RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780355|ref|YP_003064768.1| type II citrate synthase
[Candidatus Liberibacter asiaticus str. psy62]
(429 letters)
>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 = 693 bits (1791), Expect = 0.0
Identities = 251/401 (62%), Positives = 312/401 (77%), Gaps = 2/401 (0%)
Query: 17 LPIKEGSLGSSVLDISFLHKN-GIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQ 75
LP+ EG+ G V+DIS L K G+FTYDP F +TASC+S IT+IDG GIL YRGYPIEQ
Sbjct: 1 LPVLEGTEGEKVIDISSLRKKTGVFTYDPGFMNTASCESAITYIDGEKGILRYRGYPIEQ 60
Query: 76 LSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLV 135
L+EKS FLEVCYLLL+GEL Q ++F ++I+RH L++E M RFF GFP AHPMA+L
Sbjct: 61 LAEKSSFLEVCYLLLYGELPTAEQLQEFREEITRHTLVHEQMKRFFNGFPRDAHPMAILS 120
Query: 136 SAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYAS 195
+ V ALS+FY V D EQ ++R+IAK+ TIAAM Y+YSIGQPF+YP +DL Y
Sbjct: 121 AMVNALSAFYPDSLDVNDPEQRELAAIRLIAKVPTIAAMAYRYSIGQPFIYPDNDLSYVE 180
Query: 196 NFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAG 255
NFLHM F+VP Y+V+P++ +A++ I ILHADHEQNASTSTVR+ GSSGA+ FA I+AG
Sbjct: 181 NFLHMMFAVPYEPYEVDPVVVKALDTILILHADHEQNASTSTVRMVGSSGANLFASISAG 240
Query: 256 VACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRC 315
+A L G HGGANE L ML EIGS+ + YI +AKDKNDPFR+MGFGHRVY+N+DPR
Sbjct: 241 IAALWGPLHGGANEAVLEMLEEIGSVGNVDKYIAKAKDKNDPFRLMGFGHRVYKNYDPRA 300
Query: 316 RIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGF 375
+I+++T EVL G+ +DP+ ++A+ELE IAL+D+YFIERKLYPNVDFYSGI LRALG
Sbjct: 301 KILKKTCDEVLAELGK-DDPLLEIAMELEEIALKDDYFIERKLYPNVDFYSGIILRALGI 359
Query: 376 PTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416
PT +FTVLFA+ RT GW++QW EM DP +IGRPRQLYTG
Sbjct: 360 PTEMFTVLFALGRTPGWIAQWREMHEDPELKIGRPRQLYTG 400
>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 = 511 bits (1318), Expect = e-145
Identities = 207/391 (52%), Positives = 269/391 (68%), Gaps = 21/391 (5%)
Query: 38 GIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANV 97
G+ YDP + +TA C+S IT+IDG+ GILLYRGYPIEQL+E S + EV YLLL GEL
Sbjct: 1 GLRVYDPGYLNTAVCESSITYIDGDKGILLYRGYPIEQLAESSTYEEVAYLLLWGELPTQ 60
Query: 98 SQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSF------------Y 145
Q +F ++S H ++ E++ R FP AHPM +L + + ALS+F Y
Sbjct: 61 EQYDEFQRRLSEHMMVPESVHRLIQTFPRDAHPMGILCAGLSALSAFYPEAIPAHTGDLY 120
Query: 146 YSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVP 205
+ V+D + +R +AK+ TIAA Y + IG+PFVYPR++L Y NFL+M V
Sbjct: 121 QNNPEVRDKQ-----IIRTLAKMPTIAAAAYCHRIGRPFVYPRANLSYIENFLYMMGYVD 175
Query: 206 CAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHG 265
Y+ NP LARA++R++ILHADHE N STS R GSS ADP +C+AA +A L G HG
Sbjct: 176 QEPYEPNPRLARALDRLWILHADHEMNCSTSAARHTGSSLADPISCMAAAIAALYGPLHG 235
Query: 266 GANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEV 325
GANE AL ML EIG+ E +P +I R K+ R+MGFGHRVY+N+DPR +++RE ++EV
Sbjct: 236 GANEAALKMLREIGTPENVPAFIERVKNGK--RRLMGFGHRVYKNYDPRAKVIREILHEV 293
Query: 326 LEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFA 385
L + DP+ +VA+ELERIALEDEYF+ RKLYPNVDFYSG +ALGFP FTVLFA
Sbjct: 294 LTEVEK--DPLLKVAMELERIALEDEYFVSRKLYPNVDFYSGFIYKALGFPPEFFTVLFA 351
Query: 386 VARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416
VART+GW++ W EM+ DP +RI RPRQ+YTG
Sbjct: 352 VARTSGWMAHWREMMEDPLQRIWRPRQVYTG 382
>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 = 502 bits (1293), Expect = e-143
Identities = 215/388 (55%), Positives = 279/388 (71%), Gaps = 4/388 (1%)
Query: 38 GIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANV 97
G+ TYDPA+ +TASCKS IT+IDG GIL YRGYPIEQL+E+S +LEV YLLLHGEL
Sbjct: 1 GLMTYDPAYLNTASCKSAITYIDGEKGILRYRGYPIEQLAEQSSYLEVAYLLLHGELPTK 60
Query: 98 SQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQC 157
+ + I+RH + +EN+ +F GF AHPM +L+S+V ALS+FY + D EQ
Sbjct: 61 ERLAQWVYDITRHTMTHENLKKFMDGFRYDAHPMGILISSVAALSTFYPEAKNIGDEEQR 120
Query: 158 VNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLAR 217
+R+I K+ TIAA Y++ +G P+V P +DL Y NFL M F + +Y+ NP+LA+
Sbjct: 121 NKQIIRLIGKMPTIAAFAYRHRLGLPYVLPDNDLSYTGNFLSMLFKMTEPKYEPNPVLAK 180
Query: 218 AMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLME 277
A++ +FILHADHEQN STS +R GSS ADP+ +AA VA L G HGGANE L ML +
Sbjct: 181 ALDVLFILHADHEQNCSTSAMRSVGSSRADPYTAVAAAVAALYGPLHGGANEAVLRMLQQ 240
Query: 278 IGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIA 337
IGS + IP +I K + R+MGFGHRVY+N+DPR RI+++ EV E TGR +P+
Sbjct: 241 IGSPKNIPDFIETVKQGKE--RLMGFGHRVYKNYDPRARIIKKIADEVFEATGR--NPLL 296
Query: 338 QVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWT 397
+A+ELE+IALEDEYFI RKLYPNVDFYSG+ +ALGFPT FTVLFA+ RT+GW++QW
Sbjct: 297 DIAVELEKIALEDEYFISRKLYPNVDFYSGLIYQALGFPTEAFTVLFAIPRTSGWLAQWI 356
Query: 398 EMIVDPSRRIGRPRQLYTGALKRDYVPL 425
EM+ DP ++I RPRQ+YTG RDYVP+
Sbjct: 357 EMLRDPEQKIARPRQVYTGPRDRDYVPI 384
>gnl|CDD|144026 pfam00285, Citrate_synt, Citrate synthase.
