RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018252
(359 letters)
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 484 bits (1248), Expect = e-173
Identities = 206/264 (78%), Positives = 228/264 (86%)
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 VEKLAVHLHDTYGQSLPNILISLQ 344
V+KLAVH HDTYGQ+L NIL+SLQ
Sbjct: 241 VDKLAVHFHDTYGQALANILVSLQ 264
>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 = 369 bits (949), Expect = e-128
Identities = 128/216 (59%), Positives = 154/216 (71%)
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 VPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
+LEAV+ P EKLA+H HDT GQ+L NIL +L+
Sbjct: 181 RRLLEAVLERFPDEKLALHFHDTRGQALANILAALE 216
>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
Length = 287
Score = 361 bits (930), Expect = e-125
Identities = 141/223 (63%), Positives = 168/223 (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 GTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQV 345
GTPG V +LEAV+A P E+LA H HDTYGQ+L NI SL+
Sbjct: 181 GTPGQVRAVLEAVLAEFPAERLAGHFHDTYGQALANIYASLEE 223
>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 = 233 bits (596), Expect = 3e-75
Identities = 82/217 (37%), Positives = 114/217 (52%), Gaps = 6/217 (2%)
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 VVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
V +++A+ +P L +H H+T G ++ N L +L+
Sbjct: 177 VAELVKALREALPDVPLGLHTHNTLGLAVANSLAALE 213
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 162 bits (413), Expect = 2e-46
Identities = 54/222 (24%), Positives = 90/222 (40%), Gaps = 10/222 (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-KLAVHLHDTYGQSLPNILISLQ 344
TP V ++EA+ A VP + L+VH H+ G ++ N L +++
Sbjct: 173 TPNEVADIIEALKANVPNKVILSVHCHNDLGMAVANSLAAVE 214
>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 = 148 bits (376), Expect = 7e-43
Identities = 53/210 (25%), Positives = 90/210 (42%), Gaps = 8/210 (3%)
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 VMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
+ VP + VH H+ G ++ N L +++
Sbjct: 174 LKDRVPPVIIEVHCHNDLGMAVANSLAAVE 203
>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 = 41.5 bits (98), Expect = 5e-04
Identities = 50/214 (23%), Positives = 82/214 (38%), Gaps = 27/214 (12%)
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---PNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRYRAVA-- 248
G ++ EAA G V I S+ IE L + RA
Sbjct: 62 GLPARLMAWCRARDADIEAAARCGVDAVHISIPVSDL--------QIEAKLRKDRAWVLE 113
Query: 249 HAAKVLSIPV-RG-YVSCVVGCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPG 306
A+++S RG +VS VG P + +A+ + G DT+G+ P
Sbjct: 114 RLARLVSFARDRGLFVS--VGGEDASRADPDFLVELAEVAAEAGADRFRFADTVGILDPF 171
Query: 307 TVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
+ ++ A+ V + L +H H+ G + N L
Sbjct: 172 STYELVRALRQAVDLP-LEMHAHNDLGMATANTL 204
>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 = 41.3 bits (97), Expect = 7e-04
Identities = 47/228 (20%), Positives = 92/228 (40%), Gaps = 23/228 (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--LAVHLHDTYGQSLPNILISLQ 344
+G P +++ + VP ++K L+VH H+ G ++ N L ++Q
Sbjct: 169 VGYALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVANSLAAVQ 216
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 39.0 bits (92), Expect = 0.003
Identities = 58/233 (24%), Positives = 95/233 (40%), Gaps = 43/233 (18%)
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 DMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
+ G + DT+G+ P T+ +++ ++ V + + VH H+ +G + N L
Sbjct: 156 EAGADRVRFCDTVGILDPFTMYELVKELVEAVDIP-IEVHCHNDFGMATANAL 207
>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 = 39.0 bits (91), Expect = 0.003
Identities = 52/222 (23%), Positives = 89/222 (40%), Gaps = 31/222 (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 GDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPN 338
DT+GV TP + +++ + V + ++VH H+ +G + N
Sbjct: 161 ADTVGVLTPQKMEELIKKLKENVKLP-ISVHCHNDFGLATAN 201
>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 = 36.1 bits (84), Expect = 0.020
