RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16953
(806 letters)
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 886 bits (2292), Expect = 0.0
Identities = 321/599 (53%), Positives = 432/599 (72%), Gaps = 1/599 (0%)
Query: 202 QTKAIVWGMQTRAVQSMLDFDFVCRRSEPSVAAMVYPFTGDHKLKFYWGHKEVLIPVYKK 261
T+A+ + + VQ MLDFDF+C R PSVA ++ P + K ++G +E+ IPV+
Sbjct: 10 TTQALFYNYKQLPVQRMLDFDFLCGRETPSVAGIINP-GSEGFQKLFFGQEEIAIPVHGS 68
Query: 262 MEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPENMTRKLNLLAKE 321
+E A + ADV +NFAS RSA S++E L P IR +AIIAEG+PE+ T++L A+
Sbjct: 69 IEAACKAHPTADVFINFASFRSAAASSMEALKQPTIRVVAIIAEGVPESDTKQLIAYARA 128
Query: 322 KGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSRSGGMSNELNNIIS 381
+IGPATVGG++ G FKIG+T G +DNI+ KLYRPGSV +VS+SGGMSNE+ N+I+
Sbjct: 129 NNKVVIGPATVGGIQAGAFKIGDTAGTLDNIIQCKLYRPGSVGFVSKSGGMSNEMYNVIA 188
Query: 382 KATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEVGGVEEYEVCAALKDKR 441
+ T+G+YEG+AIGGD +PG+T DH+LR+ P++KMIV+LGE+GG +EY + ALK +
Sbjct: 189 RVTDGIYEGIAIGGDVFPGSTLSDHVLRFNNIPQIKMIVVLGELGGRDEYSLVEALKQGK 248
Query: 442 ITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAVVKNKSLAQAGAHVPSSFDTLGD 501
++KP+VAW GTCA +F SEVQFGHAG+ + D E+A KNK+L AGA VP+SF+ L
Sbjct: 249 VSKPVVAWVSGTCARLFKSEVQFGHAGAKSGGDMESAQAKNKALKDAGAIVPTSFEALEA 308
Query: 502 IIGSVYKDLVSRGDIVPQPELPPPTVPMDYSWARELGLIRKPASFMTSICDERGQELLYA 561
I ++ LV G I+P E+ PP +P D + A + G +R P +++I D+RG+E YA
Sbjct: 309 AIKETFEKLVEEGKIIPVKEVTPPQIPEDLNSAIKSGKVRAPTHIVSTISDDRGEEPCYA 368
Query: 562 GMPISDVLKQNMGIGGVLSLLWFQRQLPPYVCKFLEMSLMVTADHGPAVSGAHNTIVCAR 621
G+P+S +++++ G+G V+SLLWF+R LP Y KF+EM +M+ ADHGP VSGAHNTIV AR
Sbjct: 369 GVPMSSIIEKDYGVGDVISLLWFKRSLPRYCTKFIEMCIMLCADHGPCVSGAHNTIVTAR 428
Query: 622 AGKDLVSSLVSGLLTIGDRFGGALNDAAIQFSAAYDAGLIPMEFVNEMRKKGKLIMGIGH 681
AGKDLVSSLVSGLLTIG RFGGA++DAA F AYD GL P EFV M+KKG + GIGH
Sbjct: 429 AGKDLVSSLVSGLLTIGPRFGGAIDDAARYFKDAYDRGLTPYEFVEGMKKKGIRVPGIGH 488
Query: 682 RVKSINNPDMRVKIIKEFVLQNFPTTPLLNYALEVEKITTSKKPNLILNVDGVIAVAFVD 741
R+KS +N D RV++++++ +FP+ + YA++VE T SK NL+LNVDG I F+D
Sbjct: 489 RIKSRDNRDKRVELLQKYARTHFPSVKYMEYAVQVETYTLSKANNLVLNVDGAIGSLFLD 548
Query: 742 LLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQKRLKQGLYRHPWDDISYV 800
LL SG FT++E E VE+G +NGLFVL RSIG IGH DQKRLKQ LYRHPW+D+ Y
Sbjct: 549 LLAGSGMFTKQEIDEIVEIGYLNGLFVLARSIGLIGHTFDQKRLKQPLYRHPWEDVLYT 607
>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 = 278 bits (714), Expect = 1e-88
Identities = 111/244 (45%), Positives = 132/244 (54%), Gaps = 23/244 (9%)
Query: 562 GMPISDVLKQNMGIGGVLSLLWFQRQLPPYVCKFLEMSLMVTADHGPAVSGAHNTIVCAR 621
G +SD++ + G VL LL R PY + LE L+ ADHGPA AH + A
Sbjct: 1 GYDLSDLIG-KISFGDVLYLLLKGRLPTPYEARLLEALLVALADHGPATPSAHAARLTAS 59
Query: 622 AG-KDLVSSLVSGLLTIGDRFGGALNDAAIQFSAAYDAG----LIPMEFVNEMRKKGKLI 676
AG +DL S++ +GLL IGDRFGGA AA F A D+G EFV E R K I
Sbjct: 60 AGPEDLQSAVAAGLLGIGDRFGGAGEGAARLFKEAVDSGDALDAAAAEFVAEYRAAKKRI 119
Query: 677 MGIGHRVKSINNPDMRVKIIKEFVLQNFPTTPLLNYALEVEKITTSKKP-NLILNVDGVI 735
G GH V NPD RV + E + P P L+YAL VEK T+ K L LNVDG I
Sbjct: 120 PGFGHPVHK--NPDPRVPRLLELARELGPAGPHLDYALAVEKALTAAKGKPLPLNVDGAI 177
Query: 736 AVAFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQKRLKQGLYRHPWD 795
A +DL G GA+ GLFVLGRS G I H +++KRL Q LYRHPWD
Sbjct: 178 AAILLDL----GFPP----------GALRGLFVLGRSPGLIAHALEEKRLGQPLYRHPWD 223
Query: 796 DISY 799
DI Y
Sbjct: 224 DIEY 227
>gnl|CDD|223152 COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy
production and conversion].
Length = 293
Score = 213 bits (545), Expect = 3e-63
Identities = 87/256 (33%), Positives = 134/256 (52%), Gaps = 13/256 (5%)
Query: 256 IPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPENMTRKL 315
+PV+ +E+A+ K A+ V F A D+ +E + I+ + II EGIP +L
Sbjct: 51 LPVFNTVEEAV-KETGANASVIFVPPPFAADAILEAIDAG-IKLVVIITEGIPVLDMLEL 108
Query: 316 NLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSRSGGMSNE 375
A+EKG +IGP G + PG KIG I+ +Y+PG++ VSRSG ++ E
Sbjct: 109 KRYAREKGTRLIGPNCPGIITPGECKIG--------IMPGNIYKPGNIGIVSRSGTLTYE 160
Query: 376 LNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEVGGVEEYEVCA 435
+ +++A G + IGGD PGT+F+D + ++ADPE + IV++GE+GG E E
Sbjct: 161 AVSQLTEAGLGQSTAIGIGGDPIPGTSFIDALEMFEADPETEAIVMIGEIGGPAEEEAAE 220
Query: 436 ALKDKRITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAVVKNKSLAQAGAHVPSS 495
+K KP+VA+ G A + GHAG+ + TA K +L AG V +
Sbjct: 221 YIKANATRKPVVAYIAGRTAP---EGKRMGHAGAIVSGGKGTAESKIAALEAAGVKVAET 277
Query: 496 FDTLGDIIGSVYKDLV 511
LG+++ V K
Sbjct: 278 PAELGELLLEVLKGRQ 293
>gnl|CDD|223449 COG0372, GltA, Citrate synthase [Energy production and conversion].
Length = 390
Score = 138 bits (351), Expect = 1e-35
Identities = 55/233 (23%), Positives = 90/233 (38%), Gaps = 29/233 (12%)
Query: 581 LLWFQRQLP--PYVCKFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI- 637
L + P P + ++ +L++ ADH S V A G DL + + +G+ +
Sbjct: 169 LYMLFGEPPSPPVEARAMDRALILHADHELNAS-TFTARVVASTGSDLYACIAAGIGALK 227
Query: 638 GDRFGGALNDAAIQFSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIK 697
G GGA +G +V + + + IMG GHRV N D R K++K
Sbjct: 228 GPLHGGANEAVMKMLEEIGSSGESAEAYVRKALDRKERIMGFGHRVYK--NYDPRAKVLK 285
Query: 698 EF---VLQNFPTTPLLNYALEVEKITTSKKP---NLILNVDGVIAVAFVDLLRHSGSFTR 751
E + + L A E+E+I L NVD + +
Sbjct: 286 ELAEKLGKELGDLKLYEIAEELEEIALEDLGFEKKLYPNVDFYSGIVY------------ 333
Query: 752 EEAQEYVEMGAINGLFVLGRSIGFIGHYMDQKRLKQGLYRHPWDDISYVLPEQ 804
+M LF + R++G+I H+++QK + R Y PE+
Sbjct: 334 RALGIPTDMF--TPLFAIARTVGWIAHWIEQKEDGNKIIRPRAL---YTGPEE 381
>gnl|CDD|130091 TIGR01019, sucCoAalpha, succinyl-CoA synthetase, alpha subunit.
This model describes succinyl-CoA synthetase alpha
subunits but does not discriminate between GTP-specific
and ATP-specific reactions. The model is designated as
subfamily rather than equivalog for that reason. ATP
citrate lyases appear to form an outgroup [Energy
metabolism, TCA cycle].
Length = 286
Score = 125 bits (317), Expect = 5e-32
Identities = 81/257 (31%), Positives = 131/257 (50%), Gaps = 14/257 (5%)
Query: 250 GHKEVLIPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPE 309
G + +PV+ +++A+ + A+ V F A D+ E + I I I EGIP
Sbjct: 43 GTTVLGLPVFDSVKEAV-EETGANASVIFVPAPFAADAIFEAID-AGIELIVCITEGIPV 100
Query: 310 NMTRKLNLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSRS 369
+ K+ +E G +IGP G + PG KIG I+ +++PG+V VSRS
Sbjct: 101 HDMLKVKRYMEESGTRLIGPNCPGIITPGECKIG--------IMPGHIHKPGNVGIVSRS 152
Query: 370 GGMSNELNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEVGGVE 429
G ++ E + ++KA G V IGGD GT+F+D + ++ DPE + IV++GE+GG
Sbjct: 153 GTLTYEAVHQLTKAGFGQSTCVGIGGDPVNGTSFIDVLEAFEKDPETEAIVMIGEIGGSA 212
Query: 430 EYEVCAALKDKRITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAVVKNKSLAQAG 489
E E A + ++KP+V + G A + GHAG+ + TA K ++L AG
Sbjct: 213 E-EEAADFIKQNMSKPVVGFIAGATAP---PGKRMGHAGAIISGGKGTAESKIEALEAAG 268
Query: 490 AHVPSSFDTLGDIIGSV 506
V S +G+++ +
Sbjct: 269 VTVVKSPSDIGELLAEI 285
>gnl|CDD|240307 PTZ00187, PTZ00187, succinyl-CoA synthetase alpha subunit;
Provisional.
