+ +FI T+K G+ + G+GH V + DPR + K+
Sbjct: 246 NIPDFI-ETVKQGKERLMGFGHRVYKNYDPRARIIK--------------------KIAD 284
Query: 233 PVLIETGKVKNPW-----------------------PNVDAHSGVLLQYYGLKEMNYYTV 269
V TG +NP PNVD +SG++ Q G +TV
Sbjct: 285 EVFEATG--RNPLLDIAVELEKIALEDEYFISRKLYPNVDFYSGLIYQALGFP-TEAFTV 341
Query: 270 LFGVSRALGVLASLIWDRALGLP---IERPKSLSTNDLVKQYSKI 311
LF + R G LA W L P I RP+ + T + Y I
Sbjct: 342 LFAIPRTSGWLAQ--WIEMLRDPEQKIARPRQVYTGPRDRDYVPI 384
>gnl|CDD|99866 cd06113, citrate_synt_like_1_2, 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) a carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) nucleophilic attack of this carbanion on
OAA to generate citryl-CoA, and c) hydrolysis of
citryl-CoA to produce citrate and CoA. CSs are found in
two structural types: type I (homodimeric) and type II
CSs (homohexameric). Type II CSs are unique to
gram-negative bacteria. Type I CSs are found in eukarya,
gram-positive bacteria, archaea, and in some
gram-negative bacteria. Type I CS is active as a
homodimer, both subunits participating in the active
site. Type II CS is a hexamer 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 = 406
Score = 112 bits (282), Expect = 6e-28
Identities = 83/260 (31%), Positives = 134/260 (51%), Gaps = 27/260 (10%)
Query: 43 EYVYEDSMDLIAKLPVVAATIYR--NTFQGGKG--IGAIDTNKDWSANFTSMLGFDNHQF 98
E V S+ LIA+LP +A Y+ + G+ I + N SML D +
Sbjct: 132 ENVLRQSIQLIARLPTIAVYAYQAKRHYYDGESLYIHHPQPELSTAENILSMLRPDKK-Y 190
Query: 99 TE----LMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQE 154
TE L+ L L +H++H GGN S T +V S+ +D Y + AA + L GP HG AN +
Sbjct: 191 TELEAKLLDLCLVLHAEHGGGNNSTFTTRVVSSSGTDTYSAIAAAIGSLKGPRHGGANIK 250
Query: 155 VLIWLKKLQQQVGDNVSEEKLKEFIWNTL------KSGQVVPGYGHAVLRKTDPRYTCQR 208
V+ L+ +++ V D E++++ ++ L KSG ++ G GHAV +DPR +
Sbjct: 251 VMEMLEDIKENVKDWTDEDEVRAYLRKILNKEAFDKSG-LIYGMGHAVYTLSDPRAVVLK 309
Query: 209 EFAQ-----KHLPDDSLFKLVSQVYKVVPPVLIE-TGKVKNPWPNVDAHSGVLLQYYGL- 261
++A+ K ++ F L ++ ++ P V+ E G K NVD +SG + + G+
Sbjct: 310 KYARSLAKEKGREEE--FALYERIERLAPEVIAEERGIGKTVCANVDFYSGFVYKMLGIP 367
Query: 262 KEMNYYTVLFGVSRALGVLA 281
+E+ YT LF V+R +G A
Sbjct: 368 QEL--YTPLFAVARIVGWCA 385
>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 = 110 bits (277), Expect = 2e-27
Identities = 75/287 (26%), Positives = 131/287 (45%), Gaps = 29/287 (10%)
Query: 2 LNNFPNHLHPMSQFSAAITAL-NSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
+ P HPM A++ L + + + + ++ L+AKLP +
Sbjct: 78 IEALPAESHPMDVLRTAVSYLGALDPEKFGHTPEEA---------RDIAIRLLAKLPTIV 128
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSML-GFDNHQ-FTELMRLYLTIHSDHEGGNVS 118
A YR + G I A + + NF ML G + + + + M + L ++++HE N S
Sbjct: 129 AYWYR--IRHGGEIIAPKDDDSIAGNFLYMLHGEEPTKEWEKAMDIALILYAEHEF-NAS 185
Query: 119 AHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEF 178
++ S LSD Y + A + L GPLHG AN+ V+ + ++GD +K + +
Sbjct: 186 TFAARVIASTLSDMYSAITAAIGALKGPLHGGANEAVM----AMLDEIGD---PDKAEAW 238
Query: 179 IWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIET 238
I L++ + + G+GH V + DPR +E+A K L ++ + + V+ E
Sbjct: 239 IRKALENKERIMGFGHRVYKTYDPRAKILKEYA-KKLSAKEGSSKWYEIAERLEDVMEEE 297
Query: 239 GKVKNPWPNVDAHSGVLLQYYGLK-EMNYYTVLFGVSRALGVLASLI 284
+ PNVD S + YY + + +T +F +SR G A +I
Sbjct: 298 KGIY---PNVDFFSASV--YYMMGIPTDLFTPIFAMSRVTGWTAHII 339
>gnl|CDD|233579 TIGR01798, cit_synth_I, citrate synthase I (hexameric type). This
model describes one of several distinct but closely
homologous classes of citrate synthase, the protein that
brings carbon (from acetyl-CoA) into the TCA cycle. This
form, class I, is known to be hexameric and
allosterically inhibited by NADH in Escherichia coli,
Acinetobacter anitratum, Azotobacter vinelandii,
Pseudomonas aeruginosa, etc. In most species with a
class I citrate synthase, a dimeric class II isozyme is
found. The class II enzyme may act primarily on
propionyl-CoA to make 2-methylcitrate or be
bifunctional, may be found among propionate utilization
enzymes, and may be constitutive or induced by
propionate. Some members of this model group as class I
enzymes, and may be hexameric, but have shown regulatory
properties more like class II enzymes [Energy
metabolism, TCA cycle].