Identities = 37/174 (21%), Positives = 66/174 (37%), Gaps = 24/174 (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---------MAVVPVEKLAVHLHDTYGQSLPN 338
I L DT+G G P + +V VP E L H H+ + +++ N
Sbjct: 167 IRLCDTLGYGVPYPGASLPRSVPKIIYGLRKDCGVPSENLEWHGHNDFYKAVAN 220
>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 = 35.9 bits (84), Expect = 0.024
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 270 VEGAI-----PPSKVAY---VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPV 321
VEGAI P + Y +AKEL DMG I + D G+ TP +++A+ V +
Sbjct: 134 VEGAICYTGSPVHTLEYYVKLAKELEDMGADSICIKDMAGLLTPYAAYELVKALKKEVGL 193
Query: 322 EKLAVHLHDTYGQSLPNIL 340
+ +H HDT G ++ L
Sbjct: 194 P-IHLHTHDTSGLAVATYL 211
>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 = 35.6 bits (83), Expect = 0.026
Identities = 48/215 (22%), Positives = 84/215 (39%), Gaps = 43/215 (20%)
Query: 135 RDGLQNEKNTVPTGV------KVELIRRLVSSGLPVVEATSFVSPKWVPQL-ADARDVME 187
RDG Q GV K+ + R L +G+ +E +P + + R+ +
Sbjct: 7 RDGEQA------PGVAFSREEKLAIARALDEAGVDEIEVG-------IPAMGEEEREAIR 53
Query: 188 AVRDLEGARLPVLT---PNLKGFEAAIAAGAKEVAIFASASEAFSKSNINCSIEDSLVRY 244
A+ L G ++ + EAA+ G V I + S+I+ + L +
Sbjct: 54 AIVAL-GLPARLIVWCRAVKEDIEAALRCGVTAVHI------SIPVSDIH--LAHKLGKD 104
Query: 245 RA--VAHAAKVLSIPV-RG-YVSCVVGCPVEGA--IPPSKVAYVAKELHDMGCFEISLGD 298
RA + +++ RG +VS VG E A P + A+ + G + D
Sbjct: 105 RAWVLDQLRRLVGRAKDRGLFVS--VGA--EDASRADPDFLIEFAEVAQEAGADRLRFAD 160
Query: 299 TIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYG 333
T+G+ P T ++ + A + L H H+ G
Sbjct: 161 TVGILDPFTTYELIRRLRAATDLP-LEFHAHNDLG 194
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 35.0 bits (81), Expect = 0.052
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQS 335
+AKEL +MG I + D G+ TP +++A+ +PV + +H H T G +
Sbjct: 161 LAKELLEMGVDSICIKDMAGLLTPYEAYELVKAIKKELPV-PVELHTHATSGMA 213
>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 = 33.5 bits (77), Expect = 0.14
Identities = 51/229 (22%), Positives = 93/229 (40%), Gaps = 23/229 (10%)
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 GVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQVSPMH 349
G+ TP V ++ + VV + + H H+ G ++ N +L+ H
Sbjct: 165 GIATPRQVYELVRTLRGVVSCD-IEFHGHNDTGCAIANAYAALEAGATH 212
>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 = 32.8 bits (75), Expect = 0.26
Identities = 38/225 (16%), Positives = 74/225 (32%), Gaps = 40/225 (17%)
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 IGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNILISLQ 344
+G P V ++ V+ VVP + +H H+ G ++ N +++
Sbjct: 162 VGKAAPRQVYELIRTVVRVVPGVDIELHAHNDTGCAVANAYNAIE 206
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 31.8 bits (73), Expect = 0.33
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|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 32.4 bits (74), Expect = 0.39
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYG 333
+AKE+ +MG I + D G+ TP +++ + V V L VH H T G
Sbjct: 159 LAKEMQEMGADSICIKDMAGILTPYVAYELVKRIKEAVTV-PLEVHTHATSG 209
>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 = 31.5 bits (72), Expect = 0.45
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|178767 PLN03228, PLN03228, methylthioalkylmalate synthase; Provisional.
Length = 503
Score = 31.8 bits (72), Expect = 0.54
Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 29/233 (12%)
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---GTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNIL 340
+ + DT+G+ P G +V ++A + +VH H+ G + N +
Sbjct: 253 ATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGLATANTI 305
>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 = 32.1 bits (73), Expect = 0.56
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYG 333
+A+EL +MG I + D G+ TP ++ A+ + + +H H T G
Sbjct: 154 LAEELLEMGVDSICIKDMAGILTPKAAYELVSALKKRFGLP-VHLHSHATTG 204
>gnl|CDD|168348 PRK06015, PRK06015,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 201
Score = 30.6 bits (69), Expect = 1.0
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|236327 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional.