Length = 317
Score = 124 bits (313), Expect = 3e-31
Identities = 81/262 (30%), Positives = 126/262 (48%), Gaps = 14/262 (5%)
Query: 251 HKEVLIPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPE- 309
H + +PV+ +++A K AD V + A + IE + +I + I EGIP+
Sbjct: 69 HLKHGLPVFATVKEA-KKATGADASVIYVPPPHAASAIIEAIE-AEIPLVVCITEGIPQH 126
Query: 310 NMTRKLNLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSRS 369
+M + + L + +IGP G +KPG KIG I+ +++ G + VSRS
Sbjct: 127 DMVKVKHALLSQNKTRLIGPNCPGIIKPGECKIG--------IMPGHIHKKGKIGIVSRS 178
Query: 370 GGMSNELNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEVGGVE 429
G ++ E + G V IGGD + GT F+D + + DPE + I+L+GE+GG
Sbjct: 179 GTLTYEAVAQTTAVGLGQSTCVGIGGDPFNGTNFIDCLKLFLNDPETEGIILIGEIGGTA 238
Query: 430 EYEVCAALKDKRITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAVVKNKSLAQAG 489
E E +K+ I KP+V++ G A + GHAG+ + TA K ++L AG
Sbjct: 239 EEEAAEWIKNNPIKKPVVSFIAGITAP---PGRRMGHAGAIISGGKGTAPGKIEALEAAG 295
Query: 490 AHVPSSFDTLGDIIGSVYKDLV 511
V S LG + V K
Sbjct: 296 VRVVKSPAQLGKTMLEVMKKKG 317
>gnl|CDD|180194 PRK05678, PRK05678, succinyl-CoA synthetase subunit alpha;
Validated.
Length = 291
Score = 116 bits (292), Expect = 2e-28
Identities = 78/259 (30%), Positives = 122/259 (47%), Gaps = 22/259 (8%)
Query: 256 IPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPENMTRKL 315
+PV+ + +A+ A+ V + A D+ +E + I I I EGIP ++
Sbjct: 51 LPVFNTVAEAVEA-TGANASVIYVPPPFAADAILEAID-AGIDLIVCITEGIPVLDMLEV 108
Query: 316 NLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSRSGGMSNE 375
+ K +IGP G + PG KIG I+ +++ G V VSRSG ++ E
Sbjct: 109 KAYLERKKTRLIGPNCPGIITPGECKIG--------IMPGHIHKKGRVGVVSRSGTLTYE 160
Query: 376 LNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEVGGVEEYEVCA 435
++ G V IGGD GT F+D + ++ DPE + IV++GE+GG E E
Sbjct: 161 AVAQLTDLGFGQSTCVGIGGDPINGTNFIDVLEAFEEDPETEAIVMIGEIGGSAEEEAAE 220
Query: 436 ALKDKRITKPLVAWCIGTCA----SMFTSEVQFGHAGSCANSDAETAVVKNKSLAQAGAH 491
+K +TKP+V + G A M GHAG+ + TA K ++L AG
Sbjct: 221 YIKAN-VTKPVVGYIAGVTAPPGKRM-------GHAGAIISGGKGTAEEKKEALEAAGVK 272
Query: 492 VPSSFDTLGDIIGSVYKDL 510
V + +G+++ V K L
Sbjct: 273 VARTPSEIGELLKEVLKGL 291
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 111 bits (278), Expect = 6e-26
Identities = 48/88 (54%), Positives = 65/88 (73%), Gaps = 1/88 (1%)
Query: 89 GKDQVVLITGGGIANFTNVAATFKGIVTALTEFQSKLIEHKISIFVRRAGPNYQEGLRII 148
G+ + +LI GGGIANFT+VAATF GI+ AL E +SKL ++ IFVRR GPNYQ+GL +
Sbjct: 330 GRKRALLI-GGGIANFTDVAATFNGIIRALREKESKLKAARMHIFVRRGGPNYQKGLAKM 388
Query: 149 REVGKTLGIPLFVFGPETHMTAIVGMAL 176
R +G+ +G+P+ V+GPE MT I A+
Sbjct: 389 RALGEEIGVPIEVYGPEATMTGICKQAI 416
Score = 70.6 bits (173), Expect = 1e-12
Identities = 33/76 (43%), Positives = 44/76 (57%)
Query: 29 RFAAVKEETSWAELVRNEPWLESSKLVAKPDQLIKRRGKLGLIKVNTDFKGAQSWISERM 88
R A V E T + EL EPWL S+KLV KPD L +RGK GL+ +N D +++ ER+
Sbjct: 30 RSAQVTESTDFNELANKEPWLSSTKLVVKPDMLFGKRGKSGLVALNLDLAQVATFVKERL 89
Query: 89 GKDQVVLITGGGIANF 104
GK+ + G I F
Sbjct: 90 GKEVEMGGCKGPITTF 105
>gnl|CDD|215988 pfam00549, Ligase_CoA, CoA-ligase. This family includes the CoA
ligases Succinyl-CoA synthetase alpha and beta chains,
malate CoA ligase and ATP-citrate lyase. Some members of
the family utilise ATP others use GTP.
Length = 128
Score = 99.3 bits (248), Expect = 1e-24
Identities = 39/130 (30%), Positives = 60/130 (46%), Gaps = 8/130 (6%)
Query: 366 VSRSGGMSNELNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEV 425
+ G ++ E ++I A G + + +GGD + TT +D + ADPEVK+I+L +
Sbjct: 1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVL 60
Query: 426 G-GVEEYEVCAALKDKR----ITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAVV 480
G G E LK + P+VA GT A + + A + A S A
Sbjct: 61 GYGACEDPAGGLLKAIKEARARELPVVARVCGTEAD---PQGREEQAKALAESGVLIASS 117
Query: 481 KNKSLAQAGA 490
N++L AGA
Sbjct: 118 NNQALRAAGA 127
>gnl|CDD|215066 PLN00125, PLN00125, Succinyl-CoA ligase [GDP-forming] subunit
alpha.
Length = 300
Score = 98.1 bits (244), Expect = 2e-22
Identities = 79/261 (30%), Positives = 133/261 (50%), Gaps = 14/261 (5%)
Query: 250 GHKEVLIPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPE 309
G + + +PV+ + +A ++ K A+ V + A + +E + ++ + I EGIP+
Sbjct: 49 GTEHLGLPVFNTVAEAKAETK-ANASVIYVPPPFAAAAILEAME-AELDLVVCITEGIPQ 106
Query: 310 -NMTRKLNLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSR 368
+M R L ++ +IGP G +KPG KIG I+ +++PG + VSR
Sbjct: 107 HDMVRVKAALNRQSKTRLIGPNCPGIIKPGECKIG--------IMPGYIHKPGRIGIVSR 158
Query: 369 SGGMSNELNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLLGEVGGV 428
SG ++ E + G V IGGD + GT F+D + ++ DP+ + I+L+GE+GG
Sbjct: 159 SGTLTYEAVFQTTAVGLGQSTCVGIGGDPFNGTNFVDCLEKFVKDPQTEGIILIGEIGGT 218
Query: 429 EEYEVCAALKDKRITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAVVKNKSLAQA 488
E + A +K+ KP+VA+ G A + GHAG+ + TA K K+L +A
Sbjct: 219 AEEDAAAFIKESGTEKPVVAFIAGLTAP---PGRRMGHAGAIVSGGKGTAQDKIKALREA 275
Query: 489 GAHVPSSFDTLGDIIGSVYKD 509
G V S +G + V+K+
Sbjct: 276 GVTVVESPAKIGVAMLEVFKE 296
>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 = 88.9 bits (221), Expect = 1e-19
Identities = 67/270 (24%), Positives = 106/270 (39%), Gaps = 46/270 (17%)
Query: 548 TSICDERGQE--LLYAGMPISDVLKQNMGIGGVLSLLWFQRQLPPYVCKFLEM------- 598
+ I G E L Y G PI + L +N V LL +LP Y FL M
Sbjct: 11 SEISVIDGDEGGLRYRGYPIEE-LAENSSFEEVAYLLLT-GELPSYAENFLYMLGGEEPD 68
Query: 599 ---------SLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDA 648
+L++ ADH S V D S++ + + + G GGA N+A
Sbjct: 69 PEFAKAMDLALILHADHEGNAS-TFTARVVGSTLSDPYSAIAAAIAALKGPLHGGA-NEA 126
Query: 649 AIQFSAAY-DAGLIPMEF-VNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEF---VLQN 703
++ P E + + +++MG GHRV D R ++K+F +L+
Sbjct: 127 VLKMLEEIGTPKNEPAEAYIRKKLNSKRVLMGFGHRVYK--KYDPRATVLKKFAEKLLKE 184
Query: 704 FPTTPLLNYALEVEKITTSKKP--NLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMG 761
P+ A E+EKI L NVD V + + + FT
Sbjct: 185 KGLDPMFELAAELEKIAPEVLYEKKLYPNVDFYSGVLYKAMGFPTELFTP---------- 234
Query: 762 AINGLFVLGRSIGFIGHYMDQKRLKQGLYR 791
LF + R++G++ H ++Q+ Q + R
Sbjct: 235 ----LFAVSRAVGWLAHLIEQREDGQRIIR 260
>gnl|CDD|235748 PRK06224, PRK06224, citrate synthase; Provisional.
