RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014369
(426 letters)
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 631 bits (1629), Expect = 0.0
Identities = 278/347 (80%), Positives = 304/347 (87%), Gaps = 1/347 (0%)
Query: 81 SFSRRTVSLGRNHKMFGSACDIYNSNCNDKDIRDITNKFLKGIPRFVKIVEVGPRDGLQN 140
S + G + Y+S+ N+ + + NK LKG+P+FVKIVEVGPRDGLQN
Sbjct: 1 SRGSTSTVSGTLGSSWSFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQN 60
Query: 141 EKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDLEGARLPVL 200
EKN VPT VKVELI+RLVSSGLPVVEATSFVSPKWVPQLADA+DVM AVR+LEGAR PVL
Sbjct: 61 EKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADAKDVMAAVRNLEGARFPVL 120
Query: 201 TPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAVAHAAKVLSIPVRG 260
TPNLKGFEAAIAAGAKEVA+FASASE+FSKSNINCSIE+SLVRYR VA AAK SIPVRG
Sbjct: 121 TPNLKGFEAAIAAGAKEVAVFASASESFSKSNINCSIEESLVRYREVALAAKKHSIPVRG 180
Query: 261 YVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVP 320
YVSCVVGCP+EG +PPSKVAYVAKEL+DMGC+EISLGDTIGVGTPGTVVPMLEAVMAVVP
Sbjct: 181 YVSCVVGCPIEGPVPPSKVAYVAKELYDMGCYEISLGDTIGVGTPGTVVPMLEAVMAVVP 240
Query: 321 VEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLS 380
V+KLAVH HDTYGQ+L NIL+SLQMGISTVD SVAGLGGCPYAKGASGNVATEDVVYML+
Sbjct: 241 VDKLAVHFHDTYGQALANILVSLQMGISTVDSSVAGLGGCPYAKGASGNVATEDVVYMLN 300
Query: 381 GLGVETNVDLRKLMLAGDFINKHLGRPSGSKTAIALN-RIAADASKI 426
GLGV TNVDL KLM AGDFI+KHLGRPSGSKTA+AL+ RI A ASKI
Sbjct: 301 GLGVSTNVDLGKLMAAGDFISKHLGRPSGSKTAVALSARITAAASKI 347
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 476 bits (1227), Expect = e-169
Identities = 162/272 (59%), Positives = 197/272 (72%)
Query: 129 IVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEA 188
IVEVGPRDGLQNEK +PT K+ELI L ++GL +E TSFVSPKWVPQ+ADA +V+
Sbjct: 1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADAEEVLAG 60
Query: 189 VRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAVA 248
+ G R L PNL+G E A+AAG EVA+F SASE FS+ NINCSI +SL R+ VA
Sbjct: 61 LPRRPGVRYSALVPNLRGAERALAAGVDEVAVFVSASETFSQKNINCSIAESLERFEPVA 120
Query: 249 HAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTV 308
AK + VRGYVS GCP EG +PP +VA VA+ L D+GC EISLGDTIGV TP V
Sbjct: 121 ELAKAAGLRVRGYVSTAFGCPYEGEVPPERVAEVAERLLDLGCDEISLGDTIGVATPAQV 180
Query: 309 VPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASG 368
+LEAV+ P EKLA+H HDT GQ+L NIL +L+ G+ D SV GLGGCP+A GA+G
Sbjct: 181 RRLLEAVLERFPDEKLALHFHDTRGQALANILAALEAGVRRFDSSVGGLGGCPFAPGATG 240
Query: 369 NVATEDVVYMLSGLGVETNVDLRKLMLAGDFI 400
NVATED+VYML G+G+ET +DL KL+ A +I
Sbjct: 241 NVATEDLVYMLEGMGIETGIDLDKLLAAARWI 272
>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
Length = 287
Score = 469 bits (1209), Expect = e-167
Identities = 185/287 (64%), Positives = 217/287 (75%)
Query: 123 IPRFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADA 182
+P+ VKIVEVGPRDGLQNEK +PT K+ LI RL ++GL +E SFVSPKWVPQ+ADA
Sbjct: 1 LPKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADA 60
Query: 183 RDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLV 242
+VM ++ G LTPNLKG EAA+AAGA EVA+FASASEAFS+ NINCSI +SL
Sbjct: 61 AEVMAGIQRRPGVTYAALTPNLKGLEAALAAGADEVAVFASASEAFSQKNINCSIAESLE 120
Query: 243 RYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGV 302
R+ VA AAK + VRGYVSCV+GCP EG +PP VA VA+ L +GC+EISLGDTIGV
Sbjct: 121 RFEPVAEAAKQAGVRVRGYVSCVLGCPYEGEVPPEAVADVAERLFALGCYEISLGDTIGV 180
Query: 303 GTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPY 362
GTPG V +LEAV+A P E+LA H HDTYGQ+L NI SL+ GI+ D SV GLGGCPY
Sbjct: 181 GTPGQVRAVLEAVLAEFPAERLAGHFHDTYGQALANIYASLEEGITVFDASVGGLGGCPY 240
Query: 363 AKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFINKHLGRPSG 409
A GASGNVATEDV+YML GLG+ET +DL KL+ AG FI LGRP
Sbjct: 241 APGASGNVATEDVLYMLHGLGIETGIDLDKLVRAGQFIQSKLGRPLP 287
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 298 bits (766), Expect = e-100
Identities = 106/273 (38%), Positives = 146/273 (53%), Gaps = 12/273 (4%)
Query: 130 VEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAV 189
+ RDGLQ+E T T K+E+ L +G+ +E S SPK VPQ+ D +V+ A+
Sbjct: 1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDDWEVLRAI 60
Query: 190 RDLE-GARLPVLTPN-LKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAV 247
R L +L L N KG E A+ AG EV IF SASE S+ N+N S E+ L
Sbjct: 61 RKLVPNVKLQALVRNREKGIERALEAGVDEVRIFDSASETHSRKNLNKSREEDLENAEEA 120
Query: 248 AHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGT 307
AAK + V G + GC P V VAK L + G EISL DT+G+ TP
Sbjct: 121 IEAAKEAGLEVEGSLEDAFGCKT----DPEYVLEVAKALEEAGADEISLKDTVGLATPEE 176
Query: 308 VVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGAS 367
V +++A+ +P L +H H+T G ++ N L +L+ G VD SV GLG +
Sbjct: 177 VAELVKALREALPDVPLGLHTHNTLGLAVANSLAALEAGADRVDGSVNGLG------ERA 230
Query: 368 GNVATEDVVYMLSGLGVETNVDLRKLMLAGDFI 400
GN ATED+V L GLG++T +DL KL+ ++
Sbjct: 231 GNAATEDLVAALEGLGIDTGIDLEKLLEISRYV 263
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 212 bits (542), Expect = 1e-64
Identities = 70/285 (24%), Positives = 116/285 (40%), Gaps = 13/285 (4%)
Query: 125 RFVKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARD 184
+ V I + RDG Q + K+ + + L G+ +EA V+ + A
Sbjct: 1 KKVIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRAIA 60
Query: 185 VMEAVRDLEGARLPVLTPNLK-GFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVR 243
A + L +K EA + AG + IF + S+ + + + E+ L R
Sbjct: 61 EKAG--LFICALIAALARAIKRDIEALLEAGVDRIHIFIATSDLHLRYKLKKTREEVLER 118
Query: 244 YRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVG 303
A+ + VR E V K + G I+L DT+GV
Sbjct: 119 AVDAVEYARDHGLEVRFSAEDATRTDPEFLAE------VVKAAIEAGADRINLPDTVGVA 172
Query: 304 TPGTVVPMLEAVMAVVPVE-KLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPY 362
