RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12516
(327 letters)
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 342 bits (878), Expect = e-117
Identities = 137/213 (64%), Positives = 161/213 (75%)
Query: 104 SMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCP 163
++ G KE+AVFASASE FSK NINC+IEESL R+ EV A + I VRGY+SCVVGCP
Sbjct: 130 AIAAGAKEVAVFASASESFSKSNINCSIEESLVRYREVALAAKKHSIPVRGYVSCVVGCP 189
Query: 164 YEGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCH 223
EG VPP V VA LY MGCYEISLGDTIGVGTPGT+ MLE V+ V+P D+LAVH H
Sbjct: 190 IEGPVPPSKVAYVAKELYDMGCYEISLGDTIGVGTPGTVVPMLEAVMAVVPVDKLAVHFH 249
Query: 224 DTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGAD 283
DTYGQALANIL +++ GIS DSS+AGLGGCPYA+GASGNVATED+VYML G+G+ T D
Sbjct: 250 DTYGQALANILVSLQMGISTVDSSVAGLGGCPYAKGASGNVATEDVVYMLNGLGVSTNVD 309
Query: 284 LTSLLRTGHYICGKLKKPSNSKVAKALPVKETS 316
L L+ G +I L +PS SK A AL + T+
Sbjct: 310 LGKLMAAGDFISKHLGRPSGSKTAVALSARITA 342
Score = 195 bits (496), Expect = 9e-60
Identities = 77/107 (71%), Positives = 88/107 (82%)
Query: 3 VASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILT 62
VA LY MGCYEISLGDTIGVGTPGT+ MLE V+ V+P D+LAVH HDTYGQALANIL
Sbjct: 202 VAKELYDMGCYEISLGDTIGVGTPGTVVPMLEAVMAVVPVDKLAVHFHDTYGQALANILV 261
Query: 63 AMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGV 109
+++ GIS DSS+AGLGGCPYA+GASGNVATED+VYML G + V
Sbjct: 262 SLQMGISTVDSSVAGLGGCPYAKGASGNVATEDVVYMLNGLGVSTNV 308
>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 = 337 bits (866), Expect = e-116
Identities = 120/192 (62%), Positives = 139/192 (72%)
Query: 105 MQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPY 164
+ GV E+AVF SASE FS++NINC+I ESLERF V A G+RVRGY+S GCPY
Sbjct: 83 LAAGVDEVAVFVSASETFSQKNINCSIAESLERFEPVAELAKAAGLRVRGYVSTAFGCPY 142
Query: 165 EGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHD 224
EG VPP V VA L +GC EISLGDTIGV TP +R +LE VL P ++LA+H HD
Sbjct: 143 EGEVPPERVAEVAERLLDLGCDEISLGDTIGVATPAQVRRLLEAVLERFPDEKLALHFHD 202
Query: 225 TYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADL 284
T GQALANIL A+E G+ FDSS+ GLGGCP+A GA+GNVATEDLVYMLEGMGIETG DL
Sbjct: 203 TRGQALANILAALEAGVRRFDSSVGGLGGCPFAPGATGNVATEDLVYMLEGMGIETGIDL 262
Query: 285 TSLLRTGHYICG 296
LL +I
Sbjct: 263 DKLLAAARWISE 274
Score = 196 bits (501), Expect = 2e-61
Identities = 68/109 (62%), Positives = 83/109 (76%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
+VA L +GC EISLGDTIGV TP +R +LE VL P ++LA+H HDT GQALANI
Sbjct: 152 AEVAERLLDLGCDEISLGDTIGVATPAQVRRLLEAVLERFPDEKLALHFHDTRGQALANI 211
Query: 61 LTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGV 109
L A+E G+ FDSS+ GLGGCP+A GA+GNVATEDLVYMLEG ++ G+
Sbjct: 212 LAALEAGVRRFDSSVGGLGGCPFAPGATGNVATEDLVYMLEGMGIETGI 260
>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
Length = 287
Score = 334 bits (860), Expect = e-115
Identities = 129/195 (66%), Positives = 152/195 (77%)
Query: 107 CGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYEG 166
G E+AVFASASE FS++NINC+I ESLERF V A G+RVRGY+SCV+GCPYEG
Sbjct: 91 AGADEVAVFASASEAFSQKNINCSIAESLERFEPVAEAAKQAGVRVRGYVSCVLGCPYEG 150
Query: 167 AVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTY 226
VPP V VA L+ +GCYEISLGDTIGVGTPG +R +LE VL PA+RLA H HDTY
Sbjct: 151 EVPPEAVADVAERLFALGCYEISLGDTIGVGTPGQVRAVLEAVLAEFPAERLAGHFHDTY 210
Query: 227 GQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTS 286
GQALANI ++E GI+VFD+S+ GLGGCPYA GASGNVATED++YML G+GIETG DL
Sbjct: 211 GQALANIYASLEEGITVFDASVGGLGGCPYAPGASGNVATEDVLYMLHGLGIETGIDLDK 270
Query: 287 LLRTGHYICGKLKKP 301
L+R G +I KL +P
Sbjct: 271 LVRAGQFIQSKLGRP 285
Score = 195 bits (499), Expect = 6e-61
Identities = 74/124 (59%), Positives = 92/124 (74%)
Query: 3 VASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILT 62
VA L+ +GCYEISLGDTIGVGTPG +R +LE VL PA+RLA H HDTYGQALANI
Sbjct: 160 VAERLFALGCYEISLGDTIGVGTPGQVRAVLEAVLAEFPAERLAGHFHDTYGQALANIYA 219
Query: 63 AMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVKEIAVFASASEMF 122
++E GI+VFD+S+ GLGGCPYA GASGNVATED++YML G ++ G+ + + +
Sbjct: 220 SLEEGITVFDASVGGLGGCPYAPGASGNVATEDVLYMLHGLGIETGIDLDKLVRAGQFIQ 279
Query: 123 SKRN 126
SK
Sbjct: 280 SKLG 283
>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 = 213 bits (546), Expect = 3e-68
Identities = 76/193 (39%), Positives = 107/193 (55%), Gaps = 10/193 (5%)
Query: 103 KSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGC 162
++++ GV E+ +F SASE S++N+N + EE LE E + A G+ V G + GC
Sbjct: 82 RALEAGVDEVRIFDSASETHSRKNLNKSREEDLENAEEAIEAAKEAGLEVEGSLEDAFGC 141
Query: 163 PYEGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHC 222
P V VA AL + G EISL DT+G+ TP + +++ + +P L +H
Sbjct: 142 KT----DPEYVLEVAKALEEAGADEISLKDTVGLATPEEVAELVKALREALPDVPLGLHT 197
Query: 223 HDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGA 282
H+T G A+AN L A+E G D S+ GLG +GN ATEDLV LEG+GI+TG
Sbjct: 198 HNTLGLAVANSLAALEAGADRVDGSVNGLG------ERAGNAATEDLVAALEGLGIDTGI 251
Query: 283 DLTSLLRTGHYIC 295
DL LL Y+
Sbjct: 252 DLEKLLEISRYVE 264
Score = 135 bits (342), Expect = 8e-38
Identities = 45/124 (36%), Positives = 66/124 (53%), Gaps = 7/124 (5%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
++VA AL + G EISL DT+G+ TP + +++ + +P L +H H+T G A+AN
Sbjct: 149 LEVAKALEEAGADEISLKDTVGLATPEEVAELVKALREALPDVPLGLHTHNTLGLAVANS 208
Query: 61 LTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVKEIAVFASASE 120
L A+E G D S+ GLG +GN ATEDLV LEG + G+ + S
Sbjct: 209 LAALEAGADRVDGSVNGLG------ERAGNAATEDLVAALEGLGIDTGID-LEKLLEISR 261
Query: 121 MFSK 124
+
Sbjct: 262 YVEE 265
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 171 bits (436), Expect = 3e-50
Identities = 53/200 (26%), Positives = 88/200 (44%), Gaps = 10/200 (5%)
Query: 103 KSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGC 162
++ GV I +F + S++ + + T EE LER + V A +G+ VR
Sbjct: 84 ALLEAGVDRIHIFIATSDLHLRYKLKKTREEVLERAVDAVEYARDHGLEVRFSAEDATR- 142
Query: 163 PYEGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPAD-RLAVH 221
P + V A + G I+L DT+GV TP + ++E + +P L+VH
Sbjct: 143 -----TDPEFLAEVVKAAIEAGADRINLPDTVGVATPNEVADIIEALKANVPNKVILSVH 197
Query: 222 CHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETG 281
CH+ G A+AN L A+E G + ++ G+G G + + + + G++TG