Length = 412
Score = 111 bits (278), Expect = 2e-27
Identities = 96/322 (29%), Positives = 152/322 (47%), Gaps = 49/322 (15%)
Query: 2 LNNFPNHLHPMSQFSAAITALNSESKFAKAYNDG--VHKSKYWEYVYEDSMDLIAKLPVV 59
N F HPM+ + AL S F Y+D ++ ++ E ++ LIAK+P +
Sbjct: 111 FNGFRRDAHPMAVMVGVVGAL---SAF---YHDSLDINDPRHREIA---AIRLIAKIPTL 161
Query: 60 AATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFD--------NHQFTELMRLYLTIHSD 111
AA Y+ + G+ + ++ NF M+ F N M +H+D
Sbjct: 162 AAMSYKYSI--GQPFVYPRNDLSYAENFLHMM-FATPCEDYKVNPVLARAMDRIFILHAD 218
Query: 112 HEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVS 171
HE N S TV L GS+ ++P+ AAG+ L GP HG AN+ L K+ +++G S
Sbjct: 219 HEQ-NASTSTVRLAGSSGANPFACIAAGIAALWGPAHGGANEAAL----KMLEEIG---S 270
Query: 172 EEKLKEFIWNTL--KSGQVVPGYGHAVLRKTDPRY-----TCQREFAQKHLPDDSLFKLV 224
+ + EFI + G+GH V + DPR TC + L DD LFKL
Sbjct: 271 VKNIPEFIKKVKDKNDPFRLMGFGHRVYKNYDPRAKVMRETCHEVLKELGLHDDPLFKLA 330
Query: 225 SQVYKVV--PPVLIETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLAS 282
++ K+ P IE + +PNVD +SG++L+ G+ + +TV+F ++R +G ++
Sbjct: 331 MELEKIALNDPYFIE----RKLYPNVDFYSGIILKAMGIP-TSMFTVIFALARTVGWISH 385
Query: 283 LIWDRALGLP---IERPKSLST 301
W + P I RP+ L T
Sbjct: 386 --WSEMISDPGQKIGRPRQLYT 405
>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 = 108 bits (272), Expect = 2e-26
Identities = 90/335 (26%), Positives = 150/335 (44%), Gaps = 54/335 (16%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNS---ESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLP 57
M+ +FP+ HPM +AI+AL++ E+ A A D ++K+K + + + ++ K P
Sbjct: 103 MIKSFPHDAHPMGMLVSAISALSAFHPEANPALAGQD-IYKNK--QVRDKQIVRILGKAP 159
Query: 58 VVAATIYRNTFQGGKGIGAIDTNKDWSANFTSML-GFDNHQFTELMRL------YLTIHS 110
+AA YR G+ + ++ NF ML ++ RL +H+
Sbjct: 160 TIAAAAYRRR--AGRPPNLPSQDLSYTENFLYMLDSLGERKYKPNPRLARALDILFILHA 217
Query: 111 DHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNV 170
+HE N S V + S+ D Y + A + L GPLHG AN+ VL ++ ++G
Sbjct: 218 EHEM-NCSTAAVRHLASSGVDVYTAVAGAVGALYGPLHGGANEAVL----RMLAEIG--- 269
Query: 171 SEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKV 230
+ E + FI + + G+GH V + DPR ++ A D +F++V
Sbjct: 270 TVENIPAFIEGVKNRKRKLSGFGHRVYKNYDPRAKIIKKLA------DEVFEIVG----- 318
Query: 231 VPPVLIETGKV-------------KNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRAL 277
P LIE + +PNVD +SG++ + G +++ VLF + R
Sbjct: 319 KDP-LIEIAVALEKAALSDEYFVKRKLYPNVDFYSGLIYRAMGFP-TDFFPVLFAIPRMA 376
Query: 278 GVLASLIWDRAL---GLPIERPKSLSTNDLVKQYS 309
G LA W +L I RP+ L T ++ Y
Sbjct: 377 GYLAH--WRESLDDPDTKIMRPQQLYTGVWLRHYV 409
>gnl|CDD|237591 PRK14036, PRK14036, citrate synthase; Provisional.