Length = 263
Score = 88.8 bits (221), Expect = 2e-19
Identities = 68/276 (24%), Positives = 104/276 (37%), Gaps = 46/276 (16%)
Query: 548 TSICDERGQELLYAGMPISDVLKQNMGIGGVLSLLWFQRQLPPYVCKFLEMSLMVTADHG 607
TSI D +E+ G + D++ + ++ LL R P + L+ L+ DHG
Sbjct: 11 TSISDVTPEEIYVRGYDLEDLIG-KLSFTDMIFLLLRGRLPTPNEARLLDAVLVALVDHG 69
Query: 608 PAVSGAHNTIVCAR----AGKDLVSSLVSGLLTIGDRFGGALNDAA---IQFSAAYDAGL 660
S AR G+ L ++ +GLL +G GGA AA + +AA DAG
Sbjct: 70 LTPS-----AAAARMTASGGESLQGAVAAGLLALGSVHGGAGEQAAELLQEIAAAADAGA 124
Query: 661 IPME----FVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTTPLLNYALEV 716
V E R GK + G GH + +P R + + A +
Sbjct: 125 DLDAAARAIVAEYRAAGKRVPGFGHPLHKPVDP--RAPRLLALAREAGVAGRHCRLAEAL 182
Query: 717 EKI--TTSKKPNLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMG----AINGLFVLG 770
E KP L LNVDG IA ++G GLFV+
Sbjct: 183 EAALAAAKGKP-LPLNVDGAIAAI------------------LADLGFPPALARGLFVIS 223
Query: 771 RSIGFIGHYMDQKRLKQG--LYRHPWDDISYVLPEQ 804
R+ G + H ++ + G ++ + + Y P
Sbjct: 224 RAAGLVAHVWEELQQPIGFRIWDPAEEAVEYTGPPP 259
>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 = 82.4 bits (204), Expect = 8e-18
Identities = 49/206 (23%), Positives = 87/206 (42%), Gaps = 26/206 (12%)
Query: 594 KFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQF 652
+ ++++L++ ADH S V G D S++ + + + G GGA N+A ++
Sbjct: 21 RAMDLALILHADHEGNAS-TFTARVVGSTGSDPYSAIAAAIGALKGPLHGGA-NEAVLKM 78
Query: 653 SAAY-DAGLIPMEF-VNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEF---VLQNFPTT 707
P E + + + ++IMG GHRV D R ++K+F +L+
Sbjct: 79 LEEIGTPKNEPAEAYIRKKLESKRVIMGFGHRVYK--KYDPRATVLKKFAEELLKEDGDD 136
Query: 708 PLLNYALEVEKITTSKKP--NLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAING 765
P+ A E+EKI L NVD V + + + FT
Sbjct: 137 PMFELAAELEKIAEEVLYEKKLYPNVDFYSGVLYKAMGFPTELFT--------------P 182
Query: 766 LFVLGRSIGFIGHYMDQKRLKQGLYR 791
LF + R++G++ H ++Q + R
Sbjct: 183 LFAVARAVGWLAHLIEQLEDNFKIIR 208
>gnl|CDD|215837 pfam00285, Citrate_synt, Citrate synthase.
Length = 352
Score = 83.7 bits (208), Expect = 3e-17
Identities = 54/202 (26%), Positives = 88/202 (43%), Gaps = 34/202 (16%)
Query: 594 KFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAI-Q 651
+ L+++L++ ADH S V A DL S++ + + + G GGA N+A +
Sbjct: 167 RALDLALILHADHELNAS-TFTARVVASTLSDLYSAISAAIGALKGPLHGGA-NEAVLRM 224
Query: 652 FSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRV-KSINNPDMRVKIIKEF---VLQNFPTT 707
+ E++ + KG+ +MG GHRV K D R KI+K+F +
Sbjct: 225 LEEIGSPENVE-EYIEKALDKGERLMGFGHRVYK---TYDPRAKILKKFARELAAELGDD 280
Query: 708 PLLNYALEVEKITTS--KKPNLILNVD---GVIAVAFVDLLRHSGSFTREEAQEYVEMGA 762
PLL A ++E++ K+ L NVD GV L G E
Sbjct: 281 PLLEIAEKIEEVALEDLKEKKLYPNVDFYSGV-------LYYALG-IPTE---------L 323
Query: 763 INGLFVLGRSIGFIGHYMDQKR 784
LF + R +G++ H ++Q+
Sbjct: 324 FTPLFAVSRVVGWLAHIIEQRE 345
>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 = 69.2 bits (170), Expect = 2e-12
Identities = 53/207 (25%), Positives = 87/207 (42%), Gaps = 30/207 (14%)
Query: 594 KFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQF 652
K ++++L++ ADH S V A D+ S++ + + + G GGA N+A ++
Sbjct: 168 KAMDLALILHADHEGNAS-TFTARVVASTLSDMYSAIAAAIAALKGPLHGGA-NEAVLKM 225
Query: 653 SAAYDAGLIPMEFVNEMRKK---GKLIMGIGHRVKSINNPDMRVKIIKEF---VLQNFPT 706
+ G P + KK + IMG GHRV D R KI+KE + +
Sbjct: 226 LL--EIG-TPENVEAYIWKKLANKRRIMGFGHRVYK--TYDPRAKILKELAEELAEEKGD 280
Query: 707 TPLLNYALEVEKITTSKKP--NLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAIN 764
L A E+E+I + NVD V + L + FT
Sbjct: 281 DKLFEIAEELEEIALEVLGEKGIYPNVDFYSGVVYKALGFPTELFT-------------- 326
Query: 765 GLFVLGRSIGFIGHYMDQKRLKQGLYR 791
LF + R++G++ H ++ + Q L R
Sbjct: 327 PLFAVSRAVGWLAHIIEYRENNQRLIR 353
>gnl|CDD|215250 PLN02456, PLN02456, citrate synthase.
Length = 455
Score = 67.4 bits (165), Expect = 1e-11
Identities = 53/201 (26%), Positives = 88/201 (43%), Gaps = 31/201 (15%)
Query: 590 PYVCKFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTIGDRFGGALNDAA 649
P + + L++ ++ ADH S A + +G D +S+ +G+ + G N+A
Sbjct: 242 PRLARLLDLYFIIHADHEGGCSTAAARHLVGSSGVDPYTSVAAGVNALAGPLHGGANEAV 301
Query: 650 IQF-SAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNF---P 705
++ IP E+V ++ K++ G GHRV N D R K I+EF L+ F
Sbjct: 302 LKMLKEIGTVENIP-EYVEGVKNSKKVLPGFGHRV--YKNYDPRAKCIREFALEVFKHVG 358
Query: 706 TTPLLNYALEVEKITTS----KKPNLILNVD---GVIAVAFVDLLRHSGSFTREEAQEYV 758
PL A +E++ K L NVD GV+ LR G F +E+
Sbjct: 359 DDPLFKVASALEEVALLDEYFKVRKLYPNVDFYSGVL-------LRALG-FP----EEFF 406
Query: 759 EMGAINGLFVLGRSIGFIGHY 779
+ LF + R+ G++ +
Sbjct: 407 TV-----LFAVSRAAGYLSQW 422
>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 = 56.2 bits (136), Expect = 3e-08
Identities = 54/216 (25%), Positives = 93/216 (43%), Gaps = 29/216 (13%)
Query: 575 IGGVLSLLWFQRQLPPYVCKFLEMSLMVTADHGPAVSGAHNTI---VCARAGKDLVSSLV 631
I G L ++ K +++SL++ A+H S T V A D S++
Sbjct: 147 IAGHFLHLLHGKKPGELEIKAMDVSLILYAEHEFNAS----TFAARVTASTLSDFYSAIT 202
Query: 632 SGLLTI-GDRFGGALNDAAIQFSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPD 690
+ T+ G GGA N+AA++ + + + + E ++ +LIMG GHRV +P
Sbjct: 203 GAIGTLRGPLHGGA-NEAAMELIERFKSPEEAEQGLLEKLERKELIMGFGHRVYKEGDP- 260
Query: 691 MRVKIIKEFVLQ---NFPTTPLLNYALEVEKITTSKKPNLILNVDGVIAVAFVDLLRHSG 747
R IIK++ + L + +E++ +K L N+D A A+ G
Sbjct: 261 -RSDIIKKWSKKLSEEGGDPLLYQISERIEEVMWEEK-KLFPNLDFYSASAY----HFCG 314
Query: 748 SFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQK 783
T E+ +FV+ R G+ H M+Q+
Sbjct: 315 IPT--------EL--FTPIFVMSRVTGWAAHIMEQR 340
>gnl|CDD|130859 TIGR01800, cit_synth_II, 2-methylcitrate synthase/citrate synthase
II. Members of this family are dimeric enzymes with
activity as 2-methylcitrate synthase, citrate synthase,
or both. Many Gram-negative species have a hexameric
citrate synthase, termed citrate synthase I (TIGR01798).
Members of this family (TIGR01800) appear as a second
citrate synthase isozyme but typically are associated
with propionate metabolism and synthesize
2-methylcitrate from propionyl-CoA; citrate synthase
activity may be incidental. A number of species,
including Thermoplasma acidophilum, Pyrococcus furiosus,
and the Antarctic bacterium DS2-3R have a bifunctional
member of this family as the only citrate synthase
isozyme.