Sbjct: 198 CHNDLGMAVANSLAAVEAGADQVEGTVNGIG---ERAGNAALEEVVLALALRKDYGVDTG 254
Query: 282 ADLTSLLRTGHYICGKLKKP 301
DL L + P
Sbjct: 255 IDLEKLTEASRLVERLTGIP 274
Score = 105 bits (263), Expect = 2e-25
Identities = 32/127 (25%), Positives = 58/127 (45%), Gaps = 5/127 (3%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPAD-RLAVHCHDTYGQALAN 59
+V A + G I+L DT+GV TP + ++E + +P L+VHCH+ G A+AN
Sbjct: 149 AEVVKAAIEAGADRINLPDTVGVATPNEVADIIEALKANVPNKVILSVHCHNDLGMAVAN 208
Query: 60 ILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVKEIAVFASAS 119
L A+E G + ++ G+G G + + + + + G+ + AS
Sbjct: 209 SLAAVEAGADQVEGTVNGIG---ERAGNAALEEVVLALALRKDYGVDTGID-LEKLTEAS 264
Query: 120 EMFSKRN 126
+ +
Sbjct: 265 RLVERLT 271
>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 (375), Expect = 4e-43
Identities = 52/171 (30%), Positives = 78/171 (45%), Gaps = 12/171 (7%)
Query: 107 CGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYEG 166
G + VF + S++ K +N EE +R V A + GI V +GC G
Sbjct: 78 AGADRVHVFIATSDLHRKYKLNKDREEVADRAVAAVEAARSAGIDVE------LGCEDAG 131
Query: 167 AVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTY 226
+ V + G I++ DT+GV TP ++ + +P + VHCH+
Sbjct: 132 RTDLAFLIEVVEVAQEAGATRINIADTVGVLTPNEAADLISALKDRVPPVIIEVHCHNDL 191
Query: 227 GQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMG 277
G A+AN L A+E G D ++ GLG +GN A E+LV LE +G
Sbjct: 192 GMAVANSLAAVEAGADRVDGTVNGLG------ERAGNAALEELVAALEVLG 236
Score = 100 bits (252), Expect = 4e-25
Identities = 34/100 (34%), Positives = 50/100 (50%), Gaps = 6/100 (6%)
Query: 3 VASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILT 62
V + G I++ DT+GV TP ++ + +P + VHCH+ G A+AN L
Sbjct: 141 VVEVAQEAGATRINIADTVGVLTPNEAADLISALKDRVPPVIIEVHCHNDLGMAVANSLA 200
Query: 63 AMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEG 102
A+E G D ++ GLG +GN A E+LV LE
Sbjct: 201 AVEAGADRVDGTVNGLG------ERAGNAALEELVAALEV 234
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 78.3 bits (194), Expect = 3e-16
Identities = 55/188 (29%), Positives = 88/188 (46%), Gaps = 18/188 (9%)
Query: 103 KSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGC 162
S+ CGV + +F + S++ K + T EE LER E V A +G+ V
Sbjct: 83 ASIDCGVDAVHIFIATSDIHIKHKLKKTREEVLERMVEAVEYAKDHGLYVS------FSA 136
Query: 163 PYEGA--VPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAV 220
E A + A A + G + DT+G+ P TM ++++++ + + V
Sbjct: 137 --EDASRTDLDFLIEFAKAAEEAGADRVRFCDTVGILDPFTMYELVKELVEAVDIP-IEV 193
Query: 221 HCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLE-GMGIE 279
HCH+ +G A AN L +E G +++ GLG R +GN A E++V L+ GI+
Sbjct: 194 HCHNDFGMATANALAGIEAGAKQVHTTVNGLG----ER--AGNAALEEVVMALKYLYGID 247
Query: 280 TGADLTSL 287
G D L
Sbjct: 248 LGIDTERL 255
Score = 54.8 bits (133), Expect = 2e-08
Identities = 34/126 (26%), Positives = 60/126 (47%), Gaps = 13/126 (10%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANIL 61
+ A A + G + DT+G+ P TM ++++++ + + VHCH+ +G A AN L
Sbjct: 149 EFAKAAEEAGADRVRFCDTVGILDPFTMYELVKELVEAVDIP-IEVHCHNDFGMATANAL 207
Query: 62 TAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVK---EIAVFASA 118
+E G +++ GLG R +GN A E++V L+ G+ +
Sbjct: 208 AGIEAGAKQVHTTVNGLG----ER--AGNAALEEVVMALK---YLYGIDLGIDTERLYEL 258
Query: 119 SEMFSK 124
S + SK
Sbjct: 259 SRLVSK 264
>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 = 69.1 bits (169), Expect = 4e-13
Identities = 50/197 (25%), Positives = 86/197 (43%), Gaps = 30/197 (15%)
Query: 103 KSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGC 162
K++ CGV I F + S + K + + +E LE+ E V A +G+ V
Sbjct: 79 KAIDCGVDSIHTFIATSPIHLKYKLKKSRDEVLEKAVEAVEYAKEHGLIV---------- 128
Query: 163 PYEGAVPPHNVTR--------VATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIP 214
+ TR V + G I++ DT+GV TP M +++ + +
Sbjct: 129 ----EFSAEDATRTDIDFLIKVFKRAEEAGADRINIADTVGVLTPQKMEELIKKLKENVK 184
Query: 215 ADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLE 274
++VHCH+ +G A AN + ++ G ++ G+G R GN A E++V L+
Sbjct: 185 LP-ISVHCHNDFGLATANSIAGVKAGAEQVHVTVNGIG----ERA--GNAALEEVVMALK 237
Query: 275 GM-GIETGADLTSLLRT 290
+ G++T L T
Sbjct: 238 YLYGVKTKIKTEKLYET 254
Score = 54.8 bits (132), Expect = 2e-08
Identities = 29/101 (28%), Positives = 52/101 (51%), Gaps = 7/101 (6%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
+KV + G I++ DT+GV TP M +++ + + ++VHCH+ +G A AN
Sbjct: 144 IKVFKRAEEAGADRINIADTVGVLTPQKMEELIKKLKENVKLP-ISVHCHNDFGLATANS 202
Query: 61 LTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLE 101
+ ++ G ++ G+G R GN A E++V L+
Sbjct: 203 IAGVKAGAEQVHVTVNGIG----ERA--GNAALEEVVMALK 237
>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 = 62.1 bits (152), Expect = 4e-11
Identities = 42/140 (30%), Positives = 63/140 (45%), Gaps = 21/140 (15%)
Query: 165 EGAV-----PPHNV---TRVATALYKMGCYEISLGDTIGVGTPGTMRL---MLEDVLTVI 213
EGA+ P H + ++A L MG I + D G+ TP L+ + +
Sbjct: 135 EGAICYTGSPVHTLEYYVKLAKELEDMGADSICIKDMAGLLTPYAAYELVKALKKEVGLP 194
Query: 214 PADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYML 273
+ +H HDT G A+A L A E G+ + D++I+ L G + +TE +V L
Sbjct: 195 ----IHLHTHDTSGLAVATYLAAAEAGVDIVDTAISPLSGG------TSQPSTESMVAAL 244
Query: 274 EGMGIETGADLTSLLRTGHY 293
G G +TG DL L Y
Sbjct: 245 RGTGRDTGLDLEKLEEISEY 264
Score = 52.0 bits (126), Expect = 9e-08
Identities = 31/105 (29%), Positives = 49/105 (46%), Gaps = 13/105 (12%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRL---MLEDVLTVIPADRLAVHCHDTYGQAL 57
+K+A L MG I + D G+ TP L+ + + + +H HDT G A+
Sbjct: 152 VKLAKELEDMGADSICIKDMAGLLTPYAAYELVKALKKEVGLP----IHLHTHDTSGLAV 207
Query: 58 ANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEG 102
A L A E G+ + D++I+ L G + +TE +V L G
Sbjct: 208 ATYLAAAEAGVDIVDTAISPLSGG------TSQPSTESMVAALRG 246
>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 = 62.1 bits (152), Expect = 5e-11
Identities = 57/195 (29%), Positives = 89/195 (45%), Gaps = 22/195 (11%)
Query: 109 VKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYEGAV 168
V I F + S++ K + T EE LER E V A ++G+ V S E A
Sbjct: 87 VDRIHTFIATSDIHLKYKLKKTREEVLERAVEAVEYAKSHGLDVE--FSA------EDAT 138
Query: 169 --PPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADR--LAVHCHD 224
+ V A + G I++ DT+G TP +++ + +P + ++VHCH+
Sbjct: 139 RTDLDFLIEVVEAAIEAGATTINIPDTVGYLTPEEFGELIKKLKENVPNIKVPISVHCHN 198