Length = 477
Score = 30.5 bits (70), Expect = 1.3
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|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 30.7 bits (70), Expect = 1.4
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQS 335
+AK+L DMG + + D G+ P ++ + V V L +H H T G S
Sbjct: 160 LAKQLEDMGVDSLCIKDMAGLLKPYAAYELVSRIKKRVDVP-LHLHCHATTGLS 212
>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 = 29.8 bits (68), Expect = 1.7
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|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 = 30.0 bits (68), Expect = 2.0
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|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 30.1 bits (67), Expect = 2.1
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQSLPNI 339
+ K+L +MGC I++ D G+ TP V E + L VHLH L +I
Sbjct: 159 LGKKLAEMGCDSIAIKDMAGLLTPTVTV---ELYAGLKQATGLPVHLHSHSTSGLASI 213
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 29.7 bits (66), Expect = 2.6
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
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 SLQ 344
+++
Sbjct: 227 AVE 229
>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 = 29.3 bits (66), Expect = 2.9
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 276 PSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAVHLHDTYGQS 335
P V + L D+ I L DT+G+ +P + ++ P H H+ Y +
Sbjct: 146 PDYVFQLVDFLSDLPIKRIMLPDTLGILSPFETYTYISDMVKRYPNLHFDFHAHNDYDLA 205
Query: 336 LPNILISLQ--VSPMHA 350
+ N+L +++ + +H
Sbjct: 206 VANVLAAVKAGIKGLHT 222
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 29.6 bits (67), Expect = 3.3
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 274 IPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVV 309
+PPS ++ V L +G G T
Sbjct: 920 VPPSHLSAVLTRLRSRNIICYPIGTVGPSGPSNTFS 955
>gnl|CDD|131081 TIGR02026, BchE, magnesium-protoporphyrin IX monomethyl ester
anaerobic oxidative cyclase. This model respresents the
cobalamin-dependent oxidative cyclase responsible for
forming the distinctive E-ring of the chlorin ring
system under anaerobic conditions. This step is
essential in the biosynthesis of both
bacteriochlorophyll and chlorophyll under anaerobic
conditions (a separate enzyme, AcsF, acts under aerobic
conditions). This model identifies two clades of
sequences, one from photosynthetic, non-cyanobacterial
bacteria and another including Synechocystis and several
non-photosynthetic bacteria. The function of the
Synechocystis gene is supported by gene clustering with
other photosynthetic genes, so the purpose of the gene
in the non-photosynthetic bacteria is uncertain. Note
that homologs of this gene are not found in plants which
rely solely on the aerobic cyclase.
Length = 497
Score = 29.1 bits (65), Expect = 3.6
Identities = 20/93 (21%), Positives = 35/93 (37%), Gaps = 19/93 (20%)
Query: 267 GCPVEGAIPPSKVAYVAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAV 326
G + G PP VAY+ L D G +++ L+A+ + EKL
Sbjct: 13 GAEIAGQWPPLWVAYIGGALLDAGYHDVTF---------------LDAMTGPLTDEKLVE 57
Query: 327 HLHDTYGQSLPNILISLQVSPMHAKPCFTFAYL 359
L P++++ ++P C T +
Sbjct: 58 RLR----AHCPDLVLITAITPAIYIACETLKFA 86
>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 = 29.0 bits (65), Expect = 4.0
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|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 = 4.4
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 = 29.1 bits (65), Expect = 4.6
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|236449 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
Length = 592
Score = 29.0 bits (66), Expect = 4.8
Identities = 27/72 (37%), Positives = 32/72 (44%), Gaps = 11/72 (15%)
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 329
+ L V LH
Sbjct: 192 LKEEVDLPVQLH 203
>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 = 28.2 bits (64), Expect = 5.9
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 294 ISLGDTIGVGTPGTVVPMLEAVMAVVPVEK--LAVHLHDTYGQSLPNIL 340
I++ DT+G TP +++ + VP K ++VH H+ G ++ N L
Sbjct: 160 INIPDTVGYLTPEEFGELIKKLKENVPNIKVPISVHCHNDLGLAVANSL 208
>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 = 28.3 bits (64), Expect = 5.9
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 209 AAIAAGAKEVAIFASASEAFSKSN 232
A+A GA+ + A EA +
Sbjct: 32 TALANGARAIIPVADIEEALALKK 55
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 28.2 bits (64), Expect = 6.7
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
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 ISLQ 344
+L+
Sbjct: 454 QALR 457
>gnl|CDD|212503 cd11644, Precorrin-6Y-methylase, Precorrin-6Y methyltransferase,
the cobalamin biosynthesis enzyme CbiE. Precorrin-6Y
methyltransferase participates in the pathway toward the
biosynthesis of cobalamin (vitamin B12). There are two
distinct cobalamin biosynthetic pathways in bacteria.