Length = 368
Score = 53.5 bits (129), Expect = 2e-07
Identities = 49/225 (21%), Positives = 91/225 (40%), Gaps = 30/225 (13%)
Query: 570 KQNMGIGG-VLSLLWFQRQLPPYVCKFLEMSLMVTADHG-PAVSGAHNTIVCARAGKDLV 627
K + I G L +L + K ++++L++ A+H A + A V A D+
Sbjct: 144 KDDDSIAGNFLYML-HGEEPTKEWEKAMDIALILYAEHEFNASTFA--ARVIASTLSDMY 200
Query: 628 SSLVSGLLTI-GDRFGGALNDAAIQFSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSI 686
S++ + + + G GGA N+A + ++ + + + IMG GHRV
Sbjct: 201 SAITAAIGALKGPLHGGA-NEAVMAMLDEIGDPDKAEAWIRKALENKERIMGFGHRVYKT 259
Query: 687 NNPDMRVKIIKEF---VLQNFPTTPLLNYALEVEKITTSKKPNLILNVDGVIAVAFVDLL 743
+P R KI+KE+ + ++ A +E + +K + NVD A + +
Sbjct: 260 YDP--RAKILKEYAKKLSAKEGSSKWYEIAERLEDVMEEEK-GIYPNVDFFSASVYYMMG 316
Query: 744 RHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGH---YMDQKRL 785
+ FT +F + R G+ H ++ RL
Sbjct: 317 IPTDLFT--------------PIFAMSRVTGWTAHIIEQVENNRL 347
>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 = 49.4 bits (118), Expect = 5e-06
Identities = 42/152 (27%), Positives = 68/152 (44%), Gaps = 14/152 (9%)
Query: 590 PYVCKFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDA 648
P + + L+ ++ ADH S + + D +S + + + + G GGA N+A
Sbjct: 183 PRLARALDRLWILHADHEMNCSTS-AARHTGSSLADPISCMAAAIAALYGPLHGGA-NEA 240
Query: 649 AIQFSAAY-DAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEF---VLQNF 704
A++ +P F+ ++ + +MG GHRV N D R K+I+E VL
Sbjct: 241 ALKMLREIGTPENVP-AFIERVKNGKRRLMGFGHRV--YKNYDPRAKVIREILHEVLTEV 297
Query: 705 PTTPLLNYALEVEKITTS----KKPNLILNVD 732
PLL A+E+E+I L NVD
Sbjct: 298 EKDPLLKVAMELERIALEDEYFVSRKLYPNVD 329
>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 = 49.4 bits (118), Expect = 5e-06
Identities = 60/227 (26%), Positives = 102/227 (44%), Gaps = 42/227 (18%)
Query: 576 GGVLSLLWFQRQ----LPPYVCKFLEMSLMVTADHGPAVS-GAHNTIVCARAGKDLVSSL 630
G LS+L+ + P + K L++ ++ ADH S A ++ +RA D +++
Sbjct: 158 GNFLSMLFKMTEPKYEPNPVLAKALDVLFILHADHEQNCSTSAMRSVGSSRA--DPYTAV 215
Query: 631 VSGLLTIGDRFGGALNDAAIQ-FSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNP 689
+ + + G N+A ++ IP +F+ +++ + +MG GHRV N
Sbjct: 216 AAAVAALYGPLHGGANEAVLRMLQQIGSPKNIP-DFIETVKQGKERLMGFGHRV--YKNY 272
Query: 690 DMRVKIIKEFVLQNFPTT---PLLNYALEVEKIT------TSKKPNLILNVD---GVIAV 737
D R +IIK+ + F T PLL+ A+E+EKI S+K L NVD G+I
Sbjct: 273 DPRARIIKKIADEVFEATGRNPLLDIAVELEKIALEDEYFISRK--LYPNVDFYSGLIYQ 330
Query: 738 AFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQKR 784
A F E A LF + R+ G++ +++ R
Sbjct: 331 AL--------GFPTE---------AFTVLFAIPRTSGWLAQWIEMLR 360
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 49.1 bits (118), Expect = 6e-06
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 13/82 (15%)
Query: 92 QVVLIT-GGGIANFTNVAATFKGIVTALTEFQSKLIEHKISIFVRRAGPNYQEGLRIIRE 150
+ + + GGI T +GI+ AL E + + VR G N +EG RI+ E
Sbjct: 311 KAIFVNIFGGI---TRCDEVAEGIIAALKEVG-----VNVPLVVRLEGTNVEEGKRILAE 362
Query: 151 VGKTLGIPLFVFGPETHMTAIV 172
G+ +
Sbjct: 363 ----SGLNIIAADDLDEAAEKA 380
Score = 39.1 bits (92), Expect = 0.007
Identities = 17/64 (26%), Positives = 24/64 (37%)
Query: 36 ETSWAELVRNEPWLESSKLVAKPDQLIKRRGKLGLIKVNTDFKGAQSWISERMGKDQVVL 95
TS E L +V K RGK G +K+ + A+ E +GK+
Sbjct: 25 ATSPEEAEEAAKELGGGPVVVKAQVHAGGRGKAGGVKLAKSPEEAKEAAEEILGKNYQTD 84
Query: 96 ITGG 99
I G
Sbjct: 85 IKGE 88
>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 = 48.3 bits (116), Expect = 1e-05
Identities = 64/212 (30%), Positives = 97/212 (45%), Gaps = 43/212 (20%)
Query: 590 PYVCKFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDA 648
P V K L+ L++ ADH S + +V +G +L +S+ +G+ + G GGA N+A
Sbjct: 198 PVVVKALDTILILHADHEQNASTSTVRMV-GSSGANLFASISAGIAALWGPLHGGA-NEA 255
Query: 649 AI-QFSAAYDAGLIPMEFVNEMRKKGKL--IMGIGHRV-KSINNPDMRVKIIKEF---VL 701
+ G + +++ + + K +MG GHRV K N D R KI+K+ VL
Sbjct: 256 VLEMLEEIGSVGNVD-KYIAKAKDKNDPFRLMGFGHRVYK---NYDPRAKILKKTCDEVL 311
Query: 702 QNFPT-TPLLNYALEVEKIT------TSKKPNLILNVD---GVIAVAFVDLLRHSGSFTR 751
PLL A+E+E+I +K L NVD G+I LR G T
Sbjct: 312 AELGKDDPLLEIAMELEEIALKDDYFIERK--LYPNVDFYSGII-------LRALGIPT- 361
Query: 752 EEAQEYVEMGAINGLFVLGRSIGFIGHYMDQK 783
EM + LF LGR+ G+I + +
Sbjct: 362 -------EMFTV--LFALGRTPGWIAQWREMH 384
>gnl|CDD|180164 PRK05614, gltA, type II citrate synthase; Reviewed.
Length = 419
Score = 47.6 bits (114), Expect = 2e-05
Identities = 62/222 (27%), Positives = 91/222 (40%), Gaps = 65/222 (29%)
Query: 590 PYVCKFLEMSLMVTADHGP----------AVSGAHNTIVCARAGKDLVSSLVSGLLTIGD 639
P + + L+ ++ ADH SGA N C AG +++L G
Sbjct: 216 PVLVRALDRIFILHADHEQNASTSTVRLAGSSGA-NPFACIAAG---IAAL------WGP 265
Query: 640 RFGGALNDAAI-QFSAAYDAGLIPMEFVNEMRKK--GKLIMGIGHRVKSINNPDMRVKII 696
GGA N+A + IP EF+ + K G +MG GHRV N D R KI+
Sbjct: 266 AHGGA-NEAVLKMLEEIGSVDNIP-EFIARAKDKNDGFRLMGFGHRV--YKNYDPRAKIM 321
Query: 697 KEF---VLQNFPT-TPLLNYALEVEKITT------SKKPNLILNVD---GVI--AVAF-V 740
+E VL+ PLL A+E+E+I +K L NVD G+I A+
Sbjct: 322 RETCHEVLKELGLNDPLLEVAMELEEIALNDEYFIERK--LYPNVDFYSGIILKALGIPT 379
Query: 741 DLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQ 782
+ FT +F L R++G+I H+ +
Sbjct: 380 SM------FT--------------VIFALARTVGWIAHWNEM 401
>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 = 45.9 bits (109), Expect = 6e-05
Identities = 45/158 (28%), Positives = 75/158 (47%), Gaps = 17/158 (10%)
Query: 590 PYVCKFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDA 648
P + + L++ ++ A+H S A + A +G D+ +++ + + G GGA N+A
Sbjct: 203 PRLARALDILFILHAEHEMNCSTAAVRHL-ASSGVDVYTAVAGAVGALYGPLHGGA-NEA 260
Query: 649 AIQFSAAY-DAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTT 707
++ A IP F+ ++ + + + G GHRV N D R KIIK+ + F
Sbjct: 261 VLRMLAEIGTVENIP-AFIEGVKNRKRKLSGFGHRV--YKNYDPRAKIIKKLADEVFEIV 317
Query: 708 ---PLLNYALEVEKITTSK----KPNLILNVD---GVI 735
PL+ A+ +EK S K L NVD G+I
Sbjct: 318 GKDPLIEIAVALEKAALSDEYFVKRKLYPNVDFYSGLI 355
>gnl|CDD|202320 pfam02629, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 96
Score = 41.4 bits (98), Expect = 1e-04
Identities = 25/107 (23%), Positives = 38/107 (35%), Gaps = 13/107 (12%)
Query: 201 EQTKAIVWGMQTRAVQSMLDFDFVCRRSEPSVAAMVYPFTGDHKLKFYWGHKEVL-IPVY 259
+ TK V G +Q + F + V + G EV IPVY
Sbjct: 2 KDTKVAVIGAGGLGIQGLYHFIQLLGYGIKMVFGVNPRKGGT----------EVGGIPVY 51
Query: 260 KKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEG 306
K +++ ++ DV V A ++ E L I+ I I G
Sbjct: 52 KSVDELE-EDTGVDVAVITVPAPFAQEAIDE-LVDAGIKGIVNITPG 96
>gnl|CDD|214881 smart00881, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 100
Score = 40.2 bits (95), Expect = 4e-04
Identities = 25/107 (23%), Positives = 34/107 (31%), Gaps = 10/107 (9%)
Query: 201 EQTKAIVWGMQTRAVQSMLDFDFVCRRSEPSVAAMVYPFTGDHKLKFYWGHKEVLIPVYK 260
T V G L V R V G +PVY
Sbjct: 4 PNTSVAVVGASGNLGSFGL---AVMRNLLEYGTKFVGGVYPGKVGPKVDG-----VPVYD 55
Query: 261 KMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGI 307
+ +A + DV V F +A D+ E + I+ I +I EGI
Sbjct: 56 SVAEAPEET-GVDVAVIFVPAEAAPDAIDEAIEAG-IKGIVVITEGI 100
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 43.5 bits (103), Expect = 4e-04
Identities = 56/250 (22%), Positives = 92/250 (36%), Gaps = 34/250 (13%)
Query: 251 HKEVL-IPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETLGFPQIRSIAIIAEGIPE 309
+ EVL + Y + D DA L + LG ++ +I+ G E
Sbjct: 48 YDEVLGVKAYTSVADL----PDAPDLAVIVVPAKVVPEIVHELGEKGVKGAIVISAGFRE 103
Query: 310 ------NMTRKLNLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSV 363
+ ++L A++ G+ IIGP +G + P I D + G
Sbjct: 104 AGEEGMELEKELVEAARKYGMRIIGPNCLGLINP----IIGLNATFDPVFGLGR--GGGG 157
Query: 364 AYVSRSGGMSNELNNIISKATNGVYEGVAIGGDRYPG----TTFMDHILRYQADPEVKMI 419
A+VS+SG +S + + ++ +G+ G D + DP K I
Sbjct: 158 AFVSQSGAVSFAILDWANE------DGMGFSIKVSLGNAADRDESDLLEYLADDPRTKAI 211
Query: 420 VLLGEVGGVEEYEVCAALKDKRITKPLVAWCIGTCASMFTSEVQFGHAGSCANSDAETAV 479
L E + AA +R KP++A + S ++ H GS A SD
Sbjct: 212 GLYIEGVKDGRKFLNAARAAER-KKPIIA--LKAGRSEAGAKAAASHTGSLAGSDE---- 264
Query: 480 VKNKSLAQAG 489
+ + QAG
Sbjct: 265 AYDAAFKQAG 274
>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 = 42.6 bits (101), Expect = 5e-04
Identities = 43/199 (21%), Positives = 75/199 (37%), Gaps = 31/199 (15%)
Query: 594 KFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQF 652
+ +++L++ ADH S V A D+ S++ + + + G GGA N+ ++
Sbjct: 168 RAFDVALILHADHELNAS-TFAARVVASTLSDMYSAVTAAIGALKGPLHGGA-NERVMKM 225
Query: 653 SAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQ---NFPTTPL 709
+ +V + + IMG GHRV D R K ++E +
Sbjct: 226 LLEIGSVDNVAAYVKDKLANKEKIMGFGHRV--YKTGDPRAKHLREMSRRLGKETGEPKW 283
Query: 710 LNYALEVEKITTSKKPNLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFV- 768
+ +E+ +K L NVD F +S S Y +G LF
Sbjct: 284 YEMSEAIEQAMRDEK-GLNPNVD------F-----YSASV-------YYMLGIPVDLFTP 324
Query: 769 ---LGRSIGFIGHYMDQKR 784
+ R G+ H ++Q
Sbjct: 325 IFAISRVSGWCAHILEQYF 343
>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 = 42.3 bits (100), Expect = 7e-04
Identities = 51/196 (26%), Positives = 77/196 (39%), Gaps = 25/196 (12%)
Query: 596 LEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQFSA 654
L+ L+ ADHG S V A DL S+++ + + G GGA A
Sbjct: 159 LDAYLVTVADHGMNAS-TFTARVIASTEADLTSAVLGAIGALKGPLHGGAPGPVLDMLDA 217
Query: 655 AYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTTPLLNYAL 714
++ E +G+ +MG GHRV + +P R ++K + L +A
Sbjct: 218 IGTPENAE-AWLREALARGERLMGFGHRVYRVRDP--RADVLKAAAERLGAPDERLEFAE 274
Query: 715 EVEKITTS----KKPN--LILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFV 768
VE+ + KP L NV+ A+ LL G RE A F
Sbjct: 275 AVEQAALALLREYKPGRPLETNVEFYTAL----LLEALG-LPRE---------AFTPTFA 320
Query: 769 LGRSIGFIGHYMDQKR 784
GR+ G+ H ++Q R
Sbjct: 321 AGRTAGWTAHVLEQAR 336
>gnl|CDD|184470 PRK14037, PRK14037, citrate synthase; Provisional.