Length = 352
Score = 473 bits (1219), Expect = e-134
Identities = 161/365 (44%), Positives = 229/365 (62%), Gaps = 14/365 (3%)
Query: 46 FSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFND 105
+C+++I++IDG GIL YRGY IE L+EKS F EV YLLL+GEL + +F+
Sbjct: 2 LRGVVACETEISYIDGEKGILRYRGYDIEDLAEKSSFEEVAYLLLYGELPTAEELAEFSS 61
Query: 106 KISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMI 165
+++ L E++ P AHPMA+L +AV AL+++ + E + ++R+I
Sbjct: 62 ELAARRALPEDVKEVIDALPKDAHPMAVLRAAVSALAAYDPMLY-DESPEDVLEDAIRLI 120
Query: 166 AKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFIL 225
AK+ TIAA IY++ G P + P DL YA NFL+M F + +P ARA++ IL
Sbjct: 121 AKLPTIAAAIYRHRKGLPPIAPDPDLSYAENFLYMLF-----GEEPDPEEARALDLALIL 175
Query: 226 HADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIP 285
HADHE NAST T R+ S+ +D ++ I+A + L G HGGANE L ML EIGS E +
Sbjct: 176 HADHELNASTFTARVVASTLSDLYSAISAAIGALKGPLHGGANEAVLEMLEEIGSPENVE 235
Query: 286 HYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELER 345
YI +A DK + R+MGFGHRVY+ +DPR RI+++ E+ G +DP+ ++A ++E
Sbjct: 236 EYIEKALDKGE--RLMGFGHRVYKTYDPRARILKKFARELAAELG--DDPLLEIAEKIEE 291
Query: 346 IALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSR 405
+ALED E+KLYPNVDFYSG+ +ALG PT LFT LFAV+R GW++ E +
Sbjct: 292 VALED--LKEKKLYPNVDFYSGVLYKALGIPTELFTPLFAVSRVVGWLAHIIEQRENN-- 347
Query: 406 RIGRP 410
++ RP
Sbjct: 348 KLIRP 352
>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 = 467 bits (1203), Expect = e-132
Identities = 190/395 (48%), Positives = 261/395 (66%), Gaps = 11/395 (2%)
Query: 37 NGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELAN 96
G+ YDP + +TA +SKI++IDG+ GIL YRGYPIE+L+EKS FLEV YLL++G L
Sbjct: 20 KGLRLYDPGYLNTAVVRSKISYIDGDKGILRYRGYPIEELAEKSTFLEVAYLLIYGNLPT 79
Query: 97 VSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFY--YSPS-GVQD 153
SQ D+ +S+H + + FP AHPM MLVSA+ ALS+F+ +P+ QD
Sbjct: 80 KSQLSDWEFAVSQHTAVPTGVLDMIKSFPHDAHPMGMLVSAISALSAFHPEANPALAGQD 139
Query: 154 LEQCVNVS----LRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEY 209
+ + V +R++ K TIAA Y+ G+P P DL Y NFL+M S+ +Y
Sbjct: 140 IYKNKQVRDKQIVRILGKAPTIAAAAYRRRAGRPPNLPSQDLSYTENFLYMLDSLGERKY 199
Query: 210 QVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANE 269
+ NP LARA++ +FILHA+HE N ST+ VR SSG D + +A V L G HGGANE
Sbjct: 200 KPNPRLARALDILFILHAEHEMNCSTAAVRHLASSGVDVYTAVAGAVGALYGPLHGGANE 259
Query: 270 EALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVT 329
L ML EIG++E IP +I K++ ++ GFGHRVY+N+DPR +I+++ EV E+
Sbjct: 260 AVLRMLAEIGTVENIPAFIEGVKNRKR--KLSGFGHRVYKNYDPRAKIIKKLADEVFEIV 317
Query: 330 GRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVART 389
G+ DP+ ++A+ LE+ AL DEYF++RKLYPNVDFYSG+ RA+GFPT+ F VLFA+ R
Sbjct: 318 GK--DPLIEIAVALEKAALSDEYFVKRKLYPNVDFYSGLIYRAMGFPTDFFPVLFAIPRM 375
Query: 390 AGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVP 424
AG+++ W E + DP +I RP+QLYTG R YVP
Sbjct: 376 AGYLAHWRESLDDPDTKIMRPQQLYTGVWLRHYVP 410
>gnl|CDD|30721 COG0372, GltA, Citrate synthase [Energy production and conversion].