TP V ++EA+ A VP + L+VH H+ G ++ N L +++ G V+ +V G+G
Sbjct: 173 TPNEVADIIEALKANVPNKVILSVHCHNDLGMAVANSLAAVEAGADQVEGTVNGIG---E 229
Query: 363 AKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFINKHLGRP 407
G + + + GV+T +DL KL A + + G P
Sbjct: 230 RAGNAALEEVVLALALRKDYGVDTGIDLEKLTEASRLVERLTGIP 274
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 182 bits (465), Expect = 2e-55
Identities = 68/249 (27%), Positives = 109/249 (43%), Gaps = 14/249 (5%)
Query: 136 DGLQNEKNTVPTGVKVELIRRLVSSGLPVVEAT-SFVSPKWVPQLADARDVMEAVRDLEG 194
DG Q K+ + R L +G+ +E F+SP + +V++ + ++
Sbjct: 1 DGEQALGAAFSVEEKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAIAEVLKKAK-IQA 59
Query: 195 ARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAVAHAAKVL 254
PV EAA AGA V +F + S+ K +N E+ R A AA+
Sbjct: 60 LLRPVEHDIDAAVEAAKGAGADRVHVFIATSDLHRKYKLNKDREEVADRAVAAVEAARSA 119
Query: 255 SIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEA 314
I V +GC G + + V + + G I++ DT+GV TP ++ A
Sbjct: 120 GIDVE------LGCEDAGRTDLAFLIEVVEVAQEAGATRINIADTVGVLTPNEAADLISA 173
Query: 315 VMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATED 374
+ VP + VH H+ G ++ N L +++ G VD +V GLG +GN A E+
Sbjct: 174 LKDRVPPVIIEVHCHNDLGMAVANSLAAVEAGADRVDGTVNGLG------ERAGNAALEE 227
Query: 375 VVYMLSGLG 383
+V L LG
Sbjct: 228 LVAALEVLG 236
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 275
Score = 62.4 bits (153), Expect = 6e-11
Identities = 43/132 (32%), Positives = 67/132 (50%), Gaps = 15/132 (11%)
Query: 270 VEGAI-----PPSKVAY---VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPV 321
VEGAI P + Y +AKEL DMG I + D G+ TP +++A+ V +
Sbjct: 134 VEGAICYTGSPVHTLEYYVKLAKELEDMGADSICIKDMAGLLTPYAAYELVKALKKEVGL 193
Query: 322 EKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSG 381
+ +H HDT G ++ L + + G+ VD +++ L G + +TE +V L G
Sbjct: 194 P-IHLHTHDTSGLAVATYLAAAEAGVDIVDTAISPLSGG------TSQPSTESMVAALRG 246
Query: 382 LGVETNVDLRKL 393
G +T +DL KL
Sbjct: 247 TGRDTGLDLEKL 258
>gnl|CDD|233965 TIGR02660, nifV_homocitr, homocitrate synthase NifV. This family
consists of the NifV clade of homocitrate synthases,
most of which are found in operons for nitrogen
fixation. Members are closely homologous to enzymes that
include 2-isopropylmalate synthase, (R)-citramalate
synthase, and homocitrate synthases associated with
other processes. The homocitrate made by this enzyme
becomes a part of the iron-molybdenum cofactor of
nitrogenase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other, Central intermediary
metabolism, Nitrogen fixation].
Length = 365
Score = 62.3 bits (152), Expect = 1e-10
Identities = 64/278 (23%), Positives = 111/278 (39%), Gaps = 26/278 (9%)
Query: 135 RDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADA-RDVMEAVRDLE 193
RDG Q K+ + R L +G+ +E +P + + R V+ A+ L
Sbjct: 10 RDGEQAPGVAFTAAEKLAIARALDEAGVDELEVG-------IPAMGEEERAVIRAIVAL- 61
Query: 194 GARLPVLT---PNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAVAHA 250
G ++ EAA G V I S+ ++ + L R +
Sbjct: 62 GLPARLMAWCRARDADIEAAARCGVDAVHISIPVSDLQIEAKLRKDRAWVLERLARLVSF 121
Query: 251 AKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVP 310
A+ + +VS VG P + +A+ + G DT+G+ P +
Sbjct: 122 ARDRGL----FVS--VGGEDASRADPDFLVELAEVAAEAGADRFRFADTVGILDPFSTYE 175
Query: 311 MLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNV 370
++ A+ V + L +H H+ G + N L +++ G + V+ +V GLG +GN
Sbjct: 176 LVRALRQAVDLP-LEMHAHNDLGMATANTLAAVRAGATHVNTTVNGLG------ERAGNA 228
Query: 371 ATEDVVYMLSGL-GVETNVDLRKLMLAGDFINKHLGRP 407
A E+V L L G +T +D +L + + GRP
Sbjct: 229 ALEEVAMALKRLLGRDTGIDTSRLPALSQLVARASGRP 266
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 60.6 bits (148), Expect = 2e-10
Identities = 36/127 (28%), Positives = 63/127 (49%), Gaps = 6/127 (4%)
Query: 274 IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYG 333
P ++A AK + G + + D+ G P V + A+ + + H H+ G
Sbjct: 138 ASPEELAEQAKLMESYGADCVYVTDSAGAMLPDDVRERVRALREALDPTPVGFHGHNNLG 197
Query: 334 QSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKL 393
++ N L +++ G + +D S+AGLG +GN E +V +L +G+ET +DL KL
Sbjct: 198 LAVANSLAAVEAGATRIDGSLAGLGAG------AGNTPLEVLVAVLERMGIETGIDLYKL 251
Query: 394 MLAGDFI 400
M A + +
Sbjct: 252 MDAAEDL 258
>gnl|CDD|233719 TIGR02090, LEU1_arch, isopropylmalate/citramalate/homocitrate
synthases. Methanogenic archaea contain three closely
related homologs of the 2-isopropylmalate synthases
(LeuA) represented by TIGR00973. Two of these in
Methanococcus janaschii (MJ1392 - CimA ; MJ0503 - AksA )
have been characterized as catalyzing alternative
reactions leaving the third (MJ1195) as the presumptive
LeuA enzyme. CimA is citramalate (2-methylmalate)
synthase which condenses acetyl-CoA with pyruvate. This
enzyme is believed to be involved in the biosynthesis of
isoleucine in methanogens and possibly other species
lacking threonine dehydratase. AksA is a homocitrate
synthase which also produces (homo)2-citrate and
(homo)3-citrate in the biosynthesis of Coenzyme B which
is restricted solely to methanogenic archaea.
Methanogens, then should and aparrently do contain all
three of these enzymes. Unfortunately, phylogenetic
trees do not resolve into three unambiguous clades,
making assignment of function to particular genes
problematic. Other archaea which lack a threonine
dehydratase (mainly Euryarchaeota) should contain both a
CimA and a LeuA gene. This is true of, for example,
archaeoglobus fulgidis, but not for the Pyrococci which
have none in this clade, but one in TIGR00973 and one in
TIGRT00977 which may fulfill these roles. Other species
which have only one hit to this model and lack threonine
dehydratase are very likely LeuA enzymes.