Length = 377
Score = 107 bits (270), Expect = 3e-26
Identities = 94/330 (28%), Positives = 151/330 (45%), Gaps = 57/330 (17%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKF--AKAYNDGVHKSKYWEYVYEDSMDLIAKLP- 57
M+ FP HPM A+ AL F +A +D EY+ + + LIAK+P
Sbjct: 82 MMKCFPETGHPMDALQASAAALGL---FYSRRALDDP-------EYIRDAVVRLIAKIPT 131
Query: 58 -VVAATIYRNTFQGGKGIGAIDTNKD--WSANFTSMLGFDNHQFTE---------LMRLY 105
V A + R KG I D ++ANF ML TE +
Sbjct: 132 MVAAFQLIR------KGNDPIQPRDDLDYAANFLYML-------TEREPDPLAARIFDRC 178
Query: 106 LTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQ 165
L +H++H N S + + S L+DPY A+ + LAGPLHG AN++VL L+ +
Sbjct: 179 LILHAEHTI-NASTFSARVTASTLTDPYAVIASAVGTLAGPLHGGANEDVLAMLE----E 233
Query: 166 VGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQ---KHLPDDSLFK 222
+G S E ++ ++ L + Q + G+GH + DPR T ++ A+ D ++
Sbjct: 234 IG---SVENVRPYLDERLANKQKIMGFGHREYKVKDPRATILQKLAEELFARFGHDEYYE 290
Query: 223 LVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLAS 282
+ ++ +V L K +PNVD +SG++ + G+ + +T +F ++R G LA
Sbjct: 291 IALELERVAEERLGP----KGIYPNVDFYSGLVYRKLGIPR-DLFTPIFAIARVAGWLAH 345
Query: 283 LIWDRALGL-PIERPKSLSTNDLVKQYSKI 311
W LG I RP + T ++Y +
Sbjct: 346 --WREQLGANRIFRPTQIYTGSHNRRYIPL 373
>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 = 97.1 bits (242), Expect = 1e-22
Identities = 64/282 (22%), Positives = 124/282 (43%), Gaps = 29/282 (10%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVA 60
++ + P + HPM A++ L +E + + ++ L+A+LP V
Sbjct: 77 LIASLPKNCHPMDVLRTAVSVLGAEDSETDDSSP--------DANLAKAIRLLAQLPTVV 128
Query: 61 ATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLY---LTIHSDHEGGNV 117
A R + G D++ + NF M F E++R + L ++++H N
Sbjct: 129 AADIR--RRKGLDPIPPDSDLGIAENFLHMC-FGEVPSPEVVRAFDVSLILYAEH-SFNA 184
Query: 118 SAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKE 177
S T ++ S LSD Y + + L GPLHG AN+ V+ + ++ EK +
Sbjct: 185 STFTARVITSTLSDIYSAITGAIGALKGPLHGGANEAVMHMMLEID-------DPEKAAQ 237
Query: 178 FIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIE 237
++ + L + V G+GH V + D R + ++ K + +Y + ++
Sbjct: 238 WMLDALARKEKVMGFGHRVYKSGDSRVPTMEKALRRVAAVHDGQKWL-AMYDALEDAMVA 296
Query: 238 TGKVKNPWPNVDAHSGVLLQYYGLK-EMNYYTVLFGVSRALG 278
+K PN+D +G YY + +++++T +F ++R G
Sbjct: 297 AKGIK---PNLDFPAGP--AYYLMGFDIDFFTPIFVMARITG 333
>gnl|CDD|184468 PRK14035, PRK14035, citrate synthase; Provisional.
Length = 371
Score = 96.4 bits (240), Expect = 2e-22
Identities = 71/282 (25%), Positives = 124/282 (43%), Gaps = 35/282 (12%)
Query: 7 NHLHPMSQFSAAITALNSESKFAKAYNDGVH-KSKYWEYVYEDSMDLIAKLPVVAATIYR 65
+H+HPM TAL + + ++ + + E YE ++ + AK+ + R
Sbjct: 86 DHVHPM-------TALRTSVSYLAHFD--PDAEEESDEARYERAIRIQAKVASLVTAFAR 136
Query: 66 NTFQGGKGIGAIDTNKD--WSANFTSMLGFDNHQFTEL----MRLYLTIHSDHEGGNVSA 119
+G + D ++ANF ML T++ L +H+DHE N S
Sbjct: 137 VR----QGKEPLKPRPDLSYAANFLYML--RGELPTDIEVEAFNKALVLHADHEL-NAST 189
Query: 120 HTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFI 179
T S+LSD Y A + L GPLHG AN+ V+ L +++ S + ++
Sbjct: 190 FTARCAVSSLSDMYSGVVAAVGSLKGPLHGGANERVMDMLSEIR-------SIGDVDAYL 242
Query: 180 WNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIETG 239
+ + + G+GH V + DPR RE ++K + + + + ++ + + E
Sbjct: 243 DEKFANKEKIMGFGHRVYKDGDPRAKYLREMSRK-ITKGTGREELFEMSVKIEKRMKEE- 300
Query: 240 KVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLA 281
K PNVD +S + G+ + +T +F VSR G +A
Sbjct: 301 --KGLIPNVDFYSATVYHVMGIPH-DLFTPIFAVSRVAGWIA 339
>gnl|CDD|184467 PRK14034, PRK14034, citrate synthase; Provisional.