Query: 225 TYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLV----YMLEGMGIET 280
G A+AN L A+E G + +I G+G R +GN A E++V + G+ET
Sbjct: 199 DLGLAVANSLAAVEAGARQVECTINGIG----ER--AGNAALEEVVMALKTRYDYYGVET 252
Query: 281 GADLTSLLRTGHYIC 295
G D L T +
Sbjct: 253 GIDTEELYETSRLVS 267
Score = 55.5 bits (135), Expect = 7e-09
Identities = 31/98 (31%), Positives = 53/98 (54%), Gaps = 8/98 (8%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADR--LAVHCHDTYGQALAN 59
+V A + G I++ DT+G TP +++ + +P + ++VHCH+ G A+AN
Sbjct: 147 EVVEAAIEAGATTINIPDTVGYLTPEEFGELIKKLKENVPNIKVPISVHCHNDLGLAVAN 206
Query: 60 ILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLV 97
L A+E G + +I G+G R +GN A E++V
Sbjct: 207 SLAAVEAGARQVECTINGIG----ER--AGNAALEEVV 238
>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 = 62.9 bits (153), Expect = 6e-11
Identities = 50/194 (25%), Positives = 86/194 (44%), Gaps = 21/194 (10%)
Query: 110 KEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCV-VGCPYEGAV 168
I F + S + + + T +E LER +V A + + V C G
Sbjct: 91 FRIHTFIATSPIHLEHKLKMTRDEVLERAVGMVKYA-------KNFTDDVEFSCEDAGRT 143
Query: 169 PPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPA-DR--LAVHCHDT 225
+ R+ A G I++ DT+G P +++ + +P D+ L+VHCH+
Sbjct: 144 EIPFLARIVEAAINAGATTINIPDTVGYALPAEYGNLIKGLRENVPNIDKAILSVHCHND 203
Query: 226 YGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYML----EGMGIETG 281
G A+AN L A++ G + +I G+G +GN A E++V L + +G+ETG
Sbjct: 204 LGLAVANSLAAVQNGARQVECTINGIG------ERAGNAALEEVVMALKVRKDFLGVETG 257
Query: 282 ADLTSLLRTGHYIC 295
+ + RT +
Sbjct: 258 INTKEIYRTSRLVS 271
Score = 45.5 bits (108), Expect = 2e-05
Identities = 30/102 (29%), Positives = 52/102 (50%), Gaps = 9/102 (8%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPA-DR--LAVHCHDTYGQALA 58
++ A G I++ DT+G P +++ + +P D+ L+VHCH+ G A+A
Sbjct: 150 RIVEAAINAGATTINIPDTVGYALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVA 209
Query: 59 NILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYML 100
N L A++ G + +I G+G +GN A E++V L
Sbjct: 210 NSLAAVQNGARQVECTINGIG------ERAGNAALEEVVMAL 245
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 61.6 bits (150), Expect = 1e-10
Identities = 43/138 (31%), Positives = 60/138 (43%), Gaps = 16/138 (11%)
Query: 169 PPHNV---TRVATALYKMGCYEISLGDTIGVGTP-GTMRL--MLEDVLTVIPADRLAVHC 222
P H + +A L +MG I + D G+ TP L ++ L V + +H
Sbjct: 151 PVHTLEYYVELAKELLEMGVDSICIKDMAGLLTPYEAYELVKAIKKELPV----PVELHT 206
Query: 223 HDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGA 282
H T G A L A+E G+ D++I+ P + G S ATE +V L G G +TG
Sbjct: 207 HATSGMAEMTYLKAVEAGVDGIDTAIS-----PLSGGTS-QPATETMVAALRGTGYDTGL 260
Query: 283 DLTSLLRTGHYICGKLKK 300
DL L Y KK
Sbjct: 261 DLELLEEIAEYFREVRKK 278
Score = 54.3 bits (131), Expect = 3e-08
Identities = 33/114 (28%), Positives = 51/114 (44%), Gaps = 13/114 (11%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTP-GTMRL--MLEDVLTVIPADRLAVHCHDTYGQAL 57
+++A L +MG I + D G+ TP L ++ L V + +H H T G A
Sbjct: 159 VELAKELLEMGVDSICIKDMAGLLTPYEAYELVKAIKKELPV----PVELHTHATSGMAE 214
Query: 58 ANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVKE 111
L A+E G+ D++I+ P + G S ATE +V L G G+
Sbjct: 215 MTYLKAVEAGVDGIDTAIS-----PLSGGTS-QPATETMVAALRGTGYDTGLDL 262
>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 = 59.1 bits (144), Expect = 4e-10
Identities = 47/187 (25%), Positives = 78/187 (41%), Gaps = 18/187 (9%)
Query: 104 SMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCP 163
+++CGV + + S++ + L++ +V A G+ V VG
Sbjct: 78 ALRCGVTAVHISIPVSDIHLAHKLGKDRAWVLDQLRRLVGRAKDRGLFV------SVGA- 130
Query: 164 YEGA--VPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVH 221
E A P + A + G + DT+G+ P T ++ + L H
Sbjct: 131 -EDASRADPDFLIEFAEVAQEAGADRLRFADTVGILDPFTTYELIRRLRAATDLP-LEFH 188
Query: 222 CHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGM-GIET 280
H+ G A AN L A+ G + ++ GLG R +GN A E++V L+ + G +T
Sbjct: 189 AHNDLGLATANTLAAVRAGATHVSVTVNGLG----ER--AGNAALEEVVMALKHLYGRDT 242
Query: 281 GADLTSL 287
G D T L
Sbjct: 243 GIDTTRL 249
Score = 42.1 bits (100), Expect = 2e-04
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANIL 61
+ A + G + DT+G+ P T ++ + L H H+ G A AN L
Sbjct: 143 EFAEVAQEAGADRLRFADTVGILDPFTTYELIRRLRAATDLP-LEFHAHNDLGLATANTL 201
Query: 62 TAMEFGISVFDSSIAGLG 79
A+ G + ++ GLG
Sbjct: 202 AAVRAGATHVSVTVNGLG 219
>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 = 59.0 bits (144), Expect = 4e-10
Identities = 37/83 (44%), Positives = 46/83 (55%), Gaps = 9/83 (10%)
Query: 206 LEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVA 265
L + L P + H H+ G A+AN L A+E G + D S+AGLG GA GN
Sbjct: 179 LREALDPTP---VGFHGHNNLGLAVANSLAAVEAGATRIDGSLAGLG-----AGA-GNTP 229
Query: 266 TEDLVYMLEGMGIETGADLTSLL 288
E LV +LE MGIETG DL L+
Sbjct: 230 LEVLVAVLERMGIETGIDLYKLM 252
Score = 44.8 bits (107), Expect = 2e-05
Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 33 LEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVA 92
L + L P + H H+ G A+AN L A+E G + D S+AGLG GA GN
Sbjct: 179 LREALDPTP---VGFHGHNNLGLAVANSLAAVEAGATRIDGSLAGLG-----AGA-GNTP 229
Query: 93 TEDLVYMLEGKSMQCGV 109
E LV +LE ++ G+
Sbjct: 230 LEVLVAVLERMGIETGI 246
>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 = 58.1 bits (141), Expect = 1e-09
Identities = 50/206 (24%), Positives = 88/206 (42%), Gaps = 30/206 (14%)
Query: 106 QCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYE 165
+ G+KE + S S+ + + T EE++E++ E+V AL +GI+ R ++ +
Sbjct: 85 EMGLKETGILMSVSDYHIFKKLKMTREEAMEKYLEIVEEALDHGIKPRCHLEDITRADIY 144
Query: 166 GAVPPHNVTRVATALYKMGCYE-----ISLGDTIGVGT-----------PGTMRLMLEDV 209
G V P L K+ I L DT+G G P + + +D
Sbjct: 145 GFVLP-----FVNKLMKLSKESGIPVKIRLCDTLGYGVPYPGASLPRSVPKIIYGLRKD- 198
Query: 210 LTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDL 269
+P++ L H H+ + +A+AN + A +G S + ++ G+G R +GN E +
Sbjct: 199 -CGVPSENLEWHGHNDFYKAVANAVAAWLYGASWVNCTLLGIG----ER--TGNCPLEAM 251
Query: 270 VYMLEG-MGIETGADLTSLLRTGHYI 294
V G G +L + Y
Sbjct: 252 VIEYAQLKGNFDGMNLEVITEIAEYF 277
Score = 38.1 bits (89), Expect = 0.004
Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 19/98 (19%)
Query: 15 ISLGDTIGVGT-----------PGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTA 63