Length = 390
Score = 463 bits (1192), Expect = e-131
Identities = 200/392 (51%), Positives = 260/392 (66%), Gaps = 14/392 (3%)
Query: 38 GIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANV 97
G FTYDP A+C++ I++IDG+ GIL YRGY IE L+EKS F EV YLLL+GEL
Sbjct: 12 GRFTYDPGLEGVAACETAISYIDGDGGILRYRGYDIEDLAEKSSFEEVAYLLLYGELPTK 71
Query: 98 SQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQC 157
++ F K++ L E + R P AHPMA+L +AV ALS+FY + D
Sbjct: 72 AELAAFFAKLAARRTLPEQVIRLLESLPRDAHPMAVLRTAVSALSAFYPDKLDLNDRR-- 129
Query: 158 VNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLAR 217
+LR+IAK+ TIAA +Y+YS G+P + P DL YA NFL+M F P + P+ AR
Sbjct: 130 -EAALRLIAKLPTIAAAVYRYSRGEPPIAPDPDLSYAENFLYMLFGEPPSP----PVEAR 184
Query: 218 AMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLME 277
AM+R ILHADHE NAST T R+ S+G+D +ACIAAG+ L G HGGANE + ML E
Sbjct: 185 AMDRALILHADHELNASTFTARVVASTGSDLYACIAAGIGALKGPLHGGANEAVMKMLEE 244
Query: 278 IGS-LERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPI 336
IGS E Y+ +A D+ RIMGFGHRVY+N+DPR ++++E ++ + G + +
Sbjct: 245 IGSSGESAEAYVRKALDRK--ERIMGFGHRVYKNYDPRAKVLKELAEKLGKELG--DLKL 300
Query: 337 AQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQW 396
++A ELE IALED F E+KLYPNVDFYSGI RALG PT++FT LFA+ART GW++ W
Sbjct: 301 YEIAEELEEIALEDLGF-EKKLYPNVDFYSGIVYRALGIPTDMFTPLFAIARTVGWIAHW 359
Query: 397 TEMIVDPSRRIGRPRQLYTGALKRDYVPLEER 428
E D + +I RPR LYTG +RDYVP+EER
Sbjct: 360 IEQKEDGN-KIIRPRALYTGPEERDYVPIEER 390
>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 = 447 bits (1153), Expect = e-126
Identities = 166/376 (44%), Positives = 226/376 (60%), Gaps = 23/376 (6%)
Query: 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDF 103
P + ++ I++IDG+ GIL YRGY IE+L+EKS F EV YLLL+G+L + +F
Sbjct: 1 PGLEGVKAKETSISYIDGDEGILRYRGYDIEELAEKSSFEEVAYLLLYGKLPTKEELAEF 60
Query: 104 NDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYY-----SPSGVQDLEQCV 158
K++ H L E++ P +AHPM +L +AV AL SF SP +
Sbjct: 61 KKKLASHRALPEHVVEILDLLPKNAHPMDVLRTAVSALGSFDPFARDKSPEARYE----- 115
Query: 159 NVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARA 218
++R+IAK+ TIAA IY+ G + P DL YA NFL+M F + +P A+A
Sbjct: 116 -KAIRLIAKLPTIAANIYRNREGLEIIAPDPDLSYAENFLYMLFGE-----EPDPEEAKA 169
Query: 219 MNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEI 278
M+ ILHADHE NAST T R+ S+ +D ++ IAA +A L G HGGANE L ML+EI
Sbjct: 170 MDLALILHADHEGNASTFTARVVASTLSDMYSAIAAAIAALKGPLHGGANEAVLKMLLEI 229
Query: 279 GSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQ 338
G+ E + YI K + RIMGFGHRVY+ +DPR +I++E E+ E G +D + +
Sbjct: 230 GTPENVEAYI--WKKLANKRRIMGFGHRVYKTYDPRAKILKELAEELAEEKG--DDKLFE 285
Query: 339 VAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTE 398
+A ELE IALE + +YPNVDFYSG+ +ALGFPT LFT LFAV+R GW++ E
Sbjct: 286 IAEELEEIALEVLGE--KGIYPNVDFYSGVVYKALGFPTELFTPLFAVSRAVGWLAHIIE 343
Query: 399 MIVDPSRRIGRPRQLY 414
+ R+ RPR Y
Sbjct: 344 YRENNQ-RLIRPRAEY 358
>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 = 345 bits (886), Expect = 2e-95
Identities = 156/386 (40%), Positives = 225/386 (58%), Gaps = 15/386 (3%)
Query: 42 YDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQK 101
Y P + + +S I++IDG NGIL YRGY IE+L+E S F EV LLL G+L ++ +
Sbjct: 1 YIPGLAGVPAAESSISYIDGKNGILEYRGYDIEELAEYSSFEEVALLLLDGDLPTAAELE 60
Query: 102 DFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVN-- 159
+F+ ++ +H + N+ FP + HPM ML + V AL FY P V
Sbjct: 61 EFDKELRQHRRVKYNIRDMMKCFPETGHPMDMLQATVAALGMFYPKP-EVLKPNPDYIDA 119
Query: 160 VSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAM 219
++++IAK+ T+ AM + G + PR DLDYA NFL+M F + +P A+ +
Sbjct: 120 ATVKLIAKMPTLVAMWARIRNGDDPIEPRPDLDYAENFLYMLF-----GEEPDPATAKIL 174
Query: 220 NRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIG 279
+ ILHA+H NAST + + GS+ ADP+A I++ + L G HGGANE+ L ML EIG
Sbjct: 175 DACLILHAEHTMNASTFSALVTGSTLADPYAVISSAIGTLSGPLHGGANEDVLEMLEEIG 234
Query: 280 SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQV 339
S E + Y+ + +I GFGHRVY+ DPR I+++ ++ G + ++
Sbjct: 235 SPENVKAYLDKKLANKQ--KIWGFGHRVYKTKDPRATILQKLAEDLFAKMGEL-SKLYEI 291
Query: 340 AIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEM 399
A+E+ER+ E + +YPNVDFYSGI + LG P +LFT +FAVAR AGW++ W E
Sbjct: 292 ALEVERLCE--ELLGHKGVYPNVDFYSGIVYKELGIPADLFTPIFAVARVAGWLAHWKEQ 349
Query: 400 IVDPSRRIGRPRQLYTGALKRDYVPL 425
+ D RI RP Q+Y G + R YVPL
Sbjct: 350 LGD--NRIFRPTQIYIGEIDRKYVPL 373
>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 = 307 bits (789), Expect = 3e-84
Identities = 138/367 (37%), Positives = 196/367 (53%), Gaps = 21/367 (5%)
Query: 52 CKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHA 111
SKI++IDG+ GIL+YRGY I L+E S F EV YLL +GEL + F +++