Length = 372
Score = 93.3 bits (232), Expect = 3e-21
Identities = 85/281 (30%), Positives = 133/281 (47%), Gaps = 33/281 (11%)
Query: 7 NHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRN 66
+HPMS AI+ L + A+ ++ E Y ++ L AK+P + A R
Sbjct: 86 KKVHPMSVLRTAISMLGLYDEEAEIMDE--------EANYRKAVRLQAKVPTIVAAFSRI 137
Query: 67 TFQGGKGIGAIDTNKDWS--ANFTSMLGFD--NHQFTELMRLYLTIHSDHEGGNVSAHTV 122
KG+ ++ KD S ANF ML + + E L +H+DHE N S T
Sbjct: 138 R----KGLDPVEPRKDLSLAANFLYMLNGEEPDEVEVEAFNKALVLHADHEL-NASTFTA 192
Query: 123 HLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFIWNT 182
+ + LSD Y A + L GPLHG AN+ V+ K+ ++G+ EE ++ +I N
Sbjct: 193 RVCVATLSDVYSGITAAIGALKGPLHGGANENVM----KMLTEIGE---EENVESYIHNK 245
Query: 183 LKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIE--TGK 240
L++ + + G+GH V R+ DPR RE +++ L L+ + + IE K
Sbjct: 246 LQNKEKIMGFGHRVYRQGDPRAKHLREMSKR------LTVLLGEEKWYNMSIKIEEIVTK 299
Query: 241 VKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLA 281
K PNVD +S + G+ + +T +F +SR G LA
Sbjct: 300 EKGLPPNVDFYSASVYHCLGIDH-DLFTPIFAISRMSGWLA 339
>gnl|CDD|237069 PRK12349, PRK12349, citrate synthase 3; Provisional.
Length = 369
Score = 80.5 bits (199), Expect = 6e-17
Identities = 79/299 (26%), Positives = 128/299 (42%), Gaps = 50/299 (16%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNSESKFAKAYND---GVHKSKYWEYVYEDSMDLIAKLP 57
+L P HPM ++AL + + D V+KS+ + L++K+P
Sbjct: 83 ILKALPKETHPMDGLRTGVSAL---AGYDNDIEDRSLEVNKSR--------AYKLLSKVP 131
Query: 58 VVAATIYRNTFQGGKGIGAIDTNKDWSANFTSML------GFDNHQFTELMRLYLTIHSD 111
+ A Y + +SANF ML + F + LY S+
Sbjct: 132 NIVANSYH--ILNNEEPIEPLKELSYSANFLYMLTGKKPTELEEKIFDRSLVLY----SE 185
Query: 112 HEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVS 171
HE N S T ++ S SD Y + + L G LHG AN+ V+ L V
Sbjct: 186 HEMPN-STFTARVIASTQSDLYGALTGAVASLKGSLHGGANEAVMYML-----LEAGTV- 238
Query: 172 EEKLKEFIWNTLKSGQVVPGYGHAV-LRKTDPRYTCQREFAQKHL----PDDSLFKLVSQ 226
EK +E + L + + + G+GH V ++K DPR +E A K L D +L+++
Sbjct: 239 -EKFEELLQKKLYNKEKIMGFGHRVYMKKMDPRALMMKE-ALKQLCDVKGDYTLYEMCEA 296
Query: 227 VYKVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGLK-EMNYYTVLFGVSRALGVLASLI 284
K++ K K +PN+D ++ + Y+ L + YT +F SR +G+ A +I
Sbjct: 297 GEKIME-------KEKGLYPNLDYYAAPV--YWMLGIPIQLYTPIFFSSRTVGLCAHVI 346
>gnl|CDD|237590 PRK14033, PRK14033, citrate synthase; Provisional.
Length = 375
Score = 80.4 bits (199), Expect = 7e-17
Identities = 67/281 (23%), Positives = 123/281 (43%), Gaps = 29/281 (10%)
Query: 2 LNNFPNHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVAA 61
++ P HPM A++ L +E D E ++ L A LP + A
Sbjct: 88 IDKLPTTCHPMDVVRTAVSYLGAE--------DPEADDSSPEANLAKALRLFAVLPTIVA 139
Query: 62 TIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLY---LTIHSDHEGGNVS 118
R + G A ++ ++ NF M F E++R + L ++++H N S
Sbjct: 140 ADQR--RRRGLDPIAPRSDLGYAENFLHMC-FGEVPEPEVVRAFEVSLILYAEH-SFNAS 195
Query: 119 AHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEF 178
T ++ S LSD Y + + L GPLHG AN+ V+ + ++GD + E+
Sbjct: 196 TFTARVITSTLSDIYSAVTGAIGALKGPLHGGANEAVMHTML----EIGD---PARAAEW 248
Query: 179 IWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIET 238
+ + L + V G+GH V + D R + ++ + + +Y+ + + E
Sbjct: 249 LRDALARKEKVMGFGHRVYKHGDSRVPTMKAALRRVAAVRDGQRWL-DIYEALEKAMAEA 307
Query: 239 GKVKNPWPNVDAHSGVLLQYYGLK-EMNYYTVLFGVSRALG 278
+K PN+D +G YY + +++++T +F +SR G
Sbjct: 308 TGIK---PNLDFPAGPA--YYLMGFDIDFFTPIFVMSRITG 343
>gnl|CDD|184470 PRK14037, PRK14037, citrate synthase; Provisional.