Length = 363
Score = 61.0 bits (148), Expect = 3e-10
Identities = 70/278 (25%), Positives = 116/278 (41%), Gaps = 38/278 (13%)
Query: 127 VKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATS-------FVSPKWVPQL 179
V I + RDG Q ++ KVE+ R+L G+ V+EA F + K + Q
Sbjct: 1 VYIFDTTLRDGEQTPGVSLTVEQKVEIARKLDELGVDVIEAGFPIASEGEFEAIKKISQE 60
Query: 180 ADARDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIED 239
++ R L+ K + AI G + F + S K + S ++
Sbjct: 61 GLNAEICSLARALK-----------KDIDKAIDCGVDSIHTFIATSPIHLKYKLKKSRDE 109
Query: 240 SL-VRYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAI--PPSKVAYVAKELHDMGCFEISL 296
L AV +A + G + V E A + V K + G I++
Sbjct: 110 VLEKAVEAVEYAKE------HGLI---VEFSAEDATRTDIDFLIKVFKRAEEAGADRINI 160
Query: 297 GDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAG 356
DT+GV TP + +++ + V + ++VH H+ +G + N + ++ G V +V G
Sbjct: 161 ADTVGVLTPQKMEELIKKLKENVKLP-ISVHCHNDFGLATANSIAGVKAGAEQVHVTVNG 219
Query: 357 LGGCPYAKGASGNVATEDVVYMLSGL-GVETNVDLRKL 393
+G +GN A E+VV L L GV+T + KL
Sbjct: 220 IG------ERAGNAALEEVVMALKYLYGVKTKIKTEKL 251
>gnl|CDD|130046 TIGR00973, leuA_bact, 2-isopropylmalate synthase, bacterial type.
This is the first enzyme of leucine biosynthesis. A
larger family of homologous proteins includes
homocitrate synthase, distinct lineages of
2-isopropylmalate synthase, several distinct,
uncharacterized, orthologous sets in the Archaea, and
other related enzymes. This model describes a family of
2-isopropylmalate synthases found primarily in Bacteria.
The homologous families in the Archaea may represent
isozymes and/or related enzymes [Amino acid
biosynthesis, Pyruvate family].
Length = 494
Score = 60.2 bits (146), Expect = 8e-10
Identities = 68/302 (22%), Positives = 127/302 (42%), Gaps = 33/302 (10%)
Query: 127 VKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVM 186
+ I + RDG Q+ ++ K+++ L G+ ++EA VS D V
Sbjct: 2 IIIFDTTLRDGEQSPGASLTVEEKLQIALALERLGVDIIEAGFPVSSP-----GDFEAVQ 56
Query: 187 EAVRDLEGARLPVLTPNLKG-----FEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSL 241
R ++ R+ L ++ EA A + F + S + + + ++ L
Sbjct: 57 RIARTVKNPRVCGLARCVEKDIDAAAEALKPAEKFRIHTFIATSPIHLEHKLKMTRDEVL 116
Query: 242 VRY-RAVAHAAKVLSIPVRGYVSCV-VGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDT 299
R V +A + + V C G +A + + + G I++ DT
Sbjct: 117 ERAVGMVKYA--------KNFTDDVEFSCEDAGRTEIPFLARIVEAAINAGATTINIPDT 168
Query: 300 IGVGTPGTVVPMLEAVMAVVP-VEK--LAVHLHDTYGQSLPNILISLQMGISTVDCSVAG 356
+G P +++ + VP ++K L+VH H+ G ++ N L ++Q G V+C++ G
Sbjct: 169 VGYALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVANSLAAVQNGARQVECTING 228
Query: 357 LGGCPYAKGASGNVATEDVVYML----SGLGVETNVDLRKLMLAGDFINKHLGRPSGSKT 412
+G +GN A E+VV L LGVET ++ +++ +++ G P
Sbjct: 229 IG------ERAGNAALEEVVMALKVRKDFLGVETGINTKEIYRTSRLVSQLTGMPVQPNK 282
Query: 413 AI 414
AI
Sbjct: 283 AI 284
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 59.3 bits (144), Expect = 1e-09
Identities = 35/121 (28%), Positives = 62/121 (51%), Gaps = 7/121 (5%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILI 341
+AKEL +MG I + D G+ TP +++A+ +PV + +H H T G + L
Sbjct: 161 LAKELLEMGVDSICIKDMAGLLTPYEAYELVKAIKKELPV-PVELHTHATSGMAEMTYLK 219
Query: 342 SLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFIN 401
+++ G+ +D +++ P + G S ATE +V L G G +T +DL L ++
Sbjct: 220 AVEAGVDGIDTAIS-----PLSGGTS-QPATETMVAALRGTGYDTGLDLELLEEIAEYFR 273
Query: 402 K 402
+
Sbjct: 274 E 274
>gnl|CDD|132261 TIGR03217, 4OH_2_O_val_ald, 4-hydroxy-2-oxovalerate aldolase.
Members of this protein family are
4-hydroxy-2-oxovalerate aldolase, also called
4-hydroxy-2-ketovalerate aldolase and
2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of
the pathway for the meta-cleavage of catechol, produces
pyruvate and acetaldehyde. Acetaldehyde is then
converted by acetaldehyde dehydrogenase (acylating)
(DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are
tightly associated [Energy metabolism, Other].
Length = 333
Score = 57.7 bits (140), Expect = 3e-09
Identities = 41/128 (32%), Positives = 62/128 (48%), Gaps = 7/128 (5%)
Query: 274 IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVV-PVEKLAVHLHDTY 332
PP K+A AK + G + + D+ G P V + A+ AV+ P ++ H H
Sbjct: 140 TPPEKLAEQAKLMESYGADCVYIVDSAGAMLPDDVRDRVRALKAVLKPETQVGFHAHHNL 199
Query: 333 GQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRK 392
++ N + +++ G + +D S+ GLG GA GN E V +L LG T DL K
Sbjct: 200 SLAVANSIAAIEAGATRIDASLRGLGA-----GA-GNAPLEVFVAVLDRLGWNTGCDLFK 253
Query: 393 LMLAGDFI 400
LM A + I
Sbjct: 254 LMDAAEDI 261
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 58.2 bits (141), Expect = 4e-09
Identities = 37/121 (30%), Positives = 61/121 (50%), Gaps = 7/121 (5%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILI 341
+AKE+ +MG I + D G+ TP +++ + V V L VH H T G + L
Sbjct: 159 LAKEMQEMGADSICIKDMAGILTPYVAYELVKRIKEAVTV-PLEVHTHATSGIAEMTYLK 217
Query: 342 SLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFIN 401
+++ G +D +++ P+A G S ATE +V L LG +T +DL +L ++ N
Sbjct: 218 AIEAGADIIDTAIS-----PFAGGTS-QPATESMVAALQDLGYDTGLDLEELSEIAEYFN 271
Query: 402 K 402
Sbjct: 272 P 272
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 57.5 bits (140), Expect = 5e-09
Identities = 75/287 (26%), Positives = 121/287 (42%), Gaps = 50/287 (17%)
Query: 124 PRFVKIVEVGPRDGLQNEKNTVPT-GV------KVELIRRLVSSGLPVVEATSFVSPKWV 176
P+ ++IV+ RDG Q T GV K+ + R L G+ +EA
Sbjct: 2 PKDIEIVDTTLRDGEQ-------TPGVVFTNEEKLAIARMLDEIGVDQIEAG-------F 47
Query: 177 PQLADARDVMEAVRDL--EGARLPVLT---PNLKGFEAAIAAGAKEVAIFASASEAFSKS 231
P A + D EA++ + G +L +A+I G V IF + S+ K
Sbjct: 48 P--AVSEDEKEAIKAIAKLGLNASILALNRAVKSDIDASIDCGVDAVHIFIATSDIHIKH 105
Query: 232 NINCSIEDSLVR-YRAVAHAAKVLSIPVRG-YVSCVVGCPVEGA--IPPSKVAYVAKELH 287
+ + E+ L R AV +A G YVS E A + AK