Sbjct: 9 ADSKISYIDGDAGILIYRGYDIHDLAENSTFEEVAYLLWNGELPTAEELDAFKAQLAAER 68
Query: 112 LLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSP-SGVQDLEQCVNVSLRMIAKIST 170
L + P AHPM +L +AV AL+ Y P + E + ++R+IAK+ T
Sbjct: 69 ELPAEIIDLLKLLPKDAHPMDVLRTAVSALA--LYDPEADDMSREANLRKAIRLIAKMPT 126
Query: 171 IAAMIYKYSIGQPFVYPRSDLDYASNFLHMCF-SVPCAEYQVNPLLARAMNRIFILHADH 229
I A ++ G V P DL +A+NFL+M P + ARA + ILHADH
Sbjct: 127 IVAAFHRIRNGLEPVAPDPDLSHAANFLYMLTGEKP------SEEAARAFDVALILHADH 180
Query: 230 EQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIM 289
E NAST R+ S+ +D ++ + A + L G HGGANE + ML+EIGS++ + Y+
Sbjct: 181 ELNASTFAARVVASTLSDMYSAVTAAIGALKGPLHGGANERVMKMLLEIGSVDNVAAYVK 240
Query: 290 RAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALE 349
+ +IMGFGHRVY+ DPR + +RE + + TG E+ A+E
Sbjct: 241 DKLANKE--KIMGFGHRVYKTGDPRAKHLREMSRRLGKETGE------PKWYEMSE-AIE 291
Query: 350 DEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGR 409
E+ L PNVDFYS LG P +LFT +FA++R +GW + E + R+ R
Sbjct: 292 QAMRDEKGLNPNVDFYSASVYYMLGIPVDLFTPIFAISRVSGWCAHILEQYFNN--RLIR 349
Query: 410 PRQLYTG 416
PR Y G
Sbjct: 350 PRAEYVG 356
>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 = 285 bits (732), Expect = 1e-77
Identities = 105/223 (47%), Positives = 139/223 (62%), Gaps = 10/223 (4%)
Query: 192 DYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFAC 251
YA NFL+M + +P A+AM+ ILHADHE NAST T R+ GS+ +DP++
Sbjct: 53 SYAENFLYMLGGE-----EPDPEFAKAMDLALILHADHEGNASTFTARVVGSTLSDPYSA 107
Query: 252 IAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNH 311
IAA +A L G HGGANE L ML EIG+ + P K N +MGFGHRVY+ +
Sbjct: 108 IAAAIAALKGPLHGGANEAVLKMLEEIGTPKNEPAEAYIRKKLNSKRVLMGFGHRVYKKY 167
Query: 312 DPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLR 371
DPR ++++ ++L+ G DP+ ++A ELE+IA E Y +KLYPNVDFYSG+ +
Sbjct: 168 DPRATVLKKFAEKLLKEKGL--DPMFELAAELEKIAPEVLYE--KKLYPNVDFYSGVLYK 223
Query: 372 ALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLY 414
A+GFPT LFT LFAV+R GW++ E D RI RPR Y
Sbjct: 224 AMGFPTELFTPLFAVSRAVGWLAHLIEQREDGQ-RIIRPRAEY 265
Score = 79.3 bits (196), Expect = 2e-15
Identities = 29/51 (56%), Positives = 36/51 (70%)
Query: 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGEL 94
P A+ +S+I+ IDG+ G L YRGYPIE+L+E S F EV YLLL GEL
Sbjct: 1 PGLRGVAALESEISVIDGDEGGLRYRGYPIEELAENSSFEEVAYLLLTGEL 51
>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 = 280 bits (718), Expect = 5e-76
Identities = 107/223 (47%), Positives = 139/223 (62%), Gaps = 10/223 (4%)
Query: 192 DYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFAC 251
YA NFL+M + +P ARAM+ ILHADHE NAST T R+ GS+G+DP++
Sbjct: 1 SYAENFLYMLGGE-----EPDPEFARAMDLALILHADHEGNASTFTARVVGSTGSDPYSA 55
Query: 252 IAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNH 311
IAA + L G HGGANE L ML EIG+ + P K IMGFGHRVY+ +
Sbjct: 56 IAAAIGALKGPLHGGANEAVLKMLEEIGTPKNEPAEAYIRKKLESKRVIMGFGHRVYKKY 115
Query: 312 DPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLR 371
DPR ++++ E+L+ G DP+ ++A ELE+IA E Y +KLYPNVDFYSG+ +
Sbjct: 116 DPRATVLKKFAEELLKEDGD--DPMFELAAELEKIAEEVLYE--KKLYPNVDFYSGVLYK 171
Query: 372 ALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLY 414
A+GFPT LFT LFAVAR GW++ E + D +I RPR Y
Sbjct: 172 AMGFPTELFTPLFAVARAVGWLAHLIEQLEDN-FKIIRPRSEY 213
>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 = 257 bits (659), Expect = 3e-69
Identities = 116/357 (32%), Positives = 182/357 (50%), Gaps = 19/357 (5%)
Query: 66 LLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFP 125
L YRGYP++ L+E F EV YLL +GEL N +Q +F+ + + L+ N+ P
Sbjct: 23 LTYRGYPVQDLAENCSFEEVAYLLWNGELPNAAQLAEFSQRERSYRRLDRNLLSLIASLP 82
Query: 126 SSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFV 185
+ HPM +L +AV L + + + ++R++A++ T+ A + G +
Sbjct: 83 KNCHPMDVLRTAVSVLGAEDSETD-DSSPDANLAKAIRLLAQLPTVVAADIRRRKGLDPI 141
Query: 186 YPRSDLDYASNFLHMCF-SVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSS 244
P SDL A NFLHMCF VP +P + RA + IL+A+H NAST T R+ S+
Sbjct: 142 PPDSDLGIAENFLHMCFGEVP------SPEVVRAFDVSLILYAEHSFNASTFTARVITST 195
Query: 245 GADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFG 304
+D ++ I + L G HGGANE ++M++EI E+ +++ A + + ++MGFG
Sbjct: 196 LSDIYSAITGAIGALKGPLHGGANEAVMHMMLEIDDPEKAAQWMLDALARKE--KVMGFG 253
Query: 305 HRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDF 364
HRVY++ D R M + + V V Q + + LED + + PN+DF
Sbjct: 254 HRVYKSGDSRVPTMEKALRRVAAVHD------GQKWLAMYDA-LEDAMVAAKGIKPNLDF 306
Query: 365 YSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRD 421
+G +GF + FT +F +AR GW + E D + RP Y G +R
Sbjct: 307 PAGPAYYLMGFDIDFFTPIFVMARITGWTAHIMEQRAD--NALIRPLSEYNGPEQRP 361
>gnl|CDD|37828 KOG2617, KOG2617, KOG2617, Citrate synthase [Energy production and
conversion].