Length = 377
Score = 76.3 bits (188), Expect = 2e-15
Identities = 73/245 (29%), Positives = 115/245 (46%), Gaps = 22/245 (8%)
Query: 47 EDSMDLIAKLPVVAATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTE---LMR 103
E ++ +IAK+ + A +YR + G + + ++ +F F E M
Sbjct: 118 EKAISIIAKMATIVANVYRR--KEGNKPRIPEPSDSFAESFLLA-SFAREPTAEEIKAMD 174
Query: 104 LYLTIHSDHEGGNVSAHTVH-LVG-SALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKK 161
L +++DHE V A T LV S LSD Y A + L GPLHG A +E K
Sbjct: 175 AALILYTDHE---VPASTTAALVAASTLSDMYSCITAALAALKGPLHGGAAEEAF----K 227
Query: 162 LQQQVGD-NVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSL 220
++GD N E + I N K + G+GH V + DPR +E A+ + +S
Sbjct: 228 QFVEIGDPNNVEMWFNDKIINGKKR---LMGFGHRVYKTYDPRAKIFKELAETLIERNSE 284
Query: 221 FKLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGLK-EMNYYTVLFGVSRALGV 279
K ++ + + + I+ K +PN D +SG++ +Y L + +T LF +SR LG
Sbjct: 285 AKKYFEIAQKLEELGIKQFGSKGIYPNTDFYSGIV--FYALGFPVYMFTALFALSRTLGW 342
Query: 280 LASLI 284
LA +I
Sbjct: 343 LAHII 347
>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 = 73.9 bits (182), Expect = 1e-14
Identities = 66/300 (22%), Positives = 131/300 (43%), Gaps = 49/300 (16%)
Query: 2 LNNFPNHLHPMSQF---SAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPV 58
L P HPM + + L E++F++ Y + L+A P
Sbjct: 78 LELIPKDSHPMDVMRTGCSMLGCLEPENEFSQQYEIAIR--------------LLAIFP- 122
Query: 59 VAATIYRNTFQGGKGIGAIDTNKDWSA-NFTSMLGFDNHQ------FTELMRLYLTIHSD 111
+ +Y + +T++D A +F +L H + M + L ++++
Sbjct: 123 -SILLYWYHYSHSGKRIETETDEDSIAGHFLHLL----HGKKPGELEIKAMDVSLILYAE 177
Query: 112 HEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVS 171
HE N S + S LSD Y + + L GPLHG AN+ + +++ + S
Sbjct: 178 HEF-NASTFAARVTASTLSDFYSAITGAIGTLRGPLHGGANEAAMELIERFK-------S 229
Query: 172 EEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLP---DDSLFKLVSQVY 228
E+ ++ + L+ +++ G+GH V ++ DPR +++++K D L+++ ++
Sbjct: 230 PEEAEQGLLEKLERKELIMGFGHRVYKEGDPRSDIIKKWSKKLSEEGGDPLLYQISERIE 289
Query: 229 KVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDRA 288
+V+ + K +PN+D +S + G+ +T +F +SR G A ++ RA
Sbjct: 290 EVMW-------EEKKLFPNLDFYSASAYHFCGIP-TELFTPIFVMSRVTGWAAHIMEQRA 341
>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 = 63.5 bits (155), Expect = 3e-11
Identities = 75/297 (25%), Positives = 115/297 (38%), Gaps = 38/297 (12%)
Query: 7 NHLHPMSQFSAAITALNSESKFAKAYNDGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRN 66
L PM A + L A A + L+A PV+ A + R
Sbjct: 82 AGLDPMDALRALLALLPDSPDLATA------------------LRLLAAAPVITAALLR- 122
Query: 67 TFQGGKGIGAIDTNKDWS--ANFTSML--GFDNHQFTELMRLYLTIHSDHEGGNVSAHTV 122
+G I + S A++ ML + + YL +DH G N S T
Sbjct: 123 ---LSRGKQPIAPDPSLSHAADYLRMLTGEPPSEAHVRALDAYLVTVADH-GMNASTFTA 178
Query: 123 HLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLKEFIWNT 182
++ S +D + + L GPLHG A VL L + +N +E L+E
Sbjct: 179 RVIASTEADLTSAVLGAIGALKGPLHGGAPGPVLDMLDAIGTP--EN-AEAWLRE----A 231
Query: 183 LKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVLIETGKVK 242
L G+ + G+GH V R DPR + A++ D + V + +L E +
Sbjct: 232 LARGERLMGFGHRVYRVRDPRADVLKAAAERLGAPDERLEFAEAVEQAALALLREYKPGR 291
Query: 243 NPWPNVDAHSGVLLQYYGLK-EMNYYTVLFGVSRALGVLASLIWDRALGLPIERPKS 298
NV+ ++ +LL+ GL E +T F R G A ++ G I RP+S
Sbjct: 292 PLETNVEFYTALLLEALGLPREA--FTPTFAAGRTAGWTAHVLEQARTGRLI-RPQS 345
>gnl|CDD|99856 cd06102, citrate_synt_like_2, 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. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 282
Score = 60.0 bits (146), Expect = 3e-10
Identities = 31/105 (29%), Positives = 50/105 (47%), Gaps = 8/105 (7%)