Sbjct: 106 KLKKTREEVLERMVEAVEYAKD------HGLYVS--FS--AEDASRTDLDFLIEFAKAAE 155
Query: 288 DMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGI 347
+ G + DT+G+ P T+ +++ ++ V + + VH H+ +G + N L ++ G
Sbjct: 156 EAGADRVRFCDTVGILDPFTMYELVKELVEAVDIP-IEVHCHNDFGMATANALAGIEAGA 214
Query: 348 STVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGL-GVETNVDLRKL 393
V +V GLG +GN A E+VV L L G++ +D +L
Sbjct: 215 KQVHTTVNGLG------ERAGNAALEEVVMALKYLYGIDLGIDTERL 255
>gnl|CDD|163677 cd07939, DRE_TIM_NifV, Streptomyces rubellomurinus FrbC and related
proteins, catalytic TIM barrel domain. FrbC (NifV) of
Streptomyces rubellomurinus catalyzes the condensation
of acetyl-CoA and alpha-ketoglutarate to form
homocitrate and CoA, a reaction similar to one catalyzed
by homocitrate synthase. The gene encoding FrbC is one
of several genes required for the biosynthesis of
FR900098, a potent antimalarial antibiotic. This
protein is also required for assembly of the nitrogenase
MoFe complex but its exact role is unknown. This
family also includes the NifV proteins of Heliobacterium
chlorum and Gluconacetobacter diazotrophicus, which
appear to be orthologous to FrbC. This family belongs
to the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 259
Score = 53.7 bits (130), Expect = 4e-08
Identities = 62/255 (24%), Positives = 109/255 (42%), Gaps = 38/255 (14%)
Query: 150 KVELIRRLVSSGLPVVEATSFVSPKWVPQL-ADARDVMEAVRDLEGARLPVLT---PNLK 205
K+ + R L +G+ +E +P + + R+ + A+ L G ++ +
Sbjct: 22 KLAIARALDEAGVDEIEVG-------IPAMGEEEREAIRAIVAL-GLPARLIVWCRAVKE 73
Query: 206 GFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRA--VAHAAKVLSIPV-RG-Y 261
EAA+ G V I + S+I+ + L + RA + +++ RG +
Sbjct: 74 DIEAALRCGVTAVHI------SIPVSDIH--LAHKLGKDRAWVLDQLRRLVGRAKDRGLF 125
Query: 262 VSCVVGCPVEGA--IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVV 319
VS VG E A P + A+ + G + DT+G+ P T ++ + A
Sbjct: 126 VS--VGA--EDASRADPDFLIEFAEVAQEAGADRLRFADTVGILDPFTTYELIRRLRAAT 181
Query: 320 PVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYML 379
+ L H H+ G + N L +++ G + V +V GLG +GN A E+VV L
Sbjct: 182 DLP-LEFHAHNDLGLATANTLAAVRAGATHVSVTVNGLG------ERAGNAALEEVVMAL 234
Query: 380 SGL-GVETNVDLRKL 393
L G +T +D +L
Sbjct: 235 KHLYGRDTGIDTTRL 249
>gnl|CDD|233273 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This
model describes the bacterial oxaloacetate decarboxylase
alpha subunit and its equivalents in archaea. The
oxaloacetate decarboxylase Na+ pump is the paradigm of
the family of Na+ transport decarboxylases that present
in bacteria and archaea. It a multi subunit enzyme
consisting of a peripheral alpha-subunit and integral
membrane subunits beta and gamma. The energy released by
the decarboxylation reaction of oxaloacetate is coupled
to Na+ ion pumping across the membrane [Transport and
binding proteins, Cations and iron carrying compounds,
Energy metabolism, Other].
Length = 582
Score = 53.6 bits (129), Expect = 1e-07
Identities = 28/121 (23%), Positives = 58/121 (47%), Gaps = 7/121 (5%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILI 341
+A+EL +MG I + D G+ TP ++ A+ + + +H H T G + +L
Sbjct: 154 LAEELLEMGVDSICIKDMAGILTPKAAYELVSALKKRFGLP-VHLHSHATTGMAEMALLK 212
Query: 342 SLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFIN 401
+++ G +D +++ + G + + TE +V L G G +T +D+ L+ +
Sbjct: 213 AIEAGADGIDTAISSM------SGGTSHPPTETMVAALRGTGYDTGLDIELLLEIAAYFR 266
Query: 402 K 402
+
Sbjct: 267 E 267
>gnl|CDD|163678 cd07940, DRE_TIM_IPMS, 2-isopropylmalate synthase (IPMS),
N-terminal catalytic TIM barrel domain.
2-isopropylmalate synthase (IPMS) catalyzes an
aldol-type condensation of acetyl-CoA and
2-oxoisovalerate yielding 2-isopropylmalate and CoA, the
first committed step in leucine biosynthesis. This
family includes the Arabidopsis thaliana IPMS1 and IPMS2
proteins, the Glycine max GmN56 protein, and the
Brassica insularis BatIMS protein. This family also
includes a group of archeal IPMS-like proteins
represented by the Methanocaldococcus jannaschii AksA
protein. AksA catalyzes the condensation of
alpha-ketoglutarate and acetyl-CoA to form
trans-homoaconitate, one of 13 steps in the conversion
of alpha-ketoglutarate and acetylCoA to
alpha-ketosuberate, a precursor to coenzyme B and
biotin. AksA also catalyzes the condensation of
alpha-ketoadipate or alpha-ketopimelate with acetylCoA
to form, respectively, the (R)-homocitrate homologs
(R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and
(R)-2-hydroxy-1,2,6- hexanetricarboxylic acid. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 268
Score = 50.5 bits (122), Expect = 4e-07
Identities = 32/107 (29%), Positives = 55/107 (51%), Gaps = 12/107 (11%)
Query: 294 ISLGDTIGVGTPGTVVPMLEAVMAVVPVEK--LAVHLHDTYGQSLPNILISLQMGISTVD 351
I++ DT+G TP +++ + VP K ++VH H+ G ++ N L +++ G V+
Sbjct: 160 INIPDTVGYLTPEEFGELIKKLKENVPNIKVPISVHCHNDLGLAVANSLAAVEAGARQVE 219
Query: 352 CSVAGLGGCPYAKGASGNVATEDVV----YMLSGLGVETNVDLRKLM 394
C++ G+G +GN A E+VV GVET +D +L
Sbjct: 220 CTINGIG------ERAGNAALEEVVMALKTRYDYYGVETGIDTEELY 260
>gnl|CDD|183445 PRK12330, PRK12330, oxaloacetate decarboxylase; Provisional.
Length = 499
Score = 51.3 bits (123), Expect = 6e-07
Identities = 32/125 (25%), Positives = 60/125 (48%), Gaps = 7/125 (5%)
Query: 283 AKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVM-AVVPVEKLAVHLHDTYGQSLPNILI 341
AK L DMG I + D + P +++ + A ++ +H H T G +L +++
Sbjct: 161 AKRLLDMGADSICIKDMAALLKPQPAYDIVKGIKEACGEDTRINLHCHSTTGVTLVSLMK 220
Query: 342 SLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFIN 401
+++ G+ VD +++ + P G+ TE +V ML G G T +D+ +L+ D
Sbjct: 221 AIEAGVDVVDTAISSMSLGP------GHNPTESLVEMLEGTGYTTKLDMDRLLKIRDHFK 274
Query: 402 KHLGR 406
K +
Sbjct: 275 KVRPK 279
>gnl|CDD|178767 PLN03228, PLN03228, methylthioalkylmalate synthase; Provisional.