Length = 458
Score = 232 bits (593), Expect = 1e-61
Identities = 130/438 (29%), Positives = 190/438 (43%), Gaps = 43/438 (9%)
Query: 13 EEIDLPIKE-GSLGSSVLDISFLHKNGI--FTYDPAFSSTASCKSKITFIDGNNGILLYR 69
+E + E G++G+ L + G ++ + I F G+ R
Sbjct: 40 DEYKKFVSEHGTVGNVTLKKIYGGMRGKGLLLWETSVLDPEE---GIRFRGGDIPECQKR 96
Query: 70 GYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAH 129
P E+ +E E+ +LLL G + SQ + ++++ + + + + P H
Sbjct: 97 LPPAEEGAEPL-PEELFWLLLTGNVPTQSQVAALSFELAQRSAVPQGVLDMIDSMPKDLH 155
Query: 130 PMAMLVSAVGALSSF------YYSPSGVQDLEQCV-NVSLRMIAKISTIAAMIYKYSIGQ 182
PMA L +AV AL F Y G Q L +IAK+ TIAA IY+
Sbjct: 156 PMAQLAAAVLALKIFSPFAKAYLRGIGKYKYWQYTYEDCLVLIAKLPTIAAAIYRNIYAD 215
Query: 183 PFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAG 242
P +LDY++NF M S P A+ M +HADHE ++
Sbjct: 216 GIPKPDPNLDYSANFARMLGSR-------QPDFAQLMRLYVGIHADHEGGNVSAHTGHLV 268
Query: 243 SSGADPFACIAAGVACLGGRAHGGANEEALNMLM----EIGSL---ERIPHYIMRAKDKN 295
S DP+ AAG+ L G HG AN+E L L EIG E I YI K N
Sbjct: 269 GSALDPYLSFAAGMNGLAGPLHGLANQEVLRFLGKLIEEIGKDLSKENIKEYIW--KTLN 326
Query: 296 DPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIA--LEDEYF 353
+ G+GH V R DPR ++ RE + L +DP+ + L +IA + E+
Sbjct: 327 SGRVVPGYGHAVLRKTDPRYKVQREFALKHLP-----DDPLFLLVSALYKIAPGVLTEHG 381
Query: 354 IERKLYPNVDFYSGITLRALGFPT-NLFTVLFAVARTAGWVSQ--WTEMIVDPSRRIGRP 410
+ YPNVD +SG+ L+ G P +TVLF V+R G +SQ W + P I RP
Sbjct: 382 KVKNPYPNVDAHSGVLLQYYGLPELFFYTVLFGVSRALGVLSQLIWDRALGLP---IERP 438
Query: 411 RQLYTGALKRDYVPLEER 428
+ + T L R + ER
Sbjct: 439 KSVSTDWLHRFTNMVRER 456
>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 = 228 bits (583), Expect = 3e-60
Identities = 110/360 (30%), Positives = 169/360 (46%), Gaps = 28/360 (7%)
Query: 59 IDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMS 118
+DG G L+ RGY +E L+ + F +V LL +G ++ + ++F ++ L + ++
Sbjct: 16 VDGEAGRLIIRGYSVEDLAGSASFEDVAALLWNGFFPDLPELEEFRAALAAARALPDVVA 75
Query: 119 RFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKY 178
PM L + + L DL +LR++A I A + +
Sbjct: 76 ALLPALAGLD-PMDALRALLALLP-------DSPDLAT----ALRLLAAAPVITAALLRL 123
Query: 179 SIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTV 238
S G+ + P L +A+++L M P +E V RA++ + ADH NAST T
Sbjct: 124 SRGKQPIAPDPSLSHAADYLRMLTGEPPSEAHV-----RALDAYLVTVADHGMNASTFTA 178
Query: 239 RLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPF 298
R+ S+ AD + + + L G HGGA L+ML IG+ E ++ A + +
Sbjct: 179 RVIASTEADLTSAVLGAIGALKGPLHGGAPGPVLDMLDAIGTPENAEAWLREALARGE-- 236
Query: 299 RIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALE--DEYFIER 356
R+MGFGHRVYR DPR +++ + D + A +E+ AL EY R
Sbjct: 237 RLMGFGHRVYRVRDPRADVLKAA---AERLGA--PDERLEFAEAVEQAALALLREYKPGR 291
Query: 357 KLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416
L NV+FY+ + L ALG P FT FA RTAGW + E R+ RP+ Y G
Sbjct: 292 PLETNVEFYTALLLEALGLPREAFTPTFAAGRTAGWTAHVLEQART--GRLIRPQSRYVG 349
>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 = 220 bits (563), Expect = 6e-58
Identities = 115/366 (31%), Positives = 179/366 (48%), Gaps = 22/366 (6%)
Query: 61 GNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRF 120
G G L YRGY IE L+E + F EV YLLL+G+L Q + K+ L +
Sbjct: 19 GGKG-LTYRGYDIEDLAENATFEEVAYLLLYGKLPTRKQLDAYKTKLVALRRLPAALKTV 77
Query: 121 FMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSI 180
P +HPM ++ + L Q E +++R++A +I Y YS
Sbjct: 78 LELIPKDSHPMDVMRTGCSMLGCLEPENEFSQQYE----IAIRLLAIFPSILLYWYHYSH 133
Query: 181 GQPFVYPRSDLD-YASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVR 239
+ +D D A +FLH+ E ++ +AM+ IL+A+HE NAST R
Sbjct: 134 SGKRIETETDEDSIAGHFLHLLHGKKPGELEI-----KAMDVSLILYAEHEFNASTFAAR 188
Query: 240 LAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFR 299
+ S+ +D ++ I + L G HGGANE A+ ++ S E ++ ++ +
Sbjct: 189 VTASTLSDFYSAITGAIGTLRGPLHGGANEAAMELIERFKSPEEAEQGLLEKLERKE--L 246
Query: 300 IMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLY 359
IMGFGHRVY+ DPR I+++ ++ E G + + Q++ +E + E E+KL+
Sbjct: 247 IMGFGHRVYKEGDPRSDIIKKWSKKLSEEGG--DPLLYQISERIEEVMWE-----EKKLF 299
Query: 360 PNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALK 419
PN+DFYS G PT LFT +F ++R GW + E + R+ RP Y G
Sbjct: 300 PNLDFYSASAYHFCGIPTELFTPIFVMSRVTGWAAHIMEQRAN--NRLIRPSADYIGPEP 357
Query: 420 RDYVPL 425
R +VP+
Sbjct: 358 RPFVPI 363
>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 = 186 bits (475), Expect = 7e-48
Identities = 117/387 (30%), Positives = 190/387 (49%), Gaps = 28/387 (7%)
Query: 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFN 104
A S A+ + + + + L YRGY I L+EK +F EV +LL+HG+L S+ +
Sbjct: 2 ALSGVAAGNTALCTVGRSGNDLHYRGYDILDLAEKCEFEEVAHLLVHGKLPTKSELAAYK 61
Query: 105 DKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFY-----YSPSGVQDLEQCVN 159
K+ L N+ P++AHPM ++ + V L + SG +D+
Sbjct: 62 TKLKSLRGLPANVKTALEQLPAAAHPMDVMRTGVSVLGCVLPEKEDHPVSGARDIAD--- 118