Query: 99 TELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIW 158
+L+R L + +DHE N S + S + Y + AG+ L+GP HG A V
Sbjct: 98 ADLLRRALVLLADHEL-NASTFAARVAASTGASLYAAVLAGLAALSGPRHGGATARVEAL 156
Query: 159 LKKLQQQVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPR 203
L + + +E ++E L+ G+ +PG+GH + DPR
Sbjct: 157 LDEALRAGD---AEAAVRE----RLRRGEALPGFGHPLYPDGDPR 194
>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 = 56.4 bits (136), Expect = 8e-09
Identities = 55/196 (28%), Positives = 91/196 (46%), Gaps = 16/196 (8%)
Query: 102 MRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKK 161
M + L ++++HE N S T ++ SD Y + + L GP HG AN+ +
Sbjct: 171 MHISLILYAEHEF-NASTFTARVIAGTGSDMYSAITGAIGALRGPKHGGANEVAF----E 225
Query: 162 LQQQVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLF 221
+QQ+ ++ + I +++ +VV G+GH V DPR +E A K L +
Sbjct: 226 IQQRYES---ADEAEADIRRRVENKEVVIGFGHPVYTIADPRNQVIKEVA-KQLSKEGGD 281
Query: 222 KLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGL-KEMNYYTVLFGVSRALGVL 280
+ + + + V+ E K+ +PN+D S V G+ M +T LF ++R G
Sbjct: 282 MKMFDIAERLETVMWEEKKM---FPNLDWFSAVSYHMMGVPTAM--FTPLFVIARTTGWS 336
Query: 281 ASLIWDRALGLPIERP 296
A +I R G I RP
Sbjct: 337 AHIIEQRQDG-KIIRP 351
>gnl|CDD|183463 PRK12351, PRK12351, methylcitrate synthase; Provisional.
Length = 378
Score = 50.7 bits (122), Expect = 6e-07
Identities = 57/199 (28%), Positives = 92/199 (46%), Gaps = 22/199 (11%)
Query: 102 MRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKK 161
M L ++++HE N S T ++ SD Y + + L GP HG AN EV +
Sbjct: 180 MHTSLILYAEHEF-NASTFTARVIAGTGSDMYSAITGAIGALRGPKHGGAN-EVAF---E 234
Query: 162 LQQQVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPRYTCQREFAQK---HLPDD 218
+QQ+ + ++ + I +++ +VV G+GH V +DPR +E A+K D
Sbjct: 235 IQQRYD---TPDEAEADIRRRVENKEVVIGFGHPVYTISDPRNKVIKEVAKKLSKEAGDT 291
Query: 219 SLFKLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGL-KEMNYYTVLFGVSRAL 277
L+ + ++ V+ + K +PN+D S V G+ M +T LF +SR
Sbjct: 292 KLYDIAERLETVM-------WEEKKMFPNLDWFSAVSYHMMGVPTAM--FTPLFVISRTT 342
Query: 278 GVLASLIWDRALGLPIERP 296
G A +I R I RP
Sbjct: 343 GWAAHVIEQRQDN-KIIRP 360
>gnl|CDD|237070 PRK12350, PRK12350, citrate synthase 2; Provisional.
Length = 353
Score = 46.5 bits (111), Expect = 1e-05
Identities = 54/206 (26%), Positives = 90/206 (43%), Gaps = 36/206 (17%)
Query: 105 YLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQ 164
Y ++H G N S T ++ S +D + + + L+GPLHG A VL L + +
Sbjct: 161 YWVSAAEH-GMNASTFTARVIASTGADVAAALSGAIGALSGPLHGGAPARVLPMLDAV-E 218
Query: 165 QVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKTDPR-----YTCQR------EFAQK 213
+ GD + ++ L G+ + G+GH V R DPR T +R E A+
Sbjct: 219 RTGD------ARGWVKGALDRGERLMGFGHRVYRAEDPRARVLRATAKRLGAPRYEVAE- 271
Query: 214 HLPDDSLFKLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLLQYYGL-KEMNYYTVLFG 272
+ +L +L + P +ET NV+ + VLL + G+ M +T +F
Sbjct: 272 AVEQAALAELRER----RPDRPLET--------NVEFWAAVLLDFAGVPAHM--FTAMFT 317
Query: 273 VSRALGVLASLIWDRALGLPIERPKS 298
R G A ++ + G + RP +
Sbjct: 318 CGRTAGWSAHILEQKRTGRLV-RPSA 342
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 36.0 bits (83), Expect = 0.027
Identities = 49/213 (23%), Positives = 83/213 (38%), Gaps = 30/213 (14%)
Query: 99 TELMRLYLTIHSDHEGGNVS-AHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLI 157
T+ + + + + +DH G VS AH + A D S +G+ + GP G A +
Sbjct: 400 TKFIEMCIMLCADH-GPCVSGAHNTIVTARAGKDLVSSLVSGLLTI-GPRFGGAIDDAAR 457
Query: 158 WLKKLQQQVGDNVSEEKLKEFIWNTLKSGQVVPGYGHAVLRKT--DPRYTCQREFAQKHL 215
+ K + ++ EF+ K G VPG GH + + D R +++A+ H
Sbjct: 458 YFKDAYDR---GLTPY---EFVEGMKKKGIRVPGIGHRIKSRDNRDKRVELLQKYARTHF 511