I L DT+G G P + + +D +P++ L H H+ + +A+AN + A
Sbjct: 167 IRLCDTLGYGVPYPGASLPRSVPKIIYGLRKD--CGVPSENLEWHGHNDFYKAVANAVAA 224
Query: 64 MEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLE 101
+G S + ++ G+G R +GN E +V
Sbjct: 225 WLYGASWVNCTLLGIG----ER--TGNCPLEAMVIEYA 256
>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 = 57.3 bits (139), Expect = 3e-09
Identities = 45/185 (24%), Positives = 81/185 (43%), Gaps = 14/185 (7%)
Query: 104 SMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCP 163
+ +CGV + + S++ + + LER + +VS A G+ V VG
Sbjct: 81 AARCGVDAVHISIPVSDLQIEAKLRKDRAWVLERLARLVSFARDRGLFV------SVGGE 134
Query: 164 YEGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCH 223
P + +A + G DT+G+ P + ++ + + L +H H
Sbjct: 135 DASRADPDFLVELAEVAAEAGADRFRFADTVGILDPFSTYELVRALRQAVDLP-LEMHAH 193
Query: 224 DTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGM-GIETGA 282
+ G A AN L A+ G + ++++ GLG R +GN A E++ L+ + G +TG
Sbjct: 194 NDLGMATANTLAAVRAGATHVNTTVNGLG----ER--AGNAALEEVAMALKRLLGRDTGI 247
Query: 283 DLTSL 287
D + L
Sbjct: 248 DTSRL 252
Score = 40.3 bits (95), Expect = 9e-04
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 19 DTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGL 78
DT+G+ P + ++ + + L +H H+ G A AN L A+ G + ++++ GL
Sbjct: 163 DTVGILDPFSTYELVRALRQAVDLP-LEMHAHNDLGMATANTLAAVRAGATHVNTTVNGL 221
Query: 79 GGCPYARGASGNVATEDLVYMLEG 102
G R +GN A E++ L+
Sbjct: 222 G----ER--AGNAALEEVAMALKR 239
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 56.9 bits (138), Expect = 5e-09
Identities = 40/125 (32%), Positives = 59/125 (47%), Gaps = 16/125 (12%)
Query: 169 PPHNV-TRVATA--LYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPAD---RLAVHC 222
P H + T V A L MG + + D G+ P ++++ I L +HC
Sbjct: 150 PVHTLQTWVDLAKQLEDMGVDSLCIKDMAGLLKP----YAAYELVSRIKKRVDVPLHLHC 205
Query: 223 HDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGA 282
H T G + A +L A+E GI D++I+ + Y G+ ATE LV LEG +TG
Sbjct: 206 HATTGLSTATLLKAIEAGIDGVDTAISSM-SMTY-----GHSATETLVATLEGTERDTGL 259
Query: 283 DLTSL 287
D+ L
Sbjct: 260 DILKL 264
Score = 49.2 bits (118), Expect = 2e-06
Identities = 32/103 (31%), Positives = 49/103 (47%), Gaps = 13/103 (12%)
Query: 3 VASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPAD---RLAVHCHDTYGQALAN 59
+A L MG + + D G+ P ++++ I L +HCH T G + A
Sbjct: 160 LAKQLEDMGVDSLCIKDMAGLLKP----YAAYELVSRIKKRVDVPLHLHCHATTGLSTAT 215
Query: 60 ILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEG 102
+L A+E GI D++I+ + Y G+ ATE LV LEG
Sbjct: 216 LLKAIEAGIDGVDTAISSM-SMTY-----GHSATETLVATLEG 252
>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 = 56.3 bits (136), Expect = 5e-09
Identities = 35/147 (23%), Positives = 66/147 (44%), Gaps = 6/147 (4%)
Query: 106 QCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYE 165
+ GV I +F S++ + LE E + A + G+ VR S E
Sbjct: 80 ELGVDGIDIFFGTSKLLRIAEHRSDAKSILESARETIEYAKSAGLEVR--FSAEDTFRSE 137
Query: 166 GAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDT 225
A ++ + + G + + DT+G P + ++ V+ V+P + +H H+
Sbjct: 138 LA----DLLSIYETVGVFGVDRVGIADTVGKAAPRQVYELIRTVVRVVPGVDIELHAHND 193
Query: 226 YGQALANILTAMEFGISVFDSSIAGLG 252
G A+AN A+E G ++ D+++ G+G
Sbjct: 194 TGCAVANAYNAIEGGATIVDTTVLGIG 220
Score = 45.2 bits (107), Expect = 2e-05
Identities = 20/79 (25%), Positives = 42/79 (53%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
+ + + G + + DT+G P + ++ V+ V+P + +H H+ G A+AN
Sbjct: 142 LSIYETVGVFGVDRVGIADTVGKAAPRQVYELIRTVVRVVPGVDIELHAHNDTGCAVANA 201
Query: 61 LTAMEFGISVFDSSIAGLG 79
A+E G ++ D+++ G+G
Sbjct: 202 YNAIEGGATIVDTTVLGIG 220
>gnl|CDD|237593 PRK14041, PRK14041, oxaloacetate decarboxylase; Provisional.
Length = 467
Score = 55.6 bits (134), Expect = 1e-08
Identities = 58/226 (25%), Positives = 91/226 (40%), Gaps = 41/226 (18%)
Query: 94 EDLVYMLEGKSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVR 153
+D+V + K + G+ I +F + +++ RN+ +IE + + +G V+
Sbjct: 94 DDVVELFVKKVAEYGLDIIRIFDALNDI---RNLEKSIEVAKK-----------HGAHVQ 139
Query: 154 GYISCVVGCPYEGAVPPHNVTR---VATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVL 210
G IS V P H + A L MG I + D G+ TP + E V
Sbjct: 140 GAISYTVS-------PVHTLEYYLEFARELVDMGVDSICIKDMAGLLTP---KRAYELVK 189
Query: 211 TV-----IPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVA 265
+ +P + VH H T G A L A+E G +FD++I+ P++ G S
Sbjct: 190 ALKKKFGVPVE---VHSHCTTGLASLAYLAAVEAGADMFDTAIS-----PFSMGTS-QPP 240
Query: 266 TEDLVYMLEGMGIETGADLTSLLRTGHYICGKLKKPSNSKVAKALP 311
E + Y G ET D +L Y +K S V P
Sbjct: 241 FESMYYAFRENGKETDFDRKALKFLVEYFTKVREKYSEYDVGMKSP 286
Score = 35.1 bits (81), Expect = 0.045
Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 17/115 (14%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTV-----IPADRLAVHCHDTYGQ 55
++ A L MG I + D G+ TP + E V + +P + VH H T G
Sbjct: 156 LEFARELVDMGVDSICIKDMAGLLTP---KRAYELVKALKKKFGVPVE---VHSHCTTGL 209
Query: 56 ALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVK 110
A L A+E G +FD++I+ P++ G S E + Y +
Sbjct: 210 ASLAYLAAVEAGADMFDTAIS-----PFSMGTS-QPPFESMYYAFRENGKETDFD 258
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 55.1 bits (133), Expect = 2e-08
Identities = 41/125 (32%), Positives = 63/125 (50%), Gaps = 16/125 (12%)
Query: 169 PPHNV---TRVATALYKMGCYEISLGDTIGVGTPGTMRLM---LEDVLTVIPADRLAVHC 222
P H + ++A + +MG I + D G+ TP + +++ +TV P L VH
Sbjct: 149 PVHTIDYFVKLAKEMQEMGADSICIKDMAGILTPYVAYELVKRIKEAVTV-P---LEVHT 204
Query: 223 HDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGA 282
H T G A L A+E G + D++I+ P+A G S ATE +V L+ +G +TG
Sbjct: 205 HATSGIAEMTYLKAIEAGADIIDTAIS-----PFAGGTS-QPATESMVAALQDLGYDTGL 258
Query: 283 DLTSL 287
DL L
Sbjct: 259 DLEEL 263
Score = 42.8 bits (101), Expect = 2e-04
Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 18/120 (15%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLM---LEDVLTVIPADRLAVHCHDTYGQALA 58
K+A + +MG I + D G+ TP + +++ +TV P L VH H T G A
Sbjct: 158 KLAKEMQEMGADSICIKDMAGILTPYVAYELVKRIKEAVTV-P---LEVHTHATSGIAEM 213
Query: 59 NILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCG-----VKEIA 113
L A+E G + D++I+ P+A G S ATE +V L+ G + EIA
Sbjct: 214 TYLKAIEAGADIIDTAIS-----PFAGGTS-QPATESMVAALQDLGYDTGLDLEELSEIA 267
>gnl|CDD|183445 PRK12330, PRK12330, oxaloacetate decarboxylase; Provisional.