Length = 503
Score = 51.1 bits (122), Expect = 7e-07
Identities = 67/306 (21%), Positives = 124/306 (40%), Gaps = 45/306 (14%)
Query: 126 FVKIVEVGPRDGLQNEKNTVPTGVKVELIRRL-------VSSGLPVVEATSFVSPKWVPQ 178
+V++++ RDG Q+ ++ K+E+ R+L + G P F + K +
Sbjct: 84 YVRVLDTTLRDGEQSPGGSLTPPQKLEIARQLAKLRVDIMEVGFPGSSEEEFEAVKTI-- 141
Query: 179 LADARDVMEAVRDLEGARLPVLTPNLK--------GFEAAIAAGAKEVAIFASASEAFSK 230
A+ V V D E +PV+ + +EA A + F S S+ K
Sbjct: 142 ---AKTVGNEV-DEETGYVPVICGIARCKKRDIEAAWEALKYAKRPRILAFTSTSDIHMK 197
Query: 231 SNINCSIEDSLVRYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMG 290
+ + E+ + + AK L G+ GC G + + E G
Sbjct: 198 YKLKKTKEEVIEMAVSSIRYAKSL-----GFHDIQFGCEDGGRSDKEFLCKILGEAIKAG 252
Query: 291 CFEISLGDTIGVGTP---GTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGI 347
+ + DT+G+ P G +V ++A + +VH H+ G + N + + G
Sbjct: 253 ATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGLATANTIAGICAGA 312
Query: 348 STVDCSVAGLGGCPYAKGASGNVATEDVV--------YMLSGLGVETNVDLRKLMLAGDF 399
V+ ++ G+G SGN + E+VV Y+++ GV T +D R++M
Sbjct: 313 RQVEVTINGIG------ERSGNASLEEVVMALKCRGAYLMN--GVYTGIDTRQIMATSKM 364
Query: 400 INKHLG 405
+ ++ G
Sbjct: 365 VQEYTG 370
>gnl|CDD|236449 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
Length = 592
Score = 50.6 bits (122), Expect = 1e-06
Identities = 45/147 (30%), Positives = 65/147 (44%), Gaps = 19/147 (12%)
Query: 266 VGCPVEGAI--PPSKV----AYV--AKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMA 317
G V+G I S V YV AKEL +MGC I + D G+ TP E V A
Sbjct: 135 AGAHVQGTISYTTSPVHTIEKYVELAKELEEMGCDSICIKDMAGLLTPYAAY---ELVKA 191
Query: 318 VVPVEKLAVHLH--DTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDV 375
+ L V LH T G + L +++ G+ +D +++ P A G S TE +
Sbjct: 192 LKEEVDLPVQLHSHCTSGLAPMTYLKAVEAGVDIIDTAIS-----PLAFGTS-QPPTESM 245
Query: 376 VYMLSGLGVETNVDLRKLMLAGDFINK 402
V L G +T +DL L ++ +
Sbjct: 246 VAALKGTPYDTGLDLELLFEIAEYFRE 272
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 50.3 bits (121), Expect = 1e-06
Identities = 34/112 (30%), Positives = 56/112 (50%), Gaps = 7/112 (6%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILI 341
+AK+L DMG + + D G+ P ++ + V V L +H H T G S +L
Sbjct: 160 LAKQLEDMGVDSLCIKDMAGLLKPYAAYELVSRIKKRVDVP-LHLHCHATTGLSTATLLK 218
Query: 342 SLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKL 393
+++ GI VD +++ + Y G+ ATE +V L G +T +D+ KL
Sbjct: 219 AIEAGIDGVDTAISSMS-MTY-----GHSATETLVATLEGTERDTGLDILKL 264
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 49.4 bits (119), Expect = 1e-06
Identities = 42/126 (33%), Positives = 65/126 (51%), Gaps = 7/126 (5%)
Query: 274 IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVE-KLAVHLHDTY 332
PP K+A AK + G + + D+ G P V + A+ A + + ++ H H+
Sbjct: 141 APPEKLAEQAKLMESYGAQCVYVVDSAGALLPEDVRDRVRALRAALKPDTQVGFHGHNNL 200
Query: 333 GQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRK 392
G + N L +++ G + +D S+AGLG GA GN E +V +L +G ET VDL K
Sbjct: 201 GLGVANSLAAVEAGATRIDGSLAGLGA-----GA-GNTPLEVLVAVLDRMGWETGVDLYK 254
Query: 393 LMLAGD 398
LM A +
Sbjct: 255 LMDAAE 260
>gnl|CDD|163684 cd07947, DRE_TIM_Re_CS, Clostridium kluyveri Re-citrate synthase
and related proteins, catalytic TIM barrel domain.
Re-citrate synthase (Re-CS) is a Clostridium kluyveri
enzyme that converts acetyl-CoA and oxaloacetate to
citrate. In most organisms, this reaction is catalyzed
by Si-citrate synthase which is Si-face stereospecific
with respect to C-2 of oxaloacetate, and
phylogenetically unrelated to Re-citrate synthase.
Re-citrate synthase is also found in a few other
strictly anaerobic organisms. This family belongs to
the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 279
Score = 49.2 bits (118), Expect = 2e-06
Identities = 48/218 (22%), Positives = 86/218 (39%), Gaps = 30/218 (13%)
Query: 183 RDVMEAVRDLEGARLPVLT----PNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIE 238
R+ +EA D G + P +T N + + G KE I S S+ + + E
Sbjct: 53 REAVEACLDR-GYKFPEVTGWIRANKEDLKLVKEMGLKETGILMSVSDYHIFKKLKMTRE 111
Query: 239 DSLVRYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFE----- 293
+++ +Y + A I R ++ + + G + P +L +
Sbjct: 112 EAMEKYLEIVEEALDHGIKPRCHLEDITRADIYGFVLP-----FVNKLMKLSKESGIPVK 166
Query: 294 ISLGDTIGVGTPGTVVPMLEAV---------MAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
I L DT+G G P + +V VP E L H H+ + +++ N + +
Sbjct: 167 IRLCDTLGYGVPYPGASLPRSVPKIIYGLRKDCGVPSENLEWHGHNDFYKAVANAVAAWL 226
Query: 345 MGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGL 382
G S V+C++ G+G +GN E +V + L
Sbjct: 227 YGASWVNCTLLGIG------ERTGNCPLEAMVIEYAQL 258
>gnl|CDD|237593 PRK14041, PRK14041, oxaloacetate decarboxylase; Provisional.
Length = 467
Score = 49.0 bits (117), Expect = 3e-06
Identities = 43/147 (29%), Positives = 64/147 (43%), Gaps = 21/147 (14%)
Query: 267 GCPVEGAI-----PPSKVAY---VAKELHDMGCFEISLGDTIGVGTP---GTVVPMLEAV 315
G V+GAI P + Y A+EL DMG I + D G+ TP +V L+
Sbjct: 135 GAHVQGAISYTVSPVHTLEYYLEFARELVDMGVDSICIKDMAGLLTPKRAYELVKALKKK 194
Query: 316 MAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDV 375
V PVE VH H T G + L +++ G D +++ P++ G S E +
Sbjct: 195 FGV-PVE---VHSHCTTGLASLAYLAAVEAGADMFDTAIS-----PFSMGTS-QPPFESM 244
Query: 376 VYMLSGLGVETNVDLRKLMLAGDFINK 402
Y G ET+ D + L ++ K
Sbjct: 245 YYAFRENGKETDFDRKALKFLVEYFTK 271
>gnl|CDD|163683 cd07945, DRE_TIM_CMS, Leptospira interrogans citramalate synthase
(CMS) and related proteins, N-terminal catalytic TIM
barrel domain. Citramalate synthase (CMS) catalyzes the
conversion of pyruvate and acetyl-CoA to (R)-citramalate
in the first dedicated step of the citramalate pathway.