Query: 216 PDDSLFKLVSQVYKVVPPVLIETGKVKNPWPNVDAHSGVLL-------------QYYGLK 262
P + QV K N NVD G L + +
Sbjct: 512 PSVKYMEYAVQVETYT------LSKANNLVLNVDGAIGSLFLDLLAGSGMFTKQEIDEIV 565
Query: 263 EMNYYTVLFGVSRALGVLASLIWDRALGLPIER 295
E+ Y LF ++R++G++ + L P+ R
Sbjct: 566 EIGYLNGLFVLARSIGLIGHTFDQKRLKQPLYR 598
>gnl|CDD|99854 cd06100, CCL_ACL-C, Citryl-CoA lyase (CCL), the C-terminal portion
of the single-subunit type ATP-citrate lyase (ACL) and
the C-terminal portion of the large subunit of the
two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to
acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes
an ATP- and a CoA- dependant cleavage of citrate to form
AcCoA and OAA in a multistep reaction, the final step of
which is likely to involve the cleavage of CiCoA to
generate AcCoA and OAA. In fungi, yeast, plants, and
animals ACL is cytosolic and generates AcCoA for
lipogenesis. ACL may be required for fruiting body
maturation in the filamentous fungus Sordaria
macrospore. In several groups of autotrophic prokaryotes
and archaea, ACL carries out the citrate-cleavage
reaction of the reductive tricarboxylic acid (rTCA)
cycle. In the family Aquificaceae this latter reaction
in the rTCA cycle is carried out via a two enzyme system
the second enzyme of which is CCL; the first enzyme is
citryl-CoA synthetase (CCS) which is not included in
this group. Chlorobium limicola ACL is an example of a
two-subunit type ACL. It is comprised of a large and a
small subunit; it has been speculated that the large
subunit arose from a fusion of the small subunit of the
two subunit CCS with CCL. The small ACL subunit is a
homolog of the larger CCS subunit. Mammalian ACL is of
the single-subunit type and may have arisen from the
two-subunit ACL by another gene fusion. Mammalian ACLs
are homotetramers; the ACLs of C. limicola and
Arabidopsis are a heterooctomers (alpha4beta4). In
cancer cells there is a shift in energy metabolism to
aerobic glycolysis, the glycolytic end product pyruvate
enters a truncated TCA cycle generating citrate which is
cleaved in the cytosol by ACL. Inhibiting ACL limits the
in-vitro proliferation and survival of these cancer
cells, reduces in vivo tumor growth, and induces
differentiation.
Length = 227
Score = 33.7 bits (78), Expect = 0.095
Identities = 44/182 (24%), Positives = 71/182 (39%), Gaps = 16/182 (8%)
Query: 118 SAHTVHLVGSALSDPYLS-FAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDNVSEEKLK 176
SAH L SA + S AAG+ G G G A + + ++ V + +
Sbjct: 50 SAHAARLTASAGPEDLQSAVAAGLLG-IGDRFGGAGEGAA---RLFKEAVDSGDALDAAA 105
Query: 177 EFIWNTLKS-GQVVPGYGHAVLRKTDPRYTCQREFAQKHLPDDSLFKLVSQVYKVVPPVL 235
++ + +PG+GH V + DPR E A++ P V K
Sbjct: 106 AEFVAEYRAAKKRIPGFGHPVHKNPDPRVPRLLELARELGPAGPHLDYALAVEKA----- 160
Query: 236 IETGKVKNPWPNVDAHSGVLLQYYGLKE--MNYYTVLFGVSRALGVLASLIWDRALGLPI 293
+ K K NVD +L G + LF + R+ G++A + ++ LG P+
Sbjct: 161 LTAAKGKPLPLNVDGAIAAILLDLGFPPGALR---GLFVLGRSPGLIAHALEEKRLGQPL 217
Query: 294 ER 295
R
Sbjct: 218 YR 219
>gnl|CDD|205036 pfam12715, Abhydrolase_7, Abhydrolase family. This is a family of
probable bacterial abhydrolases.
Length = 389
Score = 31.0 bits (70), Expect = 0.88
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 14/73 (19%)
Query: 180 WNTLKS----GQVVPGYG--HAVLRKTDPRYTCQREFAQKHLP--DDSLFKLVSQVYKVV 231
+KS G+ + YG H +L T+P + + K P + K + ++ K
Sbjct: 7 HAVIKSDRSDGRFLSSYGIVHTMLEDTEPACAFSPDMSPKEFPKWQKKVRKAMQEIMKFP 66
Query: 232 P------PVLIET 238
P PV ++T
Sbjct: 67 PQKDIPAPVCVKT 79
>gnl|CDD|235748 PRK06224, PRK06224, citrate synthase; Provisional.