Length = 499
Score = 55.2 bits (133), Expect = 2e-08
Identities = 40/129 (31%), Positives = 58/129 (44%), Gaps = 18/129 (13%)
Query: 169 PPHNVT---RVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVI-----PADRLAV 220
P H V A L MG I + D + P D++ I R+ +
Sbjct: 150 PIHTVEGFVEQAKRLLDMGADSICIKDMAALLKPQPAY----DIVKGIKEACGEDTRINL 205
Query: 221 HCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIET 280
HCH T G L +++ A+E G+ V D++I+ + P G+ TE LV MLEG G T
Sbjct: 206 HCHSTTGVTLVSLMKAIEAGVDVVDTAISSMSLGP------GHNPTESLVEMLEGTGYTT 259
Query: 281 GADLTSLLR 289
D+ LL+
Sbjct: 260 KLDMDRLLK 268
Score = 44.4 bits (105), Expect = 5e-05
Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 15/107 (14%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVI-----PADRLAVHCHDTYGQ 55
++ A L MG I + D + P D++ I R+ +HCH T G
Sbjct: 158 VEQAKRLLDMGADSICIKDMAALLKPQPAY----DIVKGIKEACGEDTRINLHCHSTTGV 213
Query: 56 ALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEG 102
L +++ A+E G+ V D++I+ + P G+ TE LV MLEG
Sbjct: 214 TLVSLMKAIEAGVDVVDTAISSMSLGP------GHNPTESLVEMLEG 254
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 54.9 bits (133), Expect = 2e-08
Identities = 58/222 (26%), Positives = 92/222 (41%), Gaps = 46/222 (20%)
Query: 81 CPYARGASGNVATEDLVYMLEGKSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSE 140
C +AR D+ LE C V + + S++ + + T EE LE E
Sbjct: 69 CSFARAVKV-----DIDAALE-----CDVDSVHLVVPTSDLHIEYKLKKTREEVLETAVE 118
Query: 141 VVSTALTNGIRVRGYISCVVGCPYEGAVPPHNVTRVA----TALYKMGCYEISLG----- 191
V A +G+ V + G E A +R LYK G I G
Sbjct: 119 AVEYAKDHGLIVE-----LSG---EDA------SRADLDFLKELYKAG---IEAGADRIC 161
Query: 192 --DTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIA 249
DT+G+ TP + + + ++ +++HCH+ +G A+AN L A+ G +I
Sbjct: 162 FCDTVGILTPEKTYELFKRLSELVKGP-VSIHCHNDFGLAVANTLAALAAGADQVHVTIN 220
Query: 250 GLGGCPYARGASGNVATEDLVYMLE-GMGIETGADLTSLLRT 290
G+G R +GN + E++V L+ +ETG L L
Sbjct: 221 GIG----ER--AGNASLEEVVMALKHLYDVETGIKLEELYEL 256
Score = 44.9 bits (107), Expect = 4e-05
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 19 DTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGL 78
DT+G+ TP + + + ++ +++HCH+ +G A+AN L A+ G +I G+
Sbjct: 164 DTVGILTPEKTYELFKRLSELVKGP-VSIHCHNDFGLAVANTLAALAAGADQVHVTINGI 222
Query: 79 GGCPYARGASGNVATEDLVYMLE 101
G R +GN + E++V L+
Sbjct: 223 G----ER--AGNASLEEVVMALK 239
>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 = 54.4 bits (131), Expect = 3e-08
Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 7/118 (5%)
Query: 176 VATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILT 235
+A L +MG I + D G+ TP L L + +H H T G A +L
Sbjct: 154 LAEELLEMGVDSICIKDMAGILTP-KAAYELVSALKKRFGLPVHLHSHATTGMAEMALLK 212
Query: 236 AMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTSLLRTGHY 293
A+E G D++I+ + G + + TE +V L G G +TG D+ LL Y
Sbjct: 213 AIEAGADGIDTAISSMS------GGTSHPPTETMVAALRGTGYDTGLDIELLLEIAAY 264
Score = 44.8 bits (106), Expect = 4e-05
Identities = 29/110 (26%), Positives = 46/110 (41%), Gaps = 7/110 (6%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
+ +A L +MG I + D G+ TP L L + +H H T G A +
Sbjct: 152 LDLAEELLEMGVDSICIKDMAGILTP-KAAYELVSALKKRFGLPVHLHSHATTGMAEMAL 210
Query: 61 LTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVK 110
L A+E G D++I+ + G + + TE +V L G G+
Sbjct: 211 LKAIEAGADGIDTAISSMS------GGTSHPPTETMVAALRGTGYDTGLD 254
>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 = 52.6 bits (127), Expect = 6e-08
Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 7/92 (7%)
Query: 13 YEISLGDTIGVGTPGTMRLMLEDVLTVIPAD-RLAVHCHDTYGQALANILTAMEFGISVF 71
+ D+ G P ++ ++ + + + D +L H H+ ALAN L A+E G+ +
Sbjct: 153 DVFYIVDSFGSMYPEDIKRIISLLRSNLDKDIKLGFHAHNNLQLALANTLEAIELGVEII 212
Query: 72 DSSIAGLGGCPYARGASGNVATEDLVYMLEGK 103
D+++ G+G RGA GN+ TE L+ L K
Sbjct: 213 DATVYGMG-----RGA-GNLPTELLLDYLNNK 238
Score = 52.2 bits (126), Expect = 9e-08
Identities = 27/90 (30%), Positives = 47/90 (52%), Gaps = 7/90 (7%)
Query: 186 YEISLGDTIGVGTPGTMRLMLEDVLTVIPAD-RLAVHCHDTYGQALANILTAMEFGISVF 244
+ D+ G P ++ ++ + + + D +L H H+ ALAN L A+E G+ +
Sbjct: 153 DVFYIVDSFGSMYPEDIKRIISLLRSNLDKDIKLGFHAHNNLQLALANTLEAIELGVEII 212
Query: 245 DSSIAGLGGCPYARGASGNVATEDLVYMLE 274
D+++ G+G RGA GN+ TE L+ L
Sbjct: 213 DATVYGMG-----RGA-GNLPTELLLDYLN 236
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 53.2 bits (129), Expect = 9e-08
Identities = 54/188 (28%), Positives = 85/188 (45%), Gaps = 23/188 (12%)
Query: 112 IAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYEGAV--P 169
I F + S + + + + EE LE E V A + V S E A
Sbjct: 96 IHTFIATSPIHMEYKLKMSREEVLEMAVEAVKYARSYTDDVE--FSA------EDATRTD 147
Query: 170 PHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIP-ADR--LAVHCHDTY 226
+ RV A G I++ DT+G TP +++ + +P D+ ++VHCH+
Sbjct: 148 LDFLCRVVEAAIDAGATTINIPDTVGYTTPEEFGELIKTLRERVPNIDKAIISVHCHNDL 207
Query: 227 GQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYML----EGMGIETGA 282
G A+AN L A+E G + +I G+G R +GN A E++V L + G+ETG
Sbjct: 208 GLAVANSLAAVEAGARQVECTINGIG----ER--AGNAALEEVVMALKTRKDIYGVETGI 261
Query: 283 DLTSLLRT 290
+ + RT
Sbjct: 262 NTEEIYRT 269
Score = 44.3 bits (106), Expect = 5e-05
Identities = 32/99 (32%), Positives = 53/99 (53%), Gaps = 9/99 (9%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIP-ADR--LAVHCHDTYGQALA 58
+V A G I++ DT+G TP +++ + +P D+ ++VHCH+ G A+A
Sbjct: 153 RVVEAAIDAGATTINIPDTVGYTTPEEFGELIKTLRERVPNIDKAIISVHCHNDLGLAVA 212
Query: 59 NILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLV 97
N L A+E G + +I G+G R +GN A E++V
Sbjct: 213 NSLAAVEAGARQVECTINGIG----ER--AGNAALEEVV 245
>gnl|CDD|236449 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
Length = 592
Score = 52.5 bits (127), Expect = 2e-07
Identities = 41/131 (31%), Positives = 60/131 (45%), Gaps = 16/131 (12%)