Citramalate is only found in Leptospira interrogans and
a few other microorganisms. This family belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 280
Score = 47.4 bits (113), Expect = 6e-06
Identities = 32/119 (26%), Positives = 56/119 (47%), Gaps = 7/119 (5%)
Query: 276 PSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQS 335
P V + L D+ I L DT+G+ +P + ++ P H H+ Y +
Sbjct: 146 PDYVFQLVDFLSDLPIKRIMLPDTLGILSPFETYTYISDMVKRYPNLHFDFHAHNDYDLA 205
Query: 336 LPNILISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSG-LGVETNVDLRKL 393
+ N+L +++ GI + +V GLG +GN V+ +L L V+TN+D ++L
Sbjct: 206 VANVLAAVKAGIKGLHTTVNGLG------ERAGNAPLASVIAVLKDKLKVKTNIDEKRL 258
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 46.9 bits (112), Expect = 2e-05
Identities = 32/115 (27%), Positives = 54/115 (46%), Gaps = 12/115 (10%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEK--LAVHLHDTYGQSLPNI 339
+ K + G I DT+G+ TP E + + K +++H H+ +G ++ N
Sbjct: 148 LYKAGIEAGADRICFCDTVGILTPEK---TYELFKRLSELVKGPVSIHCHNDFGLAVANT 204
Query: 340 LISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGL-GVETNVDLRKL 393
L +L G V ++ G+G +GN + E+VV L L VET + L +L
Sbjct: 205 LAALAAGADQVHVTINGIG------ERAGNASLEEVVMALKHLYDVETGIKLEEL 253
>gnl|CDD|163685 cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase
and related proteins, catalytic TIM barrel domain.
Homocitrate synthase (HCS) catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate,
the first step in the lysine biosynthesis pathway. This
family includes the Yarrowia lipolytica LYS1 protein as
well as the Saccharomyces cerevisiae LYS20 and LYS21
proteins. This family belongs to the DRE-TIM
metallolyase superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 262
Score = 43.5 bits (103), Expect = 8e-05
Identities = 55/238 (23%), Positives = 101/238 (42%), Gaps = 23/238 (9%)
Query: 127 VKIVEVGPRDGLQNEKNTVPTGVKVELIRRLVSSGLPVVEATS-FVSPKWVPQLADARDV 185
KI++ R+G Q T K+E+ + L + G+ +E TS SP+ +R
Sbjct: 1 FKIIDSTLREGEQFANAFFDTEDKIEIAKALDAFGVDYIELTSPAASPQ-------SRAD 53
Query: 186 MEAVRDLEGARLPVLTP---NLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLV 242
EA+ L G + +LT ++ A+ G V + S +++ SI + +
Sbjct: 54 CEAIAKL-GLKAKILTHIRCHMDDARIAVETGVDGVDLVFGTSPFLREASHGKSITEIIE 112
Query: 243 RYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAI--PPSKVAYVAKELHDMGCFEISLGDTI 300
V K I VR S E + + V + + +G + + DT+
Sbjct: 113 SAVEVIEFVKSKGIEVR--FSS------EDSFRSDLVDLLRVYRAVDKLGVNRVGIADTV 164
Query: 301 GVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLG 358
G+ TP V ++ + VV + + H H+ G ++ N +L+ G + +D +V G+G
Sbjct: 165 GIATPRQVYELVRTLRGVVSCD-IEFHGHNDTGCAIANAYAALEAGATHIDTTVLGIG 221
>gnl|CDD|162728 TIGR02146, LysS_fung_arch, homocitrate synthase. This model
includes the yeast LYS21 gene which carries out the
first step of the alpha-aminoadipate (AAA) lysine
biosynthesis pathway. A related pathway is found in
Thermus thermophilus. This enzyme is closely related to
2-isopropylmalate synthase (LeuA) and citramalate
synthase (CimA), both of which are present in the
euryarchaeota. Some archaea have a separate homocitrate
synthase (AksA) which also synthesizes longer
homocitrate analogs.
Length = 344
Score = 41.3 bits (97), Expect = 5e-04
Identities = 44/239 (18%), Positives = 83/239 (34%), Gaps = 40/239 (16%)
Query: 135 RDGLQNEKNTVPTGVKVELIRRLVSSGL-------PVVEATSFVSPKWVPQLADARDVME 187
R+G Q T K+E+ + L G+ P S + + + L +++
Sbjct: 7 REGEQFPGANFSTEQKIEIAKALDEFGIDYIEVTHPAASKQSRIDIEIIASLGLKANIVT 66
Query: 188 AVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAV 247
+R L + A+ G + IF S+ + + L R
Sbjct: 67 HIRCR-----------LDDAKVAVELGVDGIDIFFGTSKLLRIAEHRSDAKSILESARET 115
Query: 248 AHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAY--------VAKELHDMGCFEISLGDT 299
AK + VR + + + G + + DT
Sbjct: 116 IEYAKSAGLEVR--------------FSAEDTFRSELADLLSIYETVGVFGVDRVGIADT 161
Query: 300 IGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLG 358
+G P V ++ V+ VVP + +H H+ G ++ N +++ G + VD +V G+G
Sbjct: 162 VGKAAPRQVYELIRTVVRVVPGVDIELHAHNDTGCAVANAYNAIEGGATIVDTTVLGIG 220
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 41.6 bits (97), Expect = 7e-04
Identities = 30/108 (27%), Positives = 52/108 (48%), Gaps = 7/108 (6%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILI 341
+ KEL +MG I + D G+ TP ++ + A+ + L VH H T G S L
Sbjct: 168 LVKELVEMGADSICIKDMAGILTPKAAKELVSGIKAMTNL-PLIVHTHATSGISQMTYLA 226
Query: 342 SLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVD 389
+++ G +D +++ P+++G S ATE + L G + +D
Sbjct: 227 AVEAGADRIDTALS-----PFSEGTS-QPATESMYLALKEAGYDITLD 268
>gnl|CDD|163682 cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like,
N-terminal catalytic TIM barrel domain. This family of
bacterial enzymes is sequence-similar to
4-hydroxy-2-oxovalerate aldolase (HOA) but its exact
function is unknown. This family includes the
Bacteroides vulgatus Bvu_2661 protein and belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 266
Score = 39.9 bits (94), Expect = 0.002
Identities = 24/112 (21%), Positives = 55/112 (49%), Gaps = 11/112 (9%)
Query: 294 ISLGDTIGVGTPGTVVPMLEAVMA-VVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDC 352
+ D+ G P + ++ + + + KL H H+ +L N L ++++G+ +D
Sbjct: 155 FYIVDSFGSMYPEDIKRIISLLRSNLDKDIKLGFHAHNNLQLALANTLEAIELGVEIIDA 214
Query: 353 SVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDFINKHL 404
+V G+G +GA GN+ TE ++ L+ +L ++ + I++++
Sbjct: 215 TVYGMG-----RGA-GNLPTELLLDYLNNK-FGKKYNLEPVL---ELIDEYI 256
>gnl|CDD|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 38.2 bits (88), Expect = 0.009
Identities = 34/120 (28%), Positives = 56/120 (46%), Gaps = 11/120 (9%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNI-- 339
+ K+L +MGC I++ D G+ TP V E + L VHLH L +I
Sbjct: 159 LGKKLAEMGCDSIAIKDMAGLLTPTVTV---ELYAGLKQATGLPVHLHSHSTSGLASICH 215
Query: 340 LISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDLRKLMLAGDF 399
++ G + +D +++ G GAS + TE +V L+ +T +DL L+ D+
Sbjct: 216 YEAVLAGCNHIDTAISSFSG-----GAS-HPPTEALVAALTDTPYDTELDLNILLEIDDY 269