Length = 377
Score = 42.0 bits (99), Expect = 0.001
Identities = 49/202 (24%), Positives = 85/202 (42%), Gaps = 26/202 (12%)
Query: 594 KFLEMSLMVTADHG-PAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQ 651
K ++ +L++ DH PA + A +V A D+ S + + L + G GGA +A Q
Sbjct: 171 KAMDAALILYTDHEVPASTTA--ALVAASTLSDMYSCITAALAALKGPLHGGAAEEAFKQ 228
Query: 652 FSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRV--KIIKEFVLQNFPTTPL 709
F D + M F +++ K +MG GHRV +P ++ ++ + + +N
Sbjct: 229 FVEIGDPNNVEMWFNDKIINGKKRLMGFGHRVYKTYDPRAKIFKELAETLIERNSEAKKY 288
Query: 710 LNYALEVEK--ITTSKKPNLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLF 767
A ++E+ I + N D + F L FT LF
Sbjct: 289 FEIAQKLEELGIKQFGSKGIYPNTDFYSGIVFYALGFPVYMFT--------------ALF 334
Query: 768 VLGRSIGFIGHYM----DQKRL 785
L R++G++ H + +Q RL
Sbjct: 335 ALSRTLGWLAHIIEYVEEQHRL 356
>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 = 42.0 bits (99), Expect = 0.001
Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 28/127 (22%)
Query: 665 FVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTT----PLLNYALEVEKIT 720
++++ + I G GHRV +P R I+++ F L ALEVE++
Sbjct: 242 YLDKKLANKQKIWGFGHRVYKTKDP--RATILQKLAEDLFAKMGELSKLYEIALEVERLC 299
Query: 721 TSKKPNLILNVDGVIA-VAFVDLLRHSGSFTREEAQEYVEMGAINGL----FVLGRSIGF 775
L GV V F +SG Y E+G L F + R G+
Sbjct: 300 EEL-----LGHKGVYPNVDF-----YSGIV-------YKELGIPADLFTPIFAVARVAGW 342
Query: 776 IGHYMDQ 782
+ H+ +Q
Sbjct: 343 LAHWKEQ 349
>gnl|CDD|131764 TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP
forming), alpha domain. Although technically
reversible, it is believed that this group of
ADP-dependent acetyl-CoA synthetases (ACS) act in the
direction of acetate and ATP production in the organisms
in which it has been characterized. In most species this
protein exists as a fused alpha-beta domain polypeptide.
In Pyrococcus and related species, however the domains
exist as separate polypeptides. This model represents
the alpha (N-terminal) domain. In Pyrococcus and related
species there appears to have been the development of a
paralogous family such that four other proteins are
close relatives. In reference , one of these (along with
its beta-domain partner) was characterized as ACS-II
showing specificity for phenylacetyl-CoA. This model has
been constructed to exclude these non-ACS-I paralogs.
This may result in new, authentic ACS-I sequences
falling below the trusted cutoff.
Length = 447
Score = 40.8 bits (96), Expect = 0.002
Identities = 49/218 (22%), Positives = 90/218 (41%), Gaps = 33/218 (15%)
Query: 297 IRSIAIIAEGIPE------NMTRKLNLLAKEKGVSIIGPATVGGLKPGCFKIGNTGGMMD 350
++ +I G E + ++L +A++ G+ ++GP +G I NT ++
Sbjct: 89 VKGAVVITAGFKEVGEEGAELEQELVEIARKYGMRLLGPNCLG--------IINTHIKLN 140
Query: 351 NILHSKLYRPGSVAYVSRSGGMSNELNNIISKATNGVYEGVAIGGDRYPGTTFMDHILRY 410
+ + G +A++S+SG + L + K G V++G D +
Sbjct: 141 ATFAPTMPKKGGIAFISQSGALLTALLDWAEKNGVGFSYFVSLGNK--ADIDESDLLEYL 198
Query: 411 QADPEVKMIVLLGEVGGVEEYEVCAALKDKRIT--KPLVAWCIGTC---ASMFTSEVQFG 465
DP+ K+I+L E G+++ + I+ KP+V GT A +S
Sbjct: 199 ADDPDTKVILLYLE--GIKDGRK-FLKTAREISKKKPIVVLKSGTSEAGAKAASS----- 250
Query: 466 HAGSCANSDAETAVVKNKSLAQAGAHVPSSFDTLGDII 503
H G+ A SD + + QAG S + L D+
Sbjct: 251 HTGALAGSDE----AYDAAFKQAGVIRADSIEELFDLA 284
>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 = 39.9 bits (94), Expect = 0.003
Identities = 49/193 (25%), Positives = 73/193 (37%), Gaps = 28/193 (14%)
Query: 596 LEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQFSA 654
L +L++ ADH S V A G L +++++GL + G R GGA
Sbjct: 101 LRRALVLLADHELNAS-TFAARVAASTGASLYAAVLAGLAALSGPRHGGATARVEALLDE 159
Query: 655 AYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTTPLLNYAL 714
A AG V E ++G+ + G GH + + D R + + P A
Sbjct: 160 ALRAG-DAEAAVRERLRRGEALPGFGHPL--YPDGDPRAAALLAALRPLGP--AAPPAAR 214
Query: 715 EVEKIT---TSKKPNLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGR 771
+ + T +PN I A L R G A LF LGR
Sbjct: 215 ALIEAARALTGARPN--------IDFALAALTRALG-LPAGAAF---------ALFALGR 256
Query: 772 SIGFIGHYMDQKR 784
S G+I H ++Q+
Sbjct: 257 SAGWIAHALEQRA 269
>gnl|CDD|233579 TIGR01798, cit_synth_I, citrate synthase I (hexameric type). This
model describes one of several distinct but closely
homologous classes of citrate synthase, the protein that
brings carbon (from acetyl-CoA) into the TCA cycle. This
form, class I, is known to be hexameric and
allosterically inhibited by NADH in Escherichia coli,
Acinetobacter anitratum, Azotobacter vinelandii,
Pseudomonas aeruginosa, etc. In most species with a
class I citrate synthase, a dimeric class II isozyme is
found. The class II enzyme may act primarily on
propionyl-CoA to make 2-methylcitrate or be
bifunctional, may be found among propionate utilization
enzymes, and may be constitutive or induced by
propionate. Some members of this model group as class I
enzymes, and may be hexameric, but have shown regulatory
properties more like class II enzymes [Energy
metabolism, TCA cycle].
Length = 412
Score = 39.4 bits (92), Expect = 0.006
Identities = 57/188 (30%), Positives = 84/188 (44%), Gaps = 50/188 (26%)
Query: 611 SGAHNTIVCARAGKDLVSSLVSGLLTIGDRFGGALNDAAIQFSAAY-DAGLIPMEFVNEM 669
SGA N C AG +++L G GGA N+AA++ IP EF+ ++
Sbjct: 234 SGA-NPFACIAAG---IAAL------WGPAHGGA-NEAALKMLEEIGSVKNIP-EFIKKV 281
Query: 670 RKKGKL--IMGIGHRVKSINNPDMRVKIIKEF---VLQNFPT--TPLLNYALEVEKIT-- 720
+ K +MG GHRV N D R K+++E VL+ PL A+E+EKI
Sbjct: 282 KDKNDPFRLMGFGHRV--YKNYDPRAKVMRETCHEVLKELGLHDDPLFKLAMELEKIALN 339
Query: 721 ----TSKKPNLILNVD---GVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSI 773
+K L NVD G+I L+ G T M + +F L R++
Sbjct: 340 DPYFIERK--LYPNVDFYSGII-------LKAMGIPT--------SMFTV--IFALARTV 380
Query: 774 GFIGHYMD 781
G+I H+ +
Sbjct: 381 GWISHWSE 388
>gnl|CDD|198191 cd09938, SH2_N-SH2_Zap70_Syk_like, N-terminal Src homology 2 (SH2)
domain found in Zeta-chain-associated protein kinase 70
(ZAP-70) and Spleen tyrosine kinase (Syk) proteins.
ZAP-70 and Syk comprise a family of hematopoietic cell
specific protein tyrosine kinases (PTKs) that are
required for antigen and antibody receptor function.