The aerobic pathway requires oxygen, and cobalt is
inserted late in the pathway; the anaerobic pathway does
not requires oxygen, and cobalt insertion is the first
committed step towards cobalamin synthesis. This model
represents the CbiE subunit of precorrin-6Y
C5,15-methyltransferase from the anaerobic pathway, a
bifunctional enzyme that catalyzes two methylations (at
C-5 and C-15) in precorrin-6Y, as well as the
decarboxylation of the acetate side chain located in
ring C, in order to generate precorrin-8X. In the
anaerobic pathway, two enzymes are required to produce
precorrin-8X: CbiE and CbiT, which can be fused as CbiET
(sometimes called CobL). In the aerobic pathway, the
bifunctional enzyme is called CobL.
Length = 201
Score = 27.9 bits (63), Expect = 7.8
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 187 EAVRDLEGARLPVLTPNLKGFEAAIAAGAKEVAIFAS 223
E DL ++P+ + +L +AA + V + AS
Sbjct: 36 ELFPDLGAEKIPLPSDDLAELLERLAAAGRRVVVLAS 72
>gnl|CDD|235718 PRK06154, PRK06154, hypothetical protein; Provisional.
Length = 565
Score = 28.2 bits (63), Expect = 8.2
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 142 KNTVPTGVKVELIRRLVSSGLPVVEATSFVSPKWVPQLADARDVMEAVRDLEGARLPVL 200
+N P V +EL +++ L + S + P AD +V+EA L A PV+
Sbjct: 162 RNGRPGPVVLELPVDVLAEELDELPLDHRPSRRSRPG-ADPVEVVEAAALLLAAERPVI 219
>gnl|CDD|171527 PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional.
Length = 612
Score = 28.2 bits (63), Expect = 9.2
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 194 GARLPVLTPN----LKGFEAAIAAGAKEVAIFA 222
G R+ +L P + GF AAI AG V +FA
Sbjct: 92 GDRVAILAPQGIDYVAGFFAAIKAGTIAVPLFA 124
>gnl|CDD|233228 TIGR00998, 8a0101, efflux pump membrane protein (multidrug
resistance protein A). [Transport and binding proteins,
Other].
Length = 334
Score = 27.8 bits (62), Expect = 10.0
Identities = 32/165 (19%), Positives = 57/165 (34%), Gaps = 38/165 (23%)
Query: 176 VPQLADARDVMEAVRDLEGARLPVLTPNLKGFEAAIAAGA--KEVAIFASASEAFSKSNI 233
V QL + ++ + +L +L+ G +E A + +K+ +
Sbjct: 103 VQQLQAKVESLKIKLEQAREKLLQAELDLRRRVPLFKKGLISREELDHARKALLSAKAAL 162
Query: 234 NCSIE------------DSLVRYRAVAHAAKVLSIPVRGYVSCVVGCPVEGAIPPSKVAY 281
N +I+ L + AV A + L V+ P +G Y
Sbjct: 163 NAAIQEQLNANQALVRGTPLKKQPAVQEAKERLKTAWLALKRTVIRAPFDG--------Y 214
Query: 282 VAKELHDMGCFEISLGDTIGVGTPGTVVPMLEAVMAVVPVEKLAV 326
VA+ + +G + G P +MAVVP E++ V
Sbjct: 215 VARR-------FVQVGQVVSPGQP---------LMAVVPAEQMYV 243
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 0.134 0.401
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: 18,289,831
Number of extensions: 1764176
Number of successful extensions: 1931
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1913
Number of HSP's successfully gapped: 53
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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 (21.7 bits)
S2: 60 (26.9 bits)