Length = 263
Score = 29.8 bits (68), Expect = 1.7
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 10/72 (13%)
Query: 137 AAGMNGLAGPLHGLANQEVLIWLKKLQQQVGDN-----VSEEKLKEFIWNTLKSGQVVPG 191
AAG+ L G +HG A ++ L+++ + + E+ +G+ VPG
Sbjct: 92 AAGLLAL-GSVHGGAGEQAAELLQEIAAAADAGADLDAAARAIVAEY----RAAGKRVPG 146
Query: 192 YGHAVLRKTDPR 203
+GH + + DPR
Sbjct: 147 FGHPLHKPVDPR 158
>gnl|CDD|217621 pfam03573, OprD, outer membrane porin, OprD family. This family
includes outer membrane proteins related to OprD. OprD
has been described as a serine type peptidase. However
the proposed catalytic residues are not conserved
suggesting that many of these proteins are not
peptidases.
Length = 391
Score = 29.9 bits (68), Expect = 2.3
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 63 IYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFT 99
YR G G ID N+ +S FT H F+
Sbjct: 228 YYRTRDDGQARAGEID-NRTYSLLFT--YRHGGHTFS 261
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 29.5 bits (67), Expect = 2.8
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 172 EEKLKEFIWNTLKSGQVVPG 191
+EK KE WN+L+ G VV G
Sbjct: 464 KEKKKEETWNSLEEGDVVEG 483
>gnl|CDD|216402 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 557
Score = 29.3 bits (67), Expect = 3.2
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 37 HKSKYWEYVYEDSMDLIAKLPVVAATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDN 95
S + + +Y+ + L K+ +A IY G G+ K A + GF +
Sbjct: 431 QPSNF-KPLYDLELSLEEKIETIATEIY-----GADGVEFSPKAKKQLARIEKL-GFGH 482
>gnl|CDD|185761 cd09034, BRO1_Alix_like, Protein-interacting Bro1-like domain of
mammalian Alix and related domains. This superfamily
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also
known as PalA) from Saccharomyces cerevisiae, and
related domains. Alix, HD-PTP, Brox, Bro1 and Rim20
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1),
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP functions in cell
migration and endosomal trafficking, Bro1 in endosomal
trafficking, and Rim20 in the response to the external
pH via the Rim101 pathway. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4
(in the case of Alix, HD-PTP, and Brox) and Snf7 (in the
case of yeast Bro1, and Rim20). The single domain
protein human Brox, and the isolated Bro1-like domains
of Alix, HD-PTP and Rhophilin can bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V)
domain, which in the case of Alix, has been shown to be
a dimerization domain and to contain a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in this superfamily. Alix,
HD-PTP and Bro1 also have a proline-rich region (PRR);
the Alix PRR binds multiple partners. Rhophilin-1, and
-2, in addition to this Bro1-like domain, have an
N-terminal Rho-binding domain and a C-terminal PDZ
(PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded
by the PTPN23 gene, a tumor suppressor gene candidate
frequently absent in human kidney, breast, lung, and
cervical tumors. This protein has a C-terminal,
catalytically inactive tyrosine phosphatase domain.
Length = 345
Score = 28.1 bits (63), Expect = 7.1
Identities = 40/198 (20%), Positives = 70/198 (35%), Gaps = 37/198 (18%)
Query: 1 MLNNFPNHLHPMSQFSAAITALNS-------ESKFAKAYNDGVHKSKYWEYVYEDSMDLI 53
+L P+ L A ++AL+ E KA D K + L+
Sbjct: 158 VLPLPPDELPVDLT-EAVLSALSLIMLAQAQECFLLKAEEDKKAK-----------LSLL 205
Query: 54 AKLPVVAATIYRNTFQGGKGIGAIDTNKDWSANFTSMLGFDNHQFTELMRLYLTIHSDHE 113
A+L AA Y + G+ ++T K+ + L + F L Y H
Sbjct: 206 ARLACEAAKYYEEALKCLSGV-DLETIKNIPKKWLLFLKWKKCIFKALAYYY---HGLK- 260
Query: 114 GGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLIWLKKLQQQVGD-NVSE 172
+ +G A++ L A + + L +V LKKL++++
Sbjct: 261 -----LDEANKIGEAIA--RLQAALELLKESERLCKSFLLDVWGNLKKLKEKIEKELEKA 313
Query: 173 EKLKEFIWNTLKSGQVVP 190
E+ +FI+ + VP
Sbjct: 314 ERENDFIYF-----EEVP 326
>gnl|CDD|214809 smart00762, Cog4, COG4 transport protein. This region is found in
yeast oligomeric golgi complex component 4 which is
involved in ER to Golgi and intra Golgi transport.
Length = 324
Score = 27.7 bits (62), Expect = 9.9
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 248 VDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLASLIWDR 287
++ H V+ +YYG M Y V+ + + + +I D
Sbjct: 95 IEQHQPVIEKYYGPDGMLY--VITKLQKEADLQGGIILDT 132
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
0.317 0.134 0.400
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,257,520
Number of extensions: 1745364
Number of successful extensions: 1550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1431
Number of HSP's successfully gapped: 49
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
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: 60 (26.9 bits)