ZAP-70 is expressed in T and natural killer (NK) cells
and Syk is expressed in B cells, mast cells,
polymorphonuclear leukocytes, platelets, macrophages,
and immature T cells. They are required for the proper
development of T and B cells, immune receptors, and
activating NK cells. They consist of two N-terminal Src
homology 2 (SH2) domains and a C-terminal kinase domain
separated from the SH2 domains by a linker or hinge
region. Phosphorylation of both tyrosine residues within
the Immunoreceptor Tyrosine-based Activation Motifs
(ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the
Src-family PTKs is required for efficient interaction of
ZAP-70 and Syk with the receptor subunits and for
receptor function. ZAP-70 forms two phosphotyrosine
binding pockets, one of which is shared by both SH2
domains. In Syk the two SH2 domains do not form such a
phosphotyrosine-binding site. The SH2 domains here are
believed to function independently. In addition, the two
SH2 domains of Syk display flexibility in their relative
orientation, allowing Syk to accommodate a greater
variety of spacing sequences between the ITAM
phosphotyrosines and singly phosphorylated non-classical
ITAM ligands. This model contains the N-terminus SH2
domains of both Syk and Zap70. In general SH2 domains
are involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 104
Score = 35.4 bits (82), Expect = 0.017
Identities = 16/34 (47%), Positives = 26/34 (76%), Gaps = 1/34 (2%)
Query: 747 GSFTREEAQEYVEMGAIN-GLFVLGRSIGFIGHY 779
GS TREEA+EY+++ ++ GLF+L +S+ +G Y
Sbjct: 6 GSITREEAEEYLKLAGMSDGLFLLRQSLRSLGGY 39
>gnl|CDD|184468 PRK14035, PRK14035, citrate synthase; Provisional.
Length = 371
Score = 37.0 bits (86), Expect = 0.036
Identities = 29/112 (25%), Positives = 47/112 (41%), Gaps = 20/112 (17%)
Query: 676 IMGIGHRVKSINNPDMRVKIIKEF---VLQNFPTTPLLNYALEVEKITTSKKPNLILNVD 732
IMG GHRV +P R K ++E + + L ++++EK +K LI NVD
Sbjct: 252 IMGFGHRVYKDGDP--RAKYLREMSRKITKGTGREELFEMSVKIEKRMKEEK-GLIPNVD 308
Query: 733 GVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQKR 784
A + + FT +F + R G+I H ++Q +
Sbjct: 309 FYSATVYHVMGIPHDLFTP--------------IFAVSRVAGWIAHILEQYK 346
>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 = 36.9 bits (86), Expect = 0.037
Identities = 31/126 (24%), Positives = 59/126 (46%), Gaps = 24/126 (19%)
Query: 594 KFLEMSLMVTADHGPAVSGAHN----TIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDA 648
K L++ L++ A+HG G +N T V + +G D S++ + + ++ G R GGA N
Sbjct: 196 KLLDLCLVLHAEHG----GGNNSTFTTRVVSSSGTDTYSAIAAAIGSLKGPRHGGA-NIK 250
Query: 649 AIQFSAAYDAGLIPMEFVNEMRK------------KGKLIMGIGHRVKSINNPDMRVKII 696
++ + +E+R K LI G+GH V ++++P R ++
Sbjct: 251 VMEMLEDIKENVKDWTDEDEVRAYLRKILNKEAFDKSGLIYGMGHAVYTLSDP--RAVVL 308
Query: 697 KEFVLQ 702
K++
Sbjct: 309 KKYARS 314
>gnl|CDD|237591 PRK14036, PRK14036, citrate synthase; Provisional.
Length = 377
Score = 35.7 bits (83), Expect = 0.081
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 665 FVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQ---NFPTTPLLNYALEVEKITT 721
+++E + IMG GHR + +P R I+++ + F ALE+E++
Sbjct: 243 YLDERLANKQKIMGFGHREYKVKDP--RATILQKLAEELFARFGHDEYYEIALELERVAE 300
Query: 722 SK 723
+
Sbjct: 301 ER 302
>gnl|CDD|132933 cd07022, S49_Sppa_36K_type, Signal peptide peptidase A (SppA) 36K
type, a serine protease, has catalytic Ser-Lys dyad.
Signal peptide peptidase A (SppA; Peptidase S49;
Protease IV) 36K type: SppA is found in all three
domains of life and is involved in the cleavage of
signal peptides after their removal from the precursor
proteins by signal peptidases. Members in this subfamily
are all bacterial and include sohB peptidase and protein
C. These are sometimes referred to as 36K type since
they contain only one domain, unlike E. coli SppA that
also contains an amino-terminal domain. Site-directed
mutagenesis and sequence analysis have shown these SppAs
to be serine proteases. The predicted active site serine
for members in this family occurs in a transmembrane
domain. Mutagenesis studies also suggest that the
catalytic center comprises a Ser-Lys dyad and not the
usual Ser-His-Asp catalytic triad found in the majority
of serine proteases.
Length = 214
Score = 34.8 bits (81), Expect = 0.11
Identities = 22/50 (44%), Positives = 28/50 (56%), Gaps = 7/50 (14%)
Query: 412 ADPEVKMIVLL-----GEVGGVEEYEVCAALKDKRITKPLVAWCIGTCAS 456
ADP+V+ IVL GEV GV E A++ R KP+VA+ G AS
Sbjct: 39 ADPDVRAIVLDIDSPGGEVAGVFELA--DAIRAARAGKPIVAFVNGLAAS 86
>gnl|CDD|183463 PRK12351, PRK12351, methylcitrate synthase; Provisional.
Length = 378
Score = 34.1 bits (79), Expect = 0.25
Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 618 VCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQFSAAYDAGLIPMEFVNEMR----KK 672
V A G D+ S++ + + G + GGA N+ A + YD P E ++R K
Sbjct: 201 VIAGTGSDMYSAITGAIGALRGPKHGGA-NEVAFEIQQRYDT---PDEAEADIRRRVENK 256
Query: 673 GKLIMGIGHRVKSINNPDMRVKIIKE 698
++G GH V +I++P R K+IKE
Sbjct: 257 EV-VIGFGHPVYTISDP--RNKVIKE 279
>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 = 34.2 bits (79), Expect = 0.31
Identities = 31/119 (26%), Positives = 49/119 (41%), Gaps = 27/119 (22%)
Query: 665 FVNEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTTP---LLNYALEV--EKI 719
++ + G+++ G GH V + D R +EF L++ P P L+ ++ +
Sbjct: 300 YIWDTLNSGRVVPGYGHAV--LRKTDPRFTCQREFALKHLPDDPLFKLVAQCYKIIPGVL 357
Query: 720 TTSKK-PNLILNVD---GVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIG 774
K N NVD GV LL+H G E Q Y LF + R++G
Sbjct: 358 KEHGKVKNPYPNVDAHSGV-------LLQHYGM---TEPQYYTV------LFGVSRALG 400
>gnl|CDD|130853 TIGR01793, cit_synth_euk, citrate (Si)-synthase, eukaryotic. This
model includes both mitochondrial and peroxisomal forms
of citrate synthase. Citrate synthase is the entry point
to the TCA cycle from acetyl-CoA. Peroxisomal forms,
such as SP:P08679 from yeast (recognized by the
C-terminal targeting motif SKL) act in the glyoxylate
cycle. Eukaryotic homologs excluded by the high trusted
cutoff of this model include a Tetrahymena thermophila
citrate synthase that doubles as a filament protein, a
putative citrate synthase from Plasmodium falciparum (no
TCA cycle), and a methylcitrate synthase from
Aspergillus nidulans.
Length = 427
Score = 34.1 bits (78), Expect = 0.31
Identities = 44/199 (22%), Positives = 67/199 (33%), Gaps = 30/199 (15%)
Query: 590 PYVCKFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTIGDRFGGALNDAA 649
P + + + L + +DH AH + A D S + L + G N
Sbjct: 219 PSFQELMRLYLTIHSDHEGGNVSAHTGHLVGSALSDPYLSFAAALNGLAGPLHGLANQEV 278
Query: 650 IQFSAAYDAGLIPMEFVNEMRKK--------GKLIMGIGHRVKSINNPDMRVKIIKEFVL 701
+ + + E K GK++ G GH V + D R +EF L
Sbjct: 279 LLWLKSV-VSECGENVTKEQLKDYIWKTLNSGKVVPGYGHAV--LRKTDPRYICQREFAL 335
Query: 702 QNFPTTPLLNYALEVEKITT------SKKPNLILNVDGVIAVAFVDLLRHSGSFTREEAQ 755
++ P PL + KI K N NVD V LL++ G
Sbjct: 336 KHLPDDPLFKLVSNLYKIVPGILTELGKVKNPWPNVDAHSGV----LLQYYG-------- 383
Query: 756 EYVEMGAINGLFVLGRSIG 774
E LF + R++G
Sbjct: 384 -LTEARYYTVLFGVSRALG 401
>gnl|CDD|180395 PRK06091, PRK06091, membrane protein FdrA; Validated.
Length = 555
Score = 33.9 bits (78), Expect = 0.36
Identities = 34/150 (22%), Positives = 63/150 (42%), Gaps = 28/150 (18%)
Query: 314 KLNLLAKEKGVSIIGP----ATVGGLKPGCFKIGNTGGMMDNILHSKLYRPGSVAYVSRS 369
+L A+EKG+ ++GP A + G P F N++ G++ + S
Sbjct: 158 RLKTRAREKGLLVMGPDCGTAMIAGT-PLAFA---------NVMP-----EGNIGVIGAS 202
Query: 370 GGMSNELNNIISKATNGVYEGVAIGG----DRYPGTTFMDHILRYQADPEVKMIVLLGE- 424
G EL + I+ A G+ + +GG G + + + AD + ++I + +
Sbjct: 203 GTGIQELCSQIALAGEGITHAIGLGGRDLSAEVGGISALTALEMLSADEKSEVIAFVSKP 262
Query: 425 -VGGVEEYEVCAALKDKRITKPLVAWCIGT 453
V ++ A+ K KP+VA +G
Sbjct: 263 PAEAVRL-KIINAM--KATGKPVVALFLGY 289
>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 = 33.7 bits (77), Expect = 0.39
Identities = 46/197 (23%), Positives = 92/197 (46%), Gaps = 29/197 (14%)
Query: 594 KFLEMSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDAAIQF 652
K + +SL++ A+H S V A G D+ S++ + + G + GGA N+ A +
Sbjct: 169 KAMHISLILYAEHEFNAS-TFTARVIAGTGSDMYSAITGAIGALRGPKHGGA-NEVAFEI 226
Query: 653 SAAYDAGLIPMEFVNEMRKK---GKLIMGIGHRVKSINNPDMRVKIIKEF---VLQNFPT 706
Y++ E ++R++ ++++G GH V +I +P R ++IKE + +
Sbjct: 227 QQRYES---ADEAEADIRRRVENKEVVIGFGHPVYTIADP--RNQVIKEVAKQLSKEGGD 281
Query: 707 TPLLNYALEVEKITTSKKPNLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGL 766
+ + A +E + +K + N+D AV++ + + FT L
Sbjct: 282 MKMFDIAERLETVMWEEK-KMFPNLDWFSAVSYHMMGVPTAMFTP--------------L 326
Query: 767 FVLGRSIGFIGHYMDQK 783
FV+ R+ G+ H ++Q+
Sbjct: 327 FVIARTTGWSAHIIEQR 343
>gnl|CDD|132934 cd07023, S49_Sppa_N_C, Signal peptide peptidase A (SppA), a serine
protease, has catalytic Ser-Lys dyad. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppA is
found in all three domains of life and is involved in
the cleavage of signal peptides after their removal from
the precursor proteins by signal peptidases. This
subfamily contains members with either a single domain
(sometimes referred to as 36K type), such as sohB
peptidase, protein C and archaeal signal peptide
peptidase, or an amino-terminal domain in addition to
the carboxyl-terminal protease domain that is conserved
in all the S49 family members (sometimes referred to as
67K type), similar to E. coli and Arabidopsis thaliana
SppA peptidases. Site-directed mutagenesis and sequence
analysis have shown these SppAs to be serine proteases.