Query: 160 VSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLD-YASNFLHMCFSVPCAEYQVNPLLARA 218
R++A + +I Y YS + +D D +FLH+ +E +A
Sbjct: 119 ---RLMASLGSILLYWYHYSHNGKRIEVETDDDSIGGHFLHLLHGEKPSE-----SWEKA 170
Query: 219 MNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEI 278
M+ IL+A+HE NAST T R+ +G+D ++ I + L G HGGANE A +
Sbjct: 171 MHISLILYAEHEFNASTFTARVIAGTGSDMYSAITGAIGALRGPKHGGANEVAFEIQQRY 230
Query: 279 GSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQ 338
S + I R + + ++GFGH VY DPR ++++E ++ + G + +
Sbjct: 231 ESADEAEADIRRRVENKEV--VIGFGHPVYTIADPRNQVIKEVAKQLSKEGG--DMKMFD 286
Query: 339 VAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTE 398
+A LE + E E+K++PN+D++S ++ +G PT +FT LF +ART GW + E
Sbjct: 287 IAERLETVMWE-----EKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTTGWSAHIIE 341
Query: 399 MIVDPSRRIGRPRQLYTGALKRDYVPL 425
D +I RP YTG +VP+
Sbjct: 342 QRQD--GKIIRPSANYTGPEDLKFVPI 366
>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 = 180 bits (459), Expect = 6e-46
Identities = 120/376 (31%), Positives = 183/376 (48%), Gaps = 40/376 (10%)
Query: 64 GILLYRGYPIEQL---SEKSD---FLEVCYLLLHGELANVSQQKDFNDKISRHALLNENM 117
G L YRGY +E L ++K + F E YLLL G L N + ++F + +S + L +N
Sbjct: 36 GKLYYRGYDVEDLVNGAQKENRFGFEETAYLLLFGYLPNKEELEEFCEILSSYRTLPDNF 95
Query: 118 SR-FFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIY 176
+ PS M L +V AL S+ P + LE + S+++IA++ TIA Y
Sbjct: 96 VEDVILKAPSK-DIMNKLQRSVLALYSYDDKPDDI-SLENVLRQSIQLIARLPTIAVYAY 153
Query: 177 K----YSIGQPFV--YPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHE 230
+ Y G+ +P+ +L A N L M P +Y L A+ ++ +LHA+H
Sbjct: 154 QAKRHYYDGESLYIHHPQPELSTAENILSML--RPDKKY--TELEAKLLDLCLVLHAEHG 209
Query: 231 Q-NASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEI----------G 279
N ST T R+ SSG D ++ IAA + L G HGGAN + + ML +I
Sbjct: 210 GGNNSTFTTRVVSSSGTDTYSAIAAAIGSLKGPRHGGANIKVMEMLEDIKENVKDWTDED 269
Query: 280 SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGR-----FND 334
+ I+ + + I G GH VY DPR ++++ + + GR +
Sbjct: 270 EVRAYLRKILNKEAFDKSGLIYGMGHAVYTLSDPRAVVLKKYARSLAKEKGREEEFALYE 329
Query: 335 PIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVS 394
I ++A E+ + +E I + + NVDFYSG + LG P L+T LFAVAR GW +
Sbjct: 330 RIERLAPEV----IAEERGIGKTVCANVDFYSGFVYKMLGIPQELYTPLFAVARIVGWCA 385
Query: 395 QWTEMIVDPSRRIGRP 410
E +++ RI RP
Sbjct: 386 HRIEELLNSG-RIIRP 400
>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 = 152 bits (385), Expect = 2e-37
Identities = 109/409 (26%), Positives = 165/409 (40%), Gaps = 104/409 (25%)
Query: 59 IDGNNGILLYRGYPIEQLSEK--------SDFLEVC-YLLLHGELANVSQQKDFNDKISR 109
+D + GI +RG I + E E +LLL GE+ Q + + + ++
Sbjct: 53 LDPDEGIR-FRGKTIPECQELLPKADGGGEPLPEGLFWLLLTGEVPTEEQVDELSKEWAK 111
Query: 110 HALLNENMSRFFMGFPSSAHPMAMLVSAVGAL---SSF--YYSPSGVQD-------LEQC 157
A + ++ + P + HPM L +A+ AL S F Y+ + E
Sbjct: 112 RAEVPSHVVKMIDNLPRNLHPMTQLSAAILALQSESKFAKAYAEGKINKTTYWEYVYEDA 171
Query: 158 VNVSLRMIAKISTIAAMIY--KYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLL 215
++ +IAK+ +AA IY KY G S LD+++NF HM Y+ +
Sbjct: 172 MD----LIAKLPVVAAKIYRRKYRKGGEIGAIDSKLDWSANFAHM------LGYE-DEEF 220
Query: 216 ARAMNRIFILHADHEQ-NASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEAL-- 272
M LH+DHE N S T L GS+ +DP+ +A + L G HG AN+E L
Sbjct: 221 TDLMRLYLTLHSDHEGGNVSAHTSHLVGSALSDPYLSFSAALNGLAGPLHGLANQEVLKW 280
Query: 273 --NMLMEIG---SLERIPHYI---MRAKDKNDPFRIMGFGHRVYRNHDPR---------- 314
M E+G S E + YI + + + G+GH V R DPR
Sbjct: 281 LLKMQKELGKDVSDEELEKYIWDTLNSGRV-----VPGYGHAVLRKTDPRFTCQREFALK 335
Query: 315 ----------CRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDF 364
+ + VL+ G+ +P YPNVD
Sbjct: 336 HLPDDPLFKLVAQCYKIIPGVLKEHGKVKNP-----------------------YPNVDA 372
Query: 365 YSGITLRALGFP-TNLFTVLFAVARTAGWVSQ--WTEMIVDPSRRIGRP 410
+SG+ L+ G +TVLF V+R G ++Q W SR +G P
Sbjct: 373 HSGVLLQHYGMTEPQYYTVLFGVSRALGVLAQLVW-------SRALGLP 414
>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 = 138 bits (350), Expect = 2e-33
Identities = 119/394 (30%), Positives = 186/394 (47%), Gaps = 54/394 (13%)
Query: 59 IDGNNGILLYRGYPIEQLSE---KSDFLE------VCYLLLHGELANVSQQKDFNDKISR 109
+D GI +RG I + + K+ E + +LLL GE+ Q + + +
Sbjct: 53 LDPEEGIR-FRGLSIPECQKLLPKAPGGEEPLPEGLFWLLLTGEVPTKEQVSALSKEWAA 111
Query: 110 HALLNENMSRFFMGFPSSAHPMAMLVSAVGAL---SSFY--YSPSGVQD---LEQCVNVS 161
A L ++ FP++ HPM+ L +A+ AL S F Y+ G+ E S
Sbjct: 112 RAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESKFAKAYA-EGIHKSKYWEYVYEDS 170
Query: 162 LRMIAKISTIAAMIYK--YSIGQPFVYPRSDLDYASNFLHMC-FSVPCAEYQVNPLLARA 218
+ +IAK+ +AA IY+ Y G+ + S+LD+++NF +M ++ +P
Sbjct: 171 MDLIAKLPCVAAKIYRNLYRGGK-IIAIDSNLDWSANFANMLGYT--------DPQFTEL 221
Query: 219 MNRIFILHADHEQ-NASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLM- 276