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 36.2 bits (85), Expect = 0.031
Identities = 32/108 (29%), Positives = 59/108 (54%), Gaps = 13/108 (12%)
Query: 294 ISLGDTIGVGTPGTVVPMLEAVMAVVP-VEK--LAVHLHDTYGQSLPNILISLQMGISTV 350
I++ DT+G TP +++ + VP ++K ++VH H+ G ++ N L +++ G V
Sbjct: 166 INIPDTVGYTTPEEFGELIKTLRERVPNIDKAIISVHCHNDLGLAVANSLAAVEAGARQV 225
Query: 351 DCSVAGLGGCPYAKGASGNVATEDVVYML----SGLGVETNVDLRKLM 394
+C++ G+G + A GN A E+VV L GVET ++ ++
Sbjct: 226 ECTINGIG-----ERA-GNAALEEVVMALKTRKDIYGVETGINTEEIY 267
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 34.4 bits (79), Expect = 0.12
Identities = 34/151 (22%), Positives = 64/151 (42%), Gaps = 19/151 (12%)
Query: 246 AVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAY---VAKELHDMGCFEISLGDTIGV 302
AVA A KV+ + C G ++ A P + Y +A EL G + + D G+
Sbjct: 660 AVAEAGKVVEAAI-----CYTGDILDPARPKYDLKYYTNLAVELEKAGAHILGIKDMAGL 714
Query: 303 GTPGTVVPMLEAVMAV--VPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVAGLGGC 360
P +++A+ +P+ H HDT G ++ ++L +++ G+ VD +V + G
Sbjct: 715 LKPAAAKLLIKALREKTDLPIH---FHTHDTSGIAVASMLAAVEAGVDVVDVAVDSMSGL 771
Query: 361 PYAKGASGNVATEDVVYMLSGLGVETNVDLR 391
+V L G + +++
Sbjct: 772 TSQPSLGA------IVAALEGSERDPGLNVA 796
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 32.3 bits (74), Expect = 0.56
Identities = 27/111 (24%), Positives = 51/111 (45%), Gaps = 11/111 (9%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVV--PVEKLAVHLHDTYGQSLPNI 339
+AKEL G +++ D G+ P ++ A+ V P+ +H HDT G +
Sbjct: 699 LAKELEKAGAHILAIKDMAGLLKPAAAYRLISALRETVDLPIH---LHTHDTSGNGVATY 755
Query: 340 LISLQMGISTVDCSVAGLGGCPYAKGASGNVATEDVVYMLSGLGVETNVDL 390
L +++ G+ VD ++A + G + +V L+G +T +D+
Sbjct: 756 LAAVEAGVDIVDVAMASMSGLTSQPSLNS------IVAALAGTERDTGLDI 800
>gnl|CDD|163679 cd07941, DRE_TIM_LeuA3, Desulfobacterium autotrophicum LeuA3 and
related proteins, N-terminal catalytic TIM barrel
domain. Desulfobacterium autotrophicum LeuA3 is
sequence-similar to alpha-isopropylmalate synthase
(LeuA) but its exact function is unknown. Members of
this family have an N-terminal TIM barrel domain that
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 273
Score = 31.7 bits (73), Expect = 0.59
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 294 ISLGDTIGVGT-PGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDC 352
+ L DT G GT P + +++ V +P L +H H+ G ++ N L +++ G + V
Sbjct: 168 LVLCDTNG-GTLPHEIAEIVKEVRERLPGVPLGIHAHNDSGLAVANSLAAVEAGATQVQG 226
Query: 353 SVAGLG 358
++ G G
Sbjct: 227 TINGYG 232
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 31.4 bits (72), Expect = 0.65
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 14/70 (20%)
Query: 151 VELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDLEGARL----PVLTPNLKG 206
+ L + L+ G+P +E T +P A + + A+ L VL P +
Sbjct: 28 LPLAKALIEGGIPAIEIT-LRTP-------AALEAIRALAKEFPEALIGAGTVLNP--EQ 77
Query: 207 FEAAIAAGAK 216
AIAAGA+
Sbjct: 78 ARQAIAAGAQ 87
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 32.0 bits (74), Expect = 0.69
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 324 LAVHLH--DTYGQSLPNILISLQMGISTVDCSVAGLGGCPYAKGAS-GNVATEDVVYMLS 380
L +HLH DT G L L + + G+ VD +VA + G S ++ + +V L
Sbjct: 735 LPIHLHTHDTSGNGLATYLAAAEAGVDIVDVAVASMSG-----LTSQPSLNS--IVAALE 787
Query: 381 GLGVETNVDLRKL 393
G +T +DL +
Sbjct: 788 GTERDTGLDLDAI 800
>gnl|CDD|188634 cd00945, Aldolase_Class_I, Class I aldolases. Class I aldolases.
The class I aldolases use an active-site lysine which
stabilizes a reaction intermediates via Schiff base
formation, and have TIM beta/alpha barrel fold. The
members of this family include
2-keto-3-deoxy-6-phosphogluconate (KDPG) and
2-keto-4-hydroxyglutarate (KHG) aldolases,
transaldolase, dihydrodipicolinate synthase sub-family,
Type I 3-dehydroquinate dehydratase, DeoC and DhnA
proteins, and metal-independent
fructose-1,6-bisphosphate aldolase. Although
structurally similar, the class II aldolases use a
different mechanism and are believed to have an
independent evolutionary origin.
Length = 201
Score = 30.8 bits (70), Expect = 1.0
Identities = 27/78 (34%), Positives = 33/78 (42%), Gaps = 2/78 (2%)
Query: 242 VRYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIG 301
V V AA L+ V VVG P KVA V +E D+G EI + IG
Sbjct: 32 VNPGYVRLAADALA-GSDVPVIVVVGFPTGLTTTEVKVAEV-EEAIDLGADEIDVVINIG 89
Query: 302 VGTPGTVVPMLEAVMAVV 319
G +LE + AVV
Sbjct: 90 SLKEGDWEEVLEEIAAVV 107
>gnl|CDD|236327 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional.
Length = 477
Score = 30.9 bits (71), Expect = 1.4
Identities = 23/53 (43%), Positives = 27/53 (50%), Gaps = 20/53 (37%)
Query: 111 DIRDITN--KF----LKGIP-RFVKIVEVGPRDGLQNEKNTVPTGVKVELIRR 156
D D T KF LKG+P R +E+GPRD L E NT V L+RR
Sbjct: 327 DRSDKTPGWKFNEWELKGVPLR----IEIGPRD-L--ENNT------VVLVRR 366
>gnl|CDD|221105 pfam11397, GlcNAc, Glycosyltransferase (GlcNAc). GlcNAc is an
enzyme that carries out the first glycosylation step of
hydroxylated Skp1, a ubiquitous eukaryotic protein, in
the cytoplasm.
Length = 321
Score = 30.4 bits (69), Expect = 1.7
Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 59 YDEYTREAFP--WRRHTRDMSHGDSFSRRTVSLGRNHKMFGSACDIYNSNCNDKDIRDI 115
+ YTR P W HTR+ R S R + A + ++ + D+
Sbjct: 240 FHLYTRPKRPKVWSDHTREAVSAAWEERNLRSRERVLYLLRRA-LLNSNTSTPEGGIDL 297
>gnl|CDD|168348 PRK06015, PRK06015,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 201
Score = 29.8 bits (67), Expect = 1.9
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 151 VELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRD-LEGARLPVLTP-NLKGFE 208
V L R L + GLP +E T + A D + AV +E A + T N K FE
Sbjct: 19 VPLARALAAGGLPAIEITL--------RTPAALDAIRAVAAEVEEAIVGAGTILNAKQFE 70
Query: 209 AAIAAGAK 216
A AG++
Sbjct: 71 DAAKAGSR 78
>gnl|CDD|130050 TIGR00977, LeuA_rel, 2-isopropylmalate synthase/homocitrate
synthase family protein. This model represents
uncharacterized proteins related to 2-isopropylmalate
synthases and homocitrate synthases but phylogenetically
distint. Each species represented in the seed alignment
also has a member of a known family of 2-isopropylmalate
synthases [Unknown function, General].