Query: 169 PPHNV---TRVATALYKMGCYEISLGDTIGVGTP-GTMRL--MLEDVLTVIPADRLAVHC 222
P H + +A L +MGC I + D G+ TP L L++ + +P +H
Sbjct: 149 PVHTIEKYVELAKELEEMGCDSICIKDMAGLLTPYAAYELVKALKEEVD-LPVQ---LHS 204
Query: 223 HDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGA 282
H T G A L A+E G+ + D++I+ P A G S TE +V L+G +TG
Sbjct: 205 HCTSGLAPMTYLKAVEAGVDIIDTAIS-----PLAFGTS-QPPTESMVAALKGTPYDTGL 258
Query: 283 DLTSLLRTGHY 293
DL L Y
Sbjct: 259 DLELLFEIAEY 269
Score = 47.1 bits (113), Expect = 7e-06
Identities = 33/105 (31%), Positives = 52/105 (49%), Gaps = 13/105 (12%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTP-GTMRL--MLEDVLTVIPADRLAVHCHDTYGQAL 57
+++A L +MGC I + D G+ TP L L++ + +P +H H T G A
Sbjct: 157 VELAKELEEMGCDSICIKDMAGLLTPYAAYELVKALKEEVD-LPVQ---LHSHCTSGLAP 212
Query: 58 ANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEG 102
L A+E G+ + D++I+ P A G S TE +V L+G
Sbjct: 213 MTYLKAVEAGVDIIDTAIS-----PLAFGTS-QPPTESMVAALKG 251
>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 = 51.6 bits (124), Expect = 2e-07
Identities = 37/128 (28%), Positives = 58/128 (45%), Gaps = 7/128 (5%)
Query: 168 VPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVI-PADRLAVHCHDTY 226
PP + A + G + + D+ G P +R + + V+ P ++ H H
Sbjct: 140 TPPEKLAEQAKLMESYGADCVYIVDSAGAMLPDDVRDRVRALKAVLKPETQVGFHAHHNL 199
Query: 227 GQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTS 286
A+AN + A+E G + D+S+ GLG GA GN E V +L+ +G TG DL
Sbjct: 200 SLAVANSIAAIEAGATRIDASLRGLGA-----GA-GNAPLEVFVAVLDRLGWNTGCDLFK 253
Query: 287 LLRTGHYI 294
L+ I
Sbjct: 254 LMDAAEDI 261
Score = 36.2 bits (84), Expect = 0.017
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 33 LEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVA 92
L+ VL P ++ H H A+AN + A+E G + D+S+ GLG GA GN
Sbjct: 181 LKAVLK--PETQVGFHAHHNLSLAVANSIAAIEAGATRIDASLRGLGA-----GA-GNAP 232
Query: 93 TEDLVYMLE 101
E V +L+
Sbjct: 233 LEVFVAVLD 241
>gnl|CDD|178767 PLN03228, PLN03228, methylthioalkylmalate synthase; Provisional.
Length = 503
Score = 51.5 bits (123), Expect = 2e-07
Identities = 44/182 (24%), Positives = 74/182 (40%), Gaps = 24/182 (13%)
Query: 112 IAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYEGAVPPH 171
I F S S++ K + T EE +E + A + G+ GC G
Sbjct: 185 ILAFTSTSDIHMKYKLKKTKEEVIEMAVSSIRYA-----KSLGFHDIQFGCEDGGRSDKE 239
Query: 172 NVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADR---LAVHCHDTYGQ 228
+ ++ K G + + DT+G+ P ++ V P +VHCH+ G
Sbjct: 240 FLCKILGEAIKAGATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGL 299
Query: 229 ALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLV--------YMLEGM--GI 278
A AN + + G + +I G+G SGN + E++V Y++ G+ GI
Sbjct: 300 ATANTIAGICAGARQVEVTINGIG------ERSGNASLEEVVMALKCRGAYLMNGVYTGI 353
Query: 279 ET 280
+T
Sbjct: 354 DT 355
Score = 41.1 bits (96), Expect = 6e-04
Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 9/106 (8%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADR---LAVHCHDTYGQALA 58
K+ K G + + DT+G+ P ++ V P +VHCH+ G A A
Sbjct: 243 KILGEAIKAGATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGLATA 302
Query: 59 NILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKS 104
N + + G + +I G+G SGN + E++V L+ +
Sbjct: 303 NTIAGICAGARQVEVTINGIG------ERSGNASLEEVVMALKCRG 342
>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 = 50.0 bits (120), Expect = 4e-07
Identities = 38/148 (25%), Positives = 69/148 (46%), Gaps = 11/148 (7%)
Query: 107 CGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVRGYISCVVGCPYEG 166
GV + + S + + +I E +E EV+ + GI VR S E
Sbjct: 83 TGVDGVDLVFGTSPFLREASHGKSITEIIESAVEVIEFVKSKGIEVR--FSS------ED 134
Query: 167 AV--PPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHD 224
+ ++ RV A+ K+G + + DT+G+ TP + ++ + V+ D + H H+
Sbjct: 135 SFRSDLVDLLRVYRAVDKLGVNRVGIADTVGIATPRQVYELVRTLRGVVSCD-IEFHGHN 193
Query: 225 TYGQALANILTAMEFGISVFDSSIAGLG 252
G A+AN A+E G + D+++ G+G
Sbjct: 194 DTGCAIANAYAALEAGATHIDTTVLGIG 221
Score = 43.9 bits (104), Expect = 4e-05
Identities = 23/79 (29%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
++V A+ K+G + + DT+G+ TP + ++ + V+ D + H H+ G A+AN
Sbjct: 144 LRVYRAVDKLGVNRVGIADTVGIATPRQVYELVRTLRGVVSCD-IEFHGHNDTGCAIANA 202
Query: 61 LTAMEFGISVFDSSIAGLG 79
A+E G + D+++ G+G
Sbjct: 203 YAALEAGATHIDTTVLGIG 221
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 47.9 bits (115), Expect = 3e-06
Identities = 31/68 (45%), Positives = 39/68 (57%), Gaps = 6/68 (8%)
Query: 221 HCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIET 280
H H+ G +AN L A+E G + D S+AGLG GA GN E LV +L+ MG ET
Sbjct: 195 HGHNNLGLGVANSLAAVEAGATRIDGSLAGLG-----AGA-GNTPLEVLVAVLDRMGWET 248
Query: 281 GADLTSLL 288
G DL L+
Sbjct: 249 GVDLYKLM 256
Score = 34.0 bits (79), Expect = 0.093
Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 48 HCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLE 101
H H+ G +AN L A+E G + D S+AGLG GA GN E LV +L+
Sbjct: 195 HGHNNLGLGVANSLAAVEAGATRIDGSLAGLG-----AGA-GNTPLEVLVAVLD 242
>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 = 46.2 bits (110), Expect = 9e-06
Identities = 38/153 (24%), Positives = 60/153 (39%), Gaps = 19/153 (12%)
Query: 108 GVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRVR--------GYISCV 159
G K + + S + T EE EV+ A+ NGI V G
Sbjct: 87 GAKVLNLLTKGSLKHCTEQLRKTPEEHFADIREVIEYAIKNGIEVNIYLEDWSNGMRD-- 144
Query: 160 VGCPYEGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLA 219
P V ++ L + I L DT+G+ +P + D++ P
Sbjct: 145 ---------SPDYVFQLVDFLSDLPIKRIMLPDTLGILSPFETYTYISDMVKRYPNLHFD 195
Query: 220 VHCHDTYGQALANILTAMEFGISVFDSSIAGLG 252
H H+ Y A+AN+L A++ GI +++ GLG
Sbjct: 196 FHAHNDYDLAVANVLAAVKAGIKGLHTTVNGLG 228
Score = 43.9 bits (104), Expect = 5e-05
Identities = 21/65 (32%), Positives = 35/65 (53%)
Query: 15 ISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSS 74