M +H+DHE N S T L GS+ +DP+ AA + L G HG AN+E L L
Sbjct: 222 MRLYLTIHSDHEGGNVSAHTTHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTK 281
Query: 277 ---EIG---SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTG 330
E+G S E++ Y+ K N + G+GH V R DPR RE + L
Sbjct: 282 LQKEVGKDVSDEQLREYVW--KTLNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLP--- 336
Query: 331 RFNDPIAQVAIELERIALE--DEYFIERKLYPNVDFYSGITLRALGFP-TNLFTVLFAVA 387
NDP+ ++ +L +I E + +PNVD +SG+ L+ G N +TVLF V+
Sbjct: 337 --NDPLFKLVSQLYKIVPPVLTEQGKAKNPWPNVDAHSGVLLQYYGLTEMNYYTVLFGVS 394
Query: 388 RTAGWVSQ--WTEMIVDPSRRIGRPRQLYTGALK 419
R G +SQ W + P + RP+ + T L+
Sbjct: 395 RALGVLSQLIWDRALGLP---LERPKSVSTDGLE 425
>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 = 129 bits (326), Expect = 2e-30
Identities = 67/207 (32%), Positives = 91/207 (43%), Gaps = 16/207 (7%)
Query: 210 QVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANE 269
++P A + R +L ADHE NAST R+A S+GA +A + AG+A L G HGGA
Sbjct: 92 GLDPAAADLLRRALVLLADHELNASTFAARVAASTGASLYAAVLAGLAALSGPRHGGATA 151
Query: 270 EALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVT 329
+L E + + + + GFGH +Y + DPR + L
Sbjct: 152 RVEALLDEALRAGDAEAAVRERLRRGEA--LPGFGHPLYPDGDPRAA----ALLAALRPL 205
Query: 330 GRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVART 389
G P A+ IE R PN+DF RALG P LFA+ R+
Sbjct: 206 GPAAPPAARALIEAARALTGA--------RPNIDFALAALTRALGLPAGAAFALFALGRS 257
Query: 390 AGWVSQWTEMIVDPSRRIGRPRQLYTG 416
AGW++ E + I RPR Y G
Sbjct: 258 AGWIAHALEQRAQG-KLI-RPRARYVG 282
>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 = 119 bits (300), Expect = 1e-27
Identities = 104/363 (28%), Positives = 160/363 (44%), Gaps = 54/363 (14%)
Query: 87 YLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGAL---SS 143
+LLL G++ Q + + +++ L + + P + HPM L V AL S
Sbjct: 89 WLLLTGKVPTFEQARGLSKELAERGKLPHYIEKLLDSLPKTLHPMTQLSIGVAALNHDSK 148
Query: 144 F------------YYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYK--YSIGQPFVYPRS 189
F Y+ P+ LE +N +IA++ +AA IY+ Y G
Sbjct: 149 FAAAYEKGIKKTEYWEPT----LEDSLN----LIARLPALAARIYRNVYGEGHGLGKIDP 200
Query: 190 DLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQ-NASTSTVRLAGSSGADP 248
++D++ NF M Y N + LH DHE N S T L GS+ +DP
Sbjct: 201 EVDWSYNFTSML------GYGDNLDFVDLLRLYIALHGDHEGGNVSAHTTHLVGSALSDP 254
Query: 249 FACIAAGVACLGGRAHGGANEEALNMLME----IGSL---ERIPHYIMRAKDKNDPFRIM 301
+ +AG+ L G HG A +E L ++E IGS + I Y+ + R++
Sbjct: 255 YLSYSAGLMGLAGPLHGLAAQEVLRWILEMQKNIGSKATDQDIRDYLWKTLKSG---RVV 311
Query: 302 -GFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIA--LEDEYFIERKL 358
G+GH V R DPR + E E+ NDP+ Q+ +L IA + E+ +
Sbjct: 312 PGYGHAVLRKPDPRFTALMEFAQTRPELE---NDPVVQLVQKLSEIAPGVLTEHGKTKNP 368
Query: 359 YPNVDFYSGITLRALGFPTNLF-TVLFAVARTAGWVSQ--WTEMIVDPSRRIGRPRQLYT 415
+PNVD SG+ G L+ TV+F V+R G ++Q W ++ P I RP+ L
Sbjct: 369 FPNVDAASGVLFYHYGIREFLYYTVIFGVSRALGPLTQLVWDRILGLP---IERPKSLSL 425
Query: 416 GAL 418
L
Sbjct: 426 EGL 428
>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 = 78.0 bits (193), Expect = 4e-15
Identities = 55/192 (28%), Positives = 80/192 (41%), Gaps = 22/192 (11%)
Query: 216 ARAMNRIFILHADH-EQNASTSTVRLAGSSGADPF-ACIAAGVACLGGRAHGGANEEALN 273
AR + + + ADH S RL S+G + + +AAG+ +G R GGA E A
Sbjct: 31 ARLLEALLVALADHGPATPSAHAARLTASAGPEDLQSAVAAGLLGIGDR-FGGAGEGAAR 89
Query: 274 MLMEI----GSLERIPHYI---MRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVL 326
+ E +L+ RA K RI GFGH V++N DPR + E+
Sbjct: 90 LFKEAVDSGDALDAAAAEFVAEYRAAKK----RIPGFGHPVHKNPDPR----VPRLLELA 141
Query: 327 EVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAV 386
G P A+ +E+ + + L NVD L LGFP LF +
Sbjct: 142 RELGPAG-PHLDYALAVEKALTAAK---GKPLPLNVDGAIAAILLDLGFPPGALRGLFVL 197
Query: 387 ARTAGWVSQWTE 398
R+ G ++ E
Sbjct: 198 GRSPGLIAHALE 209
Score = 30.6 bits (70), Expect = 0.93
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 70 GYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFN 104
GY + L K F +V YLLL G L + +
Sbjct: 1 GYDLSDLIGKISFGDVLYLLLKGRLPTPYEARLLE 35
>gnl|CDD|176004 cd04039, C2_PSD, C2 domain present in Phosphatidylserine
decarboxylase (PSD). PSD is involved in the
biosynthesis of aminophospholipid by converting
phosphatidylserine (PtdSer) to phosphatidylethanolamine
(PtdEtn). There is a single C2 domain present and it is
thought to confer PtdSer binding motif that is common to
PKC and synaptotagmin. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 108
Score = 34.5 bits (80), Expect = 0.057
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 274 MLMEIGSLERIPHY--IMRAKDKNDPFRIMGFGHRVYR 309
+ MEI S+ +P + R DPF I+ FG RV+R
Sbjct: 3 VFMEIKSITDLPPLKNMTRTGFDMDPFVIISFGRRVFR 40
>gnl|CDD|37216 KOG2005, KOG2005, KOG2005, 26S proteasome regulatory complex,
subunit RPN1/PSMD2 [Posttranslational modification,
protein turnover, chaperones].
