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)