I L DT+G+ +P + D++ P H H+ Y A+AN+L A++ GI ++
Sbjct: 164 IMLPDTLGILSPFETYTYISDMVKRYPNLHFDFHAHNDYDLAVANVLAAVKAGIKGLHTT 223
Query: 75 IAGLG 79
+ GLG
Sbjct: 224 VNGLG 228
>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 = 43.2 bits (103), Expect = 8e-05
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGT-PGTMRLMLEDVLTVIPADRLAVHCHDTYGQALAN 59
+ A + G + L DT G GT P + ++++V +P L +H H+ G A+AN
Sbjct: 154 LATLKAAAEAGADWLVLCDTNG-GTLPHEIAEIVKEVRERLPGVPLGIHAHNDSGLAVAN 212
Query: 60 ILTAMEFGISVFDSSIAGLG 79
L A+E G + +I G G
Sbjct: 213 SLAAVEAGATQVQGTINGYG 232
Score = 40.5 bits (96), Expect = 6e-04
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 188 ISLGDTIGVGT-PGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDS 246
+ L DT G GT P + ++++V +P L +H H+ G A+AN L A+E G +
Sbjct: 168 LVLCDTNG-GTLPHEIAEIVKEVRERLPGVPLGIHAHNDSGLAVANSLAAVEAGATQVQG 226
Query: 247 SIAGLG 252
+I G G
Sbjct: 227 TINGYG 232
>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 = 43.7 bits (103), Expect = 1e-04
Identities = 62/271 (22%), Positives = 113/271 (41%), Gaps = 56/271 (20%)
Query: 52 TYGQALANILTAMEFGISVFDSSIAGLGGCPYAR------------------GASGNVAT 93
T AL N+ + +G + FD ++ L P+ R GA+G T
Sbjct: 561 TTSHALPNLFSLECWGGATFDVAMRFLHEDPWERLEDLRKGVPNILFQMLLRGANGVGYT 620
Query: 94 ---EDLVYMLEGKSMQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGI 150
+++V ++ Q G+ VF S + + N+ ++ ++ +VV A+
Sbjct: 621 NYPDNVVKYFVKQAAQGGIDIFRVFDSLNWV---ENMRVGMD-AVAEAGKVVEAAI---- 672
Query: 151 RVRGYISCVVGCPYEGAVPPHNV---TRVATALYKMGCYEISLGDTIGVGTPGTMRLMLE 207
C G + A P +++ T +A L K G + + + D G+ P +L+++
Sbjct: 673 -------CYTGDILDPARPKYDLKYYTNLAVELEKAGAHILGIKDMAGLLKPAAAKLLIK 725
Query: 208 DV--LTVIPADRLAVHCHDTYGQALANILTAMEFGISVFD---SSIAGLGGCPYARGASG 262
+ T +P + H HDT G A+A++L A+E G+ V D S++GL P
Sbjct: 726 ALREKTDLP---IHFHTHDTSGIAVASMLAAVEAGVDVVDVAVDSMSGLTSQPSLGA--- 779
Query: 263 NVATEDLVYMLEGMGIETGADLTSLLRTGHY 293
+V LEG + G ++ + Y
Sbjct: 780 ------IVAALEGSERDPGLNVAWIRELSAY 804
Score = 37.1 bits (86), Expect = 0.013
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 3 VASALYKMGCYEISLGDTIGVGTPGTMRLMLEDV--LTVIPADRLAVHCHDTYGQALANI 60
+A L K G + + + D G+ P +L+++ + T +P + H HDT G A+A++
Sbjct: 694 LAVELEKAGAHILGIKDMAGLLKPAAAKLLIKALREKTDLP---IHFHTHDTSGIAVASM 750
Query: 61 LTAMEFGISVFDSSIAGLGG 80
L A+E G+ V D ++ + G
Sbjct: 751 LAAVEAGVDVVDVAVDSMSG 770
>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 = 40.3 bits (94), Expect = 0.001
Identities = 36/156 (23%), Positives = 64/156 (41%), Gaps = 19/156 (12%)
Query: 105 MQCGVKEIAVFASASEMFSKRNINCTIEESLERFSEVVSTALTNGIRV--------RGYI 156
++ + +F + ++ + T+EE+L + V+ G V GY
Sbjct: 91 IKAETPVVTIFGKSWDLHVLEALQTTLEENLAMIYDTVAYLKRQGDEVIYDAEHFFDGY- 149
Query: 157 SCVVGCPYEGAVPPHNVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPAD 216
A P + + +ATA + G + L DT G P + + V +
Sbjct: 150 ---------KANPEYALATLATAQ-QAGADWLVLCDTNGGTLPHEISEITTKVKRSLKQP 199
Query: 217 RLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLG 252
+L +H H+ G A+AN L A+E G ++ +I G G
Sbjct: 200 QLGIHAHNDSGTAVANSLLAVEAGATMVQGTINGYG 235
Score = 38.7 bits (90), Expect = 0.003
Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
+ + + G + L DT G P + + V + +L +H H+ G A+AN
Sbjct: 157 LATLATAQQAGADWLVLCDTNGGTLPHEISEITTKVKRSLKQPQLGIHAHNDSGTAVANS 216
Query: 61 LTAMEFGISVFDSSIAGLG 79
L A+E G ++ +I G G
Sbjct: 217 LLAVEAGATMVQGTINGYG 235
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 39.7 bits (92), Expect = 0.001
Identities = 32/117 (27%), Positives = 56/117 (47%), Gaps = 11/117 (9%)
Query: 180 LYKMGCYEISLGDTIGVGTPGTMRLMLEDV--LTVIPADRLAVHCHDTYGQALANILTAM 237
L +MG I + D G+ TP + ++ + +T +P L VH H T G + L A+
Sbjct: 172 LVEMGADSICIKDMAGILTPKAAKELVSGIKAMTNLP---LIVHTHATSGISQMTYLAAV 228
Query: 238 EFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTSLLRTGHYI 294
E G D++++ P++ G S ATE + L+ G + D T L + +++
Sbjct: 229 EAGADRIDTALS-----PFSEGTS-QPATESMYLALKEAGYDITLDETLLEQAANHL 279
Score = 37.0 bits (85), Expect = 0.011
Identities = 31/127 (24%), Positives = 57/127 (44%), Gaps = 11/127 (8%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDV--LTVIPADRLAVHCHDTYGQALA 58
+ + L +MG I + D G+ TP + ++ + +T +P L VH H T G +
Sbjct: 166 LSLVKELVEMGADSICIKDMAGILTPKAAKELVSGIKAMTNLP---LIVHTHATSGISQM 222
Query: 59 NILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGKSMQCGVKEIAVFASA 118
L A+E G D++++ P++ G S ATE + L+ + E + +A
Sbjct: 223 TYLAAVEAGADRIDTALS-----PFSEGTS-QPATESMYLALKEAGYDITLDETLLEQAA 276
Query: 119 SEMFSKR 125
+ + R
Sbjct: 277 NHLRQAR 283
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 38.2 bits (90), Expect = 0.005
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 12/77 (15%)
Query: 220 VHCHDTYGQALANILTAMEFGISVFD---SSIAGLGGCPYARGASGNVATEDLVYMLEGM 276
+H HDT G LA L A E G+ + D +S++GL P S N +V LEG
Sbjct: 739 LHTHDTSGNGLATYLAAAEAGVDIVDVAVASMSGLTSQP-----SLNS----IVAALEGT 789
Query: 277 GIETGADLTSLLRTGHY 293
+TG DL ++ + Y
Sbjct: 790 ERDTGLDLDAIRKLSPY 806
Score = 29.7 bits (68), Expect = 2.5
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 12/66 (18%)
Query: 47 VHCHDTYGQALANILTAMEFGISVFD---SSIAGLGGCPYARGASGNVATEDLVYMLEGK 103
+H HDT G LA L A E G+ + D +S++GL P S N +V LEG
Sbjct: 739 LHTHDTSGNGLATYLAAAEAGVDIVDVAVASMSGLTSQP-----SLNS----IVAALEGT 789
Query: 104 SMQCGV 109
G+
Sbjct: 790 ERDTGL 795
>gnl|CDD|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 37.4 bits (86), Expect = 0.009
Identities = 41/133 (30%), Positives = 57/133 (42%), Gaps = 11/133 (8%)
Query: 172 NVTRVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALA 231
N + L +MGC I++ D G+ TP + +E + A L VH H LA
Sbjct: 155 NFLELGKKLAEMGCDSIAIKDMAGLLTP---TVTVELYAGLKQATGLPVHLHSHSTSGLA 211
Query: 232 NI--LTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTSLLR 289