Length = 878
Score = 30.3 bits (68), Expect = 1.1
Identities = 16/88 (18%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 267 ANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYR-NHDPRCRIMRETMYEV 325
A EA+++LME+ ++ + Y+ D+++ R+ + P + T ++
Sbjct: 193 AEFEAIDLLMEVEGIDLLLDYV----DEHNYQRVCLYLTSCVPLLPGPDDVALLRTALKI 248
Query: 326 LEVTGRFNDPIAQVAIELERIALEDEYF 353
+ + AI L+ + E F
Sbjct: 249 YLKFNEYPRAL-VGAIRLDDMKEVKEVF 275
>gnl|CDD|35885 KOG0666, KOG0666, KOG0666, Cyclin C-dependent kinase CDK8
[Transcription].
Length = 438
Score = 29.6 bits (66), Expect = 1.6
Identities = 23/111 (20%), Positives = 38/111 (34%), Gaps = 14/111 (12%)
Query: 281 LERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVA 340
L+++P Y D + H+ Y H + + + ++L DPI ++
Sbjct: 276 LKKMPEYQTLLSDFRRHYYDNVSLHKYYHKHKVKDPSALDLLQKLLTY-----DPIKRIT 330
Query: 341 IELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAG 391
E ALE YF E L P T + F + + G
Sbjct: 331 AEQ---ALEHPYFTEDPLPPLP------TSDNVNFEGTTPIIPPQAGQQQG 372
>gnl|CDD|36468 KOG1254, KOG1254, KOG1254, ATP-citrate lyase [Energy production and
conversion].
Length = 600
Score = 28.8 bits (64), Expect = 3.0
Identities = 28/114 (24%), Positives = 46/114 (40%), Gaps = 23/114 (20%)
Query: 244 SGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHY-----IMRA--KDKND 296
+G D F+ + G+ +G R G ++I + P Y MR K +
Sbjct: 421 AGKDLFSSLVRGLLTIGDRFGGA---------LDIAARRFGPAYDKGLAPMRFVGKMRKV 471
Query: 297 PFRIMGFGHRV--YRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIAL 348
P + G GHR+ N D R I++ + T P+ A+E+E+I
Sbjct: 472 PIEVYGIGHRIKSINNPDKRVEILKAFARKNFPAT-----PLLDYALEVEKITT 520
>gnl|CDD|34713 COG5110, RPN1, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 881
Score = 28.8 bits (64), Expect = 3.3
Identities = 18/88 (20%), Positives = 39/88 (44%), Gaps = 6/88 (6%)
Query: 267 ANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGF-GHRVYRNHDPRCRIMRETMYEV 325
A +A+++L+E+G +E++ ++ D ++ R+ + V P + ET ++
Sbjct: 195 AEFDAIDLLVEVGGIEKVLDFV----DTHNYNRVCLYLEDCVPLLPPPEDVALLETALKI 250
Query: 326 LEVTGRFNDPIAQVAIELERIALEDEYF 353
G + AI L++ EY
Sbjct: 251 YLKMGDLTRAVV-GAIRLQKSKEIIEYV 277
>gnl|CDD|36139 KOG0921, KOG0921, KOG0921, Dosage compensation complex, subunit MLE
[Transcription].
Length = 1282
Score = 28.0 bits (61), Expect = 6.0
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 157 CVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFL 198
V R + +A+I+KYS+ P R ++D+ S F
Sbjct: 1001 AYYVEKRKVLTTEQSSALIHKYSVNCPN--SRQEMDFPSPFF 1040
>gnl|CDD|31919 COG1733, COG1733, Predicted transcriptional regulators
[Transcription].
Length = 120
Score = 27.7 bits (61), Expect = 7.1
Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 11/92 (11%)
Query: 322 MYEVLEVTGRFND------PIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGF 375
+ ++ + RFN+ I+ + LE++ +ER +YP L G
Sbjct: 29 LRDLFDGPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKG- 87
Query: 376 PTNLFTVLFAVARTAGWVSQWTEMIVDPSRRI 407
+L VL A+ A W +W + + + S R+
Sbjct: 88 -RDLLPVLLAL---ADWGEKWLDAVDEASLRL 115
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.323 0.138 0.412
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,368,765
Number of extensions: 291887
Number of successful extensions: 768
Number of sequences better than 10.0: 1
Number of HSP's gapped: 666
Number of HSP's successfully gapped: 34
Length of query: 429
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 332
Effective length of database: 4,167,664
Effective search space: 1383664448
Effective search space used: 1383664448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.5 bits)