The predicted active site serine for members in this
family occurs in a transmembrane domain. Mutagenesis
studies also suggest that the catalytic center comprises
a Ser-Lys dyad and not the usual Ser-His-Asp catalytic
triad found in the majority of serine proteases.
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain.
Length = 208
Score = 32.8 bits (76), Expect = 0.46
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 389 EGVAIGGDRYPGTTFMDHILRYQADPEVKMIVLL-----GEVGGVEEYEVCAALKD-KRI 442
EG G + ++ + + + D VK +VL G V E E+ ++ ++
Sbjct: 8 EGTISDGGGIGADSLIEQLRKAREDDSVKAVVLRINSPGGSVVASE--EIYREIRRLRKA 65
Query: 443 TKPLVAWCIGTCAS 456
KP+VA AS
Sbjct: 66 KKPVVASMGDVAAS 79
>gnl|CDD|184465 PRK14032, PRK14032, citrate synthase; Provisional.
Length = 447
Score = 33.3 bits (77), Expect = 0.48
Identities = 34/130 (26%), Positives = 62/130 (47%), Gaps = 36/130 (27%)
Query: 594 KFLEMSLMVTADHGPAVSGAHN----TIVCARAGKDLVSSLVSGLLTI-GDRFGGA---- 644
+ L+++L++ A+HG G +N T V + +G D S++ + + ++ G + GGA
Sbjct: 226 RLLDLALVLHAEHG----GGNNSTFTTRVVSSSGTDTYSAIAAAIGSLKGPKHGGANIKV 281
Query: 645 --------------LNDAAIQFSAAYDAGLIPMEFVNEMRKKGKLIMGIGHRVKSINNPD 690
++ I A Y ++ E + K G LI G+GH V +I++P
Sbjct: 282 MEMFEDIKENVKDWEDEDEI---ADYLTKILNKEAFD---KSG-LIYGMGHAVYTISDP- 333
Query: 691 MRVKIIKEFV 700
R I+K+F
Sbjct: 334 -RAVILKKFA 342
>gnl|CDD|205785 pfam13607, Succ_CoA_lig, Succinyl-CoA ligase like flavodoxin
domain. This domain contains the catalytic domain from
Succinyl-CoA ligase alpha subunit and other related
enzymes. A conserved histidine is involved in phosphoryl
transfer.
Length = 138
Score = 31.3 bits (72), Expect = 0.79
Identities = 37/153 (24%), Positives = 59/153 (38%), Gaps = 29/153 (18%)
Query: 360 PGSVAYVSRSGGMSNELNNIISKATNGVYEGVAIG-------GDRYPGTTFMDHILRYQA 412
PG VA VS+SG + L + ++ G V++G D +D++
Sbjct: 1 PGGVALVSQSGALGAALLDWAARRGIGFSHFVSLGNEADVDFAD------LLDYLAD--- 51
Query: 413 DPEVKMIVLLGE-VGGVEEYEVCAALKDKRITKPLVAWCIGTCASMFTSEVQFGHAGSCA 471
DPE ++I+L E + + A + KP+V G + + H G+ A
Sbjct: 52 DPETRVILLYLEGIRDGRRF--LRAARRAARKKPVVVLKSGRSEA--GARAAASHTGALA 107
Query: 472 NSDA--ETAVVKNKSLAQAGAHVPSSFDTLGDI 502
SDA + A QAG + L D
Sbjct: 108 GSDAVYDAA------FRQAGVIRVDDLEELFDA 134
>gnl|CDD|179138 PRK00831, rpmJ, 50S ribosomal protein L36; Validated.
Length = 41
Score = 28.8 bits (65), Expect = 0.87
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 43 VRNEPWLESSKLVAKPDQLIKRRGKLGLI-KVNTDFKGAQ 81
VRN L+S K + Q+++R+G++ +I K N FK Q
Sbjct: 3 VRNS--LKSLKNRHRDCQVVRRKGRVYVINKKNPRFKARQ 40
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 31.2 bits (71), Expect = 2.0
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 112 KGIVTALTEFQSKLIEHKISIFVRRAGPNYQEGLRIIREVG 152
+G+V A E + + VR AG N +EG +I+ E G
Sbjct: 330 EGVVQAAREVGID-----VPLVVRLAGTNVEEGRKILAESG 365
>gnl|CDD|143332 cd02439, DMB-PRT_CobT, Nicotinate-nucleotide-dimethylbenzimidazole
phosphoribosyltransferase (DMB-PRT), also called CobT.
Nicotinate-nucleotide-dimethylbenzimidazole
phosphoribosyltransferase (DMB-PRT/CobT, not to be
confused with the CobT subunit of cobaltochelatase,
which does not belong to this group) catalyzes the
synthesis of alpha-ribazole-5'-phosphate, from
nicotinate mononucleotide (NAMN) and
5,6-dimethylbenzimidazole (DMB). This function is
essential to the anaerobic biosynthesis pathway of
cobalamin (vitamin B12), which is the largest and most
complex cofactor in a number of enzyme-catalyzed
reactions in bacteria, archaea and eukaryotes. Only
eubacteria and archaebacteria can synthesize vitamin
B12; multicellular organisms have lost this ability
during evolution. DMB-PRT/CobT works sequentially with
CobC (a phosphatase) to couple the lower ligand of
cobalamin to a ribosyl moiety. DMB is the most common
lower ligand of cobamides; other lower ligands include
adenine, 5-methoxybenzimidazole or phenol. It has been
suggested that earlier metabolic or enzymatic steps may
control which lower ligand is available to DMB-PRT/CobT.
In Salmonella enterica, for example, the lower ligand is
DMB under aerobic conditions and adenine or
2-methyladenine under anaerobic conditions. Salmonella
enterica DMB-PRT/CobT is a homodimer with two active
sites, each active site is comprised of residues from
both monomers. This group includes two distinct
subfamilies, one archaeal-like, the other comprised of
bacterial sequences.
Length = 315
Score = 31.3 bits (72), Expect = 2.1
Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 34/101 (33%)
Query: 94 VLITG-GGIANFTNVAATFKGIVTAL------------TEFQSKLIEHKISIFVRRA--- 137
+L+ G GI N T AA ++ AL T + +E KI++ V A
Sbjct: 140 LLVIGEMGIGN-TTTAA---AVLAALGGDPAEEVSGRGTGLPDEGLERKIAV-VEEALAR 194
Query: 138 -GPNYQEGLRIIREVGKTLGIPLFVFGPETHMTAIVGMALG 177
GP+ + L ++ +VG GPE + A+ G+ LG
Sbjct: 195 NGPDPDDPLDVLAKVG----------GPE--IAAMAGLILG 223
>gnl|CDD|184467 PRK14034, PRK14034, citrate synthase; Provisional.
Length = 372
Score = 31.3 bits (71), Expect = 2.2
Identities = 33/119 (27%), Positives = 51/119 (42%), Gaps = 21/119 (17%)
Query: 667 NEMRKKGKLIMGIGHRVKSINNPDMRVKIIKEFV--LQNFPTTP-LLNYALEVEKITTSK 723
N+++ K K IMG GHRV D R K ++E L N ++++E+I T +
Sbjct: 244 NKLQNKEK-IMGFGHRV--YRQGDPRAKHLREMSKRLTVLLGEEKWYNMSIKIEEIVTKE 300
Query: 724 KPNLILNVDGVIAVAFVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMDQ 782
K L NVD A + L FT +F + R G++ H ++Q
Sbjct: 301 K-GLPPNVDFYSASVYHCLGIDHDLFTP--------------IFAISRMSGWLAHILEQ 344
>gnl|CDD|237070 PRK12350, PRK12350, citrate synthase 2; Provisional.
Length = 353
Score = 31.1 bits (71), Expect = 2.3
Identities = 33/124 (26%), Positives = 48/124 (38%), Gaps = 32/124 (25%)
Query: 672 KGKLIMGIGHRVKSINNPDMRV--KIIKEFVLQNFPTTPLLNYALEVEK----ITTSKKP 725
+G+ +MG GHRV +P RV K P A VE+ ++P
Sbjct: 233 RGERLMGFGHRVYRAEDPRARVLRATAKRL------GAPRYEVAEAVEQAALAELRERRP 286
Query: 726 NLIL--NVDGVIAVA--FVDLLRHSGSFTREEAQEYVEMGAINGLFVLGRSIGFIGHYMD 781
+ L NV+ AV F + H FT +F GR+ G+ H ++
Sbjct: 287 DRPLETNVEFWAAVLLDFAGVPAH--MFT--------------AMFTCGRTAGWSAHILE 330
Query: 782 QKRL 785
QKR
Sbjct: 331 QKRT 334
>gnl|CDD|233234 TIGR01016, sucCoAbeta, succinyl-CoA synthetase, beta subunit. This
model is designated subfamily because it does not
discriminate the ADP-forming enzyme ((EC 6.2.1.5) from
the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half
is described by the CoA-ligases model (pfam00549). The
C-terminal half is described by the ATP-grasp model
(pfam02222). This family contains a split seen both in a
maximum parsimony tree (which ignores gaps) and in the
gap pattern near position 85 of the seed alignment.
Eukaryotic and most bacterial sequences are longer and
contain a region similar to TXQTXXXG. Sequences from
Deinococcus radiodurans, Mycobacterium tuberculosis,
Streptomyces coelicolor, and the Archaea are 6 amino
acids shorter in that region and contain a motif
resembling [KR]G [Energy metabolism, TCA cycle].