+I A+ G + D++I+ G GAS + TE LV L +T DL LL
Sbjct: 212 SICHYEAVLAGCNHIDTAISSFSG-----GAS-HPPTEALVAALTDTPYDTELDLNILLE 265
Query: 290 TGHYICGKLKKPS 302
Y KK S
Sbjct: 266 IDDYFKAVRKKYS 278
Score = 30.1 bits (67), Expect = 1.6
Identities = 31/102 (30%), Positives = 48/102 (47%), Gaps = 11/102 (10%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANI 60
+++ L +MGC I++ D G+ TP + +E + A L VH H LA+I
Sbjct: 157 LELGKKLAEMGCDSIAIKDMAGLLTP---TVTVELYAGLKQATGLPVHLHSHSTSGLASI 213
Query: 61 --LTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYML 100
A+ G + D++I+ G GAS + TE LV L
Sbjct: 214 CHYEAVLAGCNHIDTAISSFSG-----GAS-HPPTEALVAAL 249
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 36.2 bits (84), Expect = 0.023
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 220 VHCHDTYGQALANILTAMEFGISVFD---SSIAGLGGCPYARGASGNVATEDLVYMLEGM 276
+H HDT G +A L A+E G+ + D +S++GL P +V L G
Sbjct: 742 LHTHDTSGNGVATYLAAVEAGVDIVDVAMASMSGLTSQPSLNS---------IVAALAGT 792
Query: 277 GIETGADLTSLLRTGHY 293
+TG D+ ++ Y
Sbjct: 793 ERDTGLDIEAVRELSFY 809
Score = 33.9 bits (78), Expect = 0.12
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 2 KVASALYKMGCYEISLGDTIGVGTPGTMRLMLEDV--LTVIPADRLAVHCHDTYGQALAN 59
K+A L K G + +++ D G+ P ++ + +P + +H HDT G +A
Sbjct: 698 KLAKELEKAGAHILAIKDMAGLLKPAAAYRLISALRETVDLP---IHLHTHDTSGNGVAT 754
Query: 60 ILTAMEFGISVFDSSIAGLGG 80
L A+E G+ + D ++A + G
Sbjct: 755 YLAAVEAGVDIVDVAMASMSG 775
>gnl|CDD|184849 PRK14847, PRK14847, hypothetical protein; Provisional.
Length = 333
Score = 32.7 bits (74), Expect = 0.24
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 218 LAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGA-SGNVATEDLVYMLEGM 276
L+VH H+ G A+A A+ G + GC + G +GNV L LE
Sbjct: 243 LSVHPHNDRGTAVAAAELAVLAGAERIE-------GCLFGNGERTGNVDLVALALNLERQ 295
Query: 277 GIETGADLTSL 287
GI +G D +
Sbjct: 296 GIASGLDFRDM 306
>gnl|CDD|237068 PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate
synthase family transferase; Provisional.
Length = 524
Score = 30.8 bits (71), Expect = 1.0
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 1 MKVASALYKMGCYEISLGDTIGVGT-PGTMRLMLEDVLTVIPADRLAVHCHDTYGQALAN 59
+ A + G + L DT G GT P + ++ +V L +H H+ G A+AN
Sbjct: 161 LATLKAAAEAGADWVVLCDTNG-GTLPHEVAEIVAEVRAAPGV-PLGIHAHNDSGCAVAN 218
Query: 60 ILTAMEFGI 68
L A+E G
Sbjct: 219 SLAAVEAGA 227
Score = 30.4 bits (70), Expect = 1.4
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 190 LGDTIGVGT-PGTMRLMLEDVLTVIPADRLAVHCHDTYGQALANILTAMEFGI 241
L DT G GT P + ++ +V L +H H+ G A+AN L A+E G
Sbjct: 177 LCDTNG-GTLPHEVAEIVAEVRAAPGV-PLGIHAHNDSGCAVANSLAAVEAGA 227
>gnl|CDD|222494 pfam14011, ESX-1_EspG, EspG family. This family of proteins
contains the the EspG1, EspG2 and EspG3 proteins from M.
tuberculosis. These proteins are involved in the ESAT-6
secretion system 1 (ESX-1) of Mycobacterium tuberculosis
which is important for virulence and intercellular
spread. Proteins in this family are typically between
254 and 295 amino acids in length.
Length = 244
Score = 28.1 bits (63), Expect = 5.4
Identities = 24/81 (29%), Positives = 30/81 (37%), Gaps = 17/81 (20%)
Query: 209 VLTVIPADRLAVHCHDTYGQALANILTAMEFGISVFDSSIAGLGGCPYARGASGNVATED 268
VL V D + + D G LA L +A L P RG S + E+
Sbjct: 98 VLAVRDGDLVTLTPVDPDG--LAAAL-------------VAALPPAPPGRGRSVTLPAEE 142
Query: 269 LVYMLEGMGIETGADLTSLLR 289
L LE + A L S LR
Sbjct: 143 LAEALEAGR--SAAALASALR 161
>gnl|CDD|215182 PLN02321, PLN02321, 2-isopropylmalate synthase.
Length = 632
Score = 28.4 bits (63), Expect = 7.0
Identities = 28/128 (21%), Positives = 52/128 (40%), Gaps = 10/128 (7%)
Query: 175 RVATALYKMGCYEISLGDTIGVGTPGTMRLMLEDVLTVIPADRLAV---HCHDTYGQALA 231
R+ + K G +++ DT+G P ++ D+ P + HC + G + A
Sbjct: 244 RILGEVIKAGATTLNIPDTVGYTLPSEFGQLIADIKANTPGIENVIISTHCQNDLGLSTA 303
Query: 232 NILTAMEFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTSLLRTG 291
N L G + +I G+G +GN + E++V ++ G E L + +
Sbjct: 304 NTLAGAHAGARQVEVTINGIG------ERAGNASLEEVVMAIKCRGDEQLGGLYTGINPV 357
Query: 292 H-YICGKL 298
H K+
Sbjct: 358 HITPTSKM 365
>gnl|CDD|132518 TIGR03478, DMSO_red_II_bet, DMSO reductase family type II enzyme,
iron-sulfur subunit. This model represents the
iron-sulfur subunit, typically called the beta subunit,
of various proteins that also contain a molybdopterin
subunit and a heme b subunit. The group includes two
distinct but very closely related periplasmic proteins
of anaerobic respiration, selenate reductase and
chlorate reductase. Other members of this family include
dimethyl sulphide dehydrogenase and ethylbenzene
dehydrogenase [Energy metabolism, Anaerobic, Energy
metabolism, Electron transport].
Length = 321
Score = 27.8 bits (62), Expect = 7.6
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 151 RVRGYISCVVGCPYEGAVPPHNVTRVATALYKMGCY 186
R +GY CV CPY+ + + + +GCY
Sbjct: 163 RCKGYRYCVEACPYK---KVYFNPQSQKSEKCIGCY 195
>gnl|CDD|225879 COG3342, COG3342, Uncharacterized conserved protein [Function
unknown].
Length = 265
Score = 27.8 bits (62), Expect = 8.3
Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 6/55 (10%)
Query: 238 EFGISVFDSSIAGLGGCPYARGASGNVATEDLVYMLEGMGIETGADLTSLLRTGH 292
E G++V IA P+A+ G VAT+ G+ LL G
Sbjct: 14 EVGVAVQSKFIAVGAIVPWAKAGVGAVATQSYA------NPALGSAGLDLLAQGL 62
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.397
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,231,968
Number of extensions: 1570877
Number of successful extensions: 1420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1372
Number of HSP's successfully gapped: 94
Length of query: 327
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 230
Effective length of database: 6,635,264
Effective search space: 1526110720
Effective search space used: 1526110720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)