Length = 526
Score = 29.9 bits (67), Expect = 2.9
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 296 LGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQMGISTVDCSVA 355
L DT G P + + V + +L +H H+ G ++ N L++++ G + V ++
Sbjct: 173 LCDTNGGTLPHEISEITTKVKRSLKQPQLGIHAHNDSGTAVANSLLAVEAGATMVQGTIN 232
Query: 356 GLG 358
G G
Sbjct: 233 GYG 235
>gnl|CDD|216654 pfam01702, TGT, Queuine tRNA-ribosyltransferase. This is a family
of queuine tRNA-ribosyltransferases EC:2.4.2.29, also
known as tRNA-guanine transglycosylase and guanine
insertion enzyme. Queuine tRNA-ribosyltransferase
modifies tRNAs for asparagine, aspartic acid, histidine
and tyrosine with queuine. It catalyzes the exchange of
guanine-34 at the wobble position with
7-aminomethyl-7-deazaguanine, and the addition of a
cyclopentenediol moiety to
7-aminomethyl-7-deazaguanine-34 tRNA; giving a
hypermodified base queuine in the wobble position. The
aligned region contains a zinc binding motif
C-x-C-x2-C-x29-H, and important tRNA and
7-aminomethyl-7deazaguanine binding residues.
Length = 237
Score = 29.6 bits (67), Expect = 2.9
Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 269 PVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTP-GTVVPMLEAVMAVVPVEKLAVH 327
V+G + A+EL + G ++G + VG ++ +++AV ++P +K +
Sbjct: 59 IVQGGLYEDLREESAEELAEDGFDGYAIGG-LSVGEEKEEMLELVDAVTPLLPEDKP-RY 116
Query: 328 LHDTYGQSLPNILISLQMGISTVDCS 353
L + +IL ++ +G+ DC
Sbjct: 117 LMGVG--TPEDILEAVALGVDMFDCV 140
>gnl|CDD|188632 cd00452, KDPG_aldolase, KDPG and KHG aldolase. KDPG and KHG
aldolase. This family belongs to the class I adolases
whose reaction mechanism involves Schiff base formation
between a substrate carbonyl and lysine residue in the
active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG)
aldolase, is best known for its role in the
Entner-Doudoroff pathway of bacteria, where it catalyzes
the reversible cleavage of KDPG to pyruvate and
glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate
(KHG) aldolase, which has enzymatic specificity toward
glyoxylate, forming KHG in the presence of pyruvate, and
is capable of regulating glyoxylate levels in the
glyoxylate bypass, an alternate pathway when bacteria
are grown on acetate carbon sources.
Length = 190
Score = 29.0 bits (66), Expect = 3.6
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 16/71 (22%)
Query: 151 VELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDLEGARLP-----VLTPNLK 205
+ L L+ G+ +E T +P A + + A+R E VLTP +
Sbjct: 19 LALAEALIEGGIRAIEIT-LRTP-------GALEAIRALRK-EFPEALIGAGTVLTP--E 67
Query: 206 GFEAAIAAGAK 216
+AAIAAGA+
Sbjct: 68 QADAAIAAGAQ 78
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 29.6 bits (67), Expect = 3.7
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 274 IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVV 309
+PPS ++ V L +G G T
Sbjct: 920 VPPSHLSAVLTRLRSRNIICYPIGTVGPSGPSNTFS 955
>gnl|CDD|233807 TIGR02275, DHB_AMP_lig, 2,3-dihydroxybenzoate-AMP ligase. Proteins
in this family belong to the AMP-binding enzyme family
(pfam00501). Members activate 2,3-dihydroxybenzoate
(DHB) by ligation of AMP from ATP with the release of
pyrophosphate; many are involved in synthesis of
siderophores such as enterobactin, vibriobactin,
vulnibactin, etc. The most closely related proteine
believed to differ in function activates salicylate
rather than DHB [Transport and binding proteins, Cations
and iron carrying compounds].
Length = 526
Score = 29.4 bits (66), Expect = 4.6
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 237 IEDSLVRYRAVAHAAKV-LSIPVRGYVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEIS 295
IE+ L+ + AV AA V + + G SC + P K A + + L + G E
Sbjct: 445 IENLLLAHPAVHDAALVSMPDELLGEKSCAFIVVRD---PALKAAQLRRFLRERGLAEYK 501
Query: 296 LGDTI 300
L D +
Sbjct: 502 LPDRV 506
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 29.0 bits (66), Expect = 5.1
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 284 KELHDMGCFEISLGDTI-GVGTPGTVVPMLEAVMAVVPVEKL--AVHLHDTYGQSLPNIL 340
K + D I LG TI GV + +L+A+ A P L A+H+H T + +P +
Sbjct: 395 KVVVDADTDRI-LGATILGVHGDEMIHEILDAMYAGAPYTTLSRAIHIHPTVSELIPTLA 453
Query: 341 ISLQMGIST 349
+L+ T
Sbjct: 454 QALRRTRLT 462
>gnl|CDD|238439 cd00862, ProRS_anticodon_zinc, ProRS Prolyl-anticodon binding
domain, long version found predominantly in eukaryotes
and archaea. ProRS belongs to class II aminoacyl-tRNA
synthetases (aaRS). This alignment contains the
anticodon binding domain, which is responsible for
specificity in tRNA-binding, so that the activated amino
acid is transferred to a ribose 3' OH group of the
appropriate tRNA only, and an additional C-terminal
zinc-binding domain specific to this subfamily of aaRSs.
Length = 202
Score = 28.4 bits (64), Expect = 5.2
Identities = 23/68 (33%), Positives = 26/68 (38%), Gaps = 27/68 (39%)
Query: 111 DIRDITN---KF----LKGIP-RFVKIVEVGPRDGLQN----------EKNTVP-----T 147
D RD KF LKG+P R E+GPRD +N EK TVP
Sbjct: 49 DDRDNYTPGWKFNDWELKGVPLRI----EIGPRDLEKNTVVIVRRDTGEKKTVPLAELVE 104
Query: 148 GVKVELIR 155
V L
Sbjct: 105 KVPELLDE 112
>gnl|CDD|184438 PRK13985, ureB, urease subunit beta; Provisional.
Length = 568
Score = 28.7 bits (64), Expect = 7.2
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 274 IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVP 310
I P +A LHDMG F I+ D+ +G G V+
Sbjct: 338 IRPQTIA-AEDTLHDMGIFSITSSDSQAMGRVGEVIT 373
>gnl|CDD|217851 pfam04029, 2-ph_phosp, 2-phosphosulpholactate phosphatase. Thought
to catalyze 2-phosphosulpholactate = sulpholactate +
phosphate. Probable magnesium cofactor. Involved in the
second step of coenzyme M biosynthesis. Inhibited by
vanadate in Methanococcus jannaschii. Also known as the
ComB family.
Length = 231
Score = 27.9 bits (63), Expect = 9.6
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 209 AAIAAGAKEVAIFASASEAFSKSN 232
A+A GA+ + A EA +
Sbjct: 32 TALANGARAIIPVADIEEALALKK 55
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
0.318 0.134 0.394
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,670,166
Number of extensions: 2118041
Number of successful extensions: 2233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2181
Number of HSP's successfully gapped: 62
Length of query: 426
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 326
Effective length of database: 6,502,202
Effective search space: 2119717852
Effective search space used: 2119717852
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)