Length = 386
Score = 30.8 bits (70), Expect = 2.8
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 99 GGIANFTNVAATFKGIVTALTEFQSKLIEHKISIFVRRAGPNYQEGLRIIREVGK 153
GGI VA KG+V AL E + + + VR G N +EG +I+ E G
Sbjct: 320 GGITRCDLVA---KGLVEALKE-----VGVNVPVVVRLEGTNVEEGKKILAESGL 366
>gnl|CDD|223404 COG0327, COG0327, Uncharacterized conserved protein [Function
unknown].
Length = 250
Score = 30.0 bits (68), Expect = 4.0
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 11/73 (15%)
Query: 29 RFAAVKEETSWAEL---VRNEPWLESSKLVAKPDQLIKRRGKLGLIKVNTDFKGAQSWIS 85
R +KE T+ EL ++ + ++V + IKR Q ++S
Sbjct: 132 RVGELKEPTTLEELAERIKAKLGRPPLRVVKDGSEEIKRVAVCS--------GSGQGFLS 183
Query: 86 ERMGKDQVVLITG 98
E + ITG
Sbjct: 184 EAAAEGVDAYITG 196
>gnl|CDD|237105 PRK12457, PRK12457, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 281
Score = 30.1 bits (68), Expect = 4.8
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 138 GPNYQEGLRIIREVGKTLGIPL 159
G EGLRI EV G+P+
Sbjct: 69 GVGLDEGLRIFEEVKARFGVPV 90
>gnl|CDD|240547 cd13142, MATE_like_12, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. The
integral membrane proteins from the MATE family are
involved in exporting metabolites across the cell
membrane and are responsible for multidrug resistance
(MDR) in many bacteria and animals. A number of family
members are involved in the synthesis of peptidoglycan
components in bacteria.
Length = 444
Score = 30.2 bits (69), Expect = 4.9
Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 537 LGLIRKPASFMTSICDERGQELLYAGMPISDVLKQNMGIGGVLSLLWFQR 586
L +IR P +++ + G ++ M IS++ + +++L WF+R
Sbjct: 396 LWVIRIPLAYLLAYVLGLGVTGIWIAMAISNI------VAALIALAWFKR 439
>gnl|CDD|181961 PRK09569, PRK09569, type I citrate synthase; Reviewed.
Length = 437
Score = 30.1 bits (68), Expect = 5.1
Identities = 33/120 (27%), Positives = 48/120 (40%), Gaps = 10/120 (8%)
Query: 598 MSLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTI-GDRFGGALNDA---AIQFS 653
M ++ +DH AH T + A A D S +GL + G G A + QF
Sbjct: 226 MYFILHSDHESGNVSAHTTHLVASALSDAYYSYSAGLNGLAGPLHGLANQEVLGWIQQFQ 285
Query: 654 AAYDAGLIPMEFVNE-MRK---KGKLIMGIGHRVKSINNPDMRVKIIKEFVLQNFPTTPL 709
E V + + G++I G GH V +P R +EF L++ P PL
Sbjct: 286 EKLGGEEPTKEQVEQALWDTLNAGQVIPGYGHAVLRKTDP--RYTAQREFCLKHLPDDPL 343
>gnl|CDD|180933 PRK07329, PRK07329, hypothetical protein; Provisional.
Length = 246
Score = 29.6 bits (67), Expect = 5.3
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 252 KEVLIPVYKKMEDAMSKNKDADVLVNF 278
KE+L ++KME+A+ + DADVL +F
Sbjct: 120 KELLQEYFEKMEEAIGRVHDADVLAHF 146
>gnl|CDD|190270 pfam02277, DBI_PRT, Phosphoribosyltransferase. This family of
proteins represent the nicotinate-nucleotide-
dimethylbenzimidazole phosphoribosyltransferase (NN:DBI
PRT) enzymes involved in dimethylbenzimidazole
synthesis. This function is essential to de novo
cobalamin (vitamin B12) production in bacteria.
Nicotinate mononucleotide
(NaMN):5,6-dimethylbenzimidazole (DMB)
phosphoribosyltransferase (CobT) from Salmonella
enterica plays a central role in the synthesis of
alpha-ribazole-5'-phosphate, an intermediate for the
lower ligand of cobalamin.
Length = 339
Score = 30.1 bits (68), Expect = 5.5
Identities = 43/185 (23%), Positives = 65/185 (35%), Gaps = 51/185 (27%)
Query: 86 ERMGKDQVVLITG-GGIANFTNVAATFKGIVTALTEFQSKLI------------EHKISI 132
E K +LI G GI N T AA ++ ALT ++ + KI++
Sbjct: 154 EAADKGADLLIIGEMGIGNTTTAAA----LLAALTGGDAEDVVGRGTGLDDEGLARKIAV 209
Query: 133 FVRRA----GPNYQEGLRIIREVGKTLGIPLFVFGPETHMTAIVGMALG--KKEIP---- 182
V A PN + L ++ +VG G E + A+ G LG + IP
Sbjct: 210 -VEEALARHRPNLADPLEVLAKVG----------GFE--IAAMAGAILGAAVRRIPVLLD 256
Query: 183 -SETSADGATAN--------FLLPGGQEQTKAIVWGMQTRAVQSMLDFDFVCRRSEPSVA 233
+A AN L ++ ++ +LD R E S A
Sbjct: 257 GFIATAAALVANRLAPGVLDHCLAAHLSAEPGHRAALEALGLEPLLDLGM--RLGEGSGA 314
Query: 234 AMVYP 238
A+ P
Sbjct: 315 ALALP 319
>gnl|CDD|176521 cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial
glycerophosphodiester phosphodiesterases. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial glycerophosphodiester
phosphodiesterases. In addition to a C-terminal GDPD
domain, most members in this family have an N-terminus
that functions as a membrane anchor.
Length = 220
Score = 29.4 bits (67), Expect = 6.4
Identities = 20/105 (19%), Positives = 40/105 (38%), Gaps = 33/105 (31%)
Query: 664 EFVNEMRKK-GKLIMGIGHRVKSIN----------NPDMRVKIIKEFVLQNFPTTPLLNY 712
+ V + K + ++ H+V S++ +P ++ I F + N P T + Y
Sbjct: 112 DLVEKFVKLYKQNLIENQHQVHSLDYRVIEKVKKLDPKIKTGYILPFNIGNLPKTNVDFY 171
Query: 713 ALE--------VEKITTSKKP------N--------LILNVDGVI 735
++E + + + K N L + VDG+I
Sbjct: 172 SIEYSTLNKEFIRQAHQNGKKVYVWTVNDPDDMQRYLAMGVDGII 216
>gnl|CDD|201611 pfam01126, Heme_oxygenase, Heme oxygenase.
Length = 204
Score = 29.3 bits (66), Expect = 6.8
Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 13/76 (17%)
Query: 212 TRAVQSMLDFDFVCRRSEPSVAAMVYPFTGDHKLKFYWGHKEVLIPVYKKMEDAMSKNKD 271
T+ V M + ++ + G + Y L VY +E+ + +N+D
Sbjct: 11 TKDVHVMAE----------NLVFVKDFLKGVVDKEAYAKLLANLYFVYSALEEELERNRD 60
Query: 272 ADV--LVNFASL-RSA 284
+ V + F L R A
Sbjct: 61 SPVAAPIYFPELNRKA 76
>gnl|CDD|115680 pfam07042, TrfA, TrfA protein. This family consists of several
bacterial TrfA proteins. The trfA operon of
broad-host-range IncP plasmids is essential to activate
the origin of vegetative replication in diverse species.
The trfA operon encodes two ORFs. The first ORF is
highly conserved and encodes a putative single-stranded
DNA binding protein (Ssb). The second, trfA, contains
two translational starts as in the IncP alpha plasmids,
generating related polypeptides of 406 (TrfA1) and 282
(TrfA2) amino acids. TrfA2 is very similar to the IncP
alpha product, whereas the N-terminal region of TrfA1
shows very little similarity to the equivalent region of
IncP alpha TrfA1. This region has been implicated in the
ability of IncP alpha plasmids to replicate efficiently
in Pseudomonas aeruginosa.
Length = 282
Score = 29.6 bits (66), Expect = 7.1
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 233 AAMVYPFTGDHKLKFYWGHKEVLIPVYKKMEDAMSKNKDADVLVNFASLRSAYDSTIETL 292
A +V F GDH KF W Y+K +S N+ + FAS + Y +ET
Sbjct: 189 AEIVVLFAGDHYTKFIWEK-------YRK----LSPNRAGRMFDYFASHKEPYPLKLETF 237
>gnl|CDD|222107 pfam13406, SLT_2, Transglycosylase SLT domain. This family is
related to the SLT domain pfam01464.
Length = 292
Score = 29.4 bits (67), Expect = 7.4
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 2/67 (2%)
Query: 133 FVRRAGPNYQEGLRIIREVGKTLGIPLFVFGPETHMTAIVGMALGKKEIPSETSADGATA 192
++++ G +Q G REV G + G + ALG + A
Sbjct: 195 YLKQHG--WQPGEPWGREVRLPAGFDYSLAGLKNRKPLAEWAALGVRPADGSPPDADLPA 252
Query: 193 NFLLPGG 199
+ LLP G
Sbjct: 253 SLLLPAG 259
>gnl|CDD|235363 PRK05198, PRK05198, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 264
Score = 29.3 bits (67), Expect = 7.6
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 138 GPNYQEGLRIIREVGKTLGIPL 159
GP +EGL+I++EV +T G+P+
Sbjct: 63 GPGLEEGLKILQEVKETFGVPV 84
>gnl|CDD|224277 COG1358, RPL8A, Ribosomal protein HS6-type (S12/L30/L7a)
[Translation, ribosomal structure and biogenesis].
Length = 116
Score = 28.1 bits (63), Expect = 7.6
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 302 IIAEGI-PENMTRKLNLLAKEKGVSII 327
+IAE + PE + + L L +EK V +
Sbjct: 48 VIAEDVSPEELVKHLPALCEEKNVPYV 74
>gnl|CDD|217454 pfam03252, Herpes_UL21, Herpesvirus UL21. The UL21 protein appears
to be a dispensable component in herpesviruses.
Length = 515
Score = 29.6 bits (67), Expect = 8.3
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 94 VLITGGGIANFTNVAATFKGIV-----TALTEF-QSKLIEHKISIFVRRAGP 139
V++TG A V + K T +++F Q K I I+I+ R+
Sbjct: 213 VIVTGKRAARTVAVGSGRKARRRGKKKTTVSDFVQVKYIPRVINIWAPRSPS 264
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.401
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 41,678,910
Number of extensions: 4231420
Number of successful extensions: 3897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3838
Number of HSP's successfully gapped: 78
Length of query: 806
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 701
Effective length of database: 6,280,432
Effective search space: 4402582832
Effective search space used: 4402582832
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (27.9 bits)