RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 015894
(398 letters)
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 612 bits (1579), Expect = 0.0
Identities = 268/331 (80%), Positives = 296/331 (89%)
Query: 68 YLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKL 127
+ YSSS + + +KLL +P FVKIVEVGPRDGLQNEKNIVP VKVELI+
Sbjct: 17 SFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQR 76
Query: 128 LVSSGLAVVEATSFVSPKWVPQLADAKDVMAAIQNVEGARFPVLTPNLKGFEAAVAAGAK 187
LVSSGL VVEATSFVSPKWVPQLADAKDVMAA++N+EGARFPVLTPNLKGFEAA+AAGAK
Sbjct: 77 LVSSGLPVVEATSFVSPKWVPQLADAKDVMAAVRNLEGARFPVLTPNLKGFEAAIAAGAK 136
Query: 188 EVAIFASASESFSKSNINCTIEDSLIRYRDVALAARELSIPVRGYLSCVVGCPVEGMVPP 247
EVA+FASASESFSKSNINC+IE+SL+RYR+VALAA++ SIPVRGY+SCVVGCP+EG VPP
Sbjct: 137 EVAVFASASESFSKSNINCSIEESLVRYREVALAAKKHSIPVRGYVSCVVGCPIEGPVPP 196
Query: 248 SKVAYVSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQAL 307
SKVAYV+K+LYDMGC EISLGDTIGVGTPGTV+PMLEAV+ VPVDKLAVHFHDTYGQAL
Sbjct: 197 SKVAYVAKELYDMGCYEISLGDTIGVGTPGTVVPMLEAVMAVVPVDKLAVHFHDTYGQAL 256
Query: 308 SNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIA 367
+NIL SLQMGISTVDSSV+GLGGCPYAKGASGNVATEDVVYMLNGLGV TNVD+ KLM A
Sbjct: 257 ANILVSLQMGISTVDSSVAGLGGCPYAKGASGNVATEDVVYMLNGLGVSTNVDLGKLMAA 316
Query: 368 GDFICKHLGRTSGSKTAIALSKTSTANASKL 398
GDFI KHLGR SGSKTA+ALS TA ASK+
Sbjct: 317 GDFISKHLGRPSGSKTAVALSARITAAASKI 347
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 480 bits (1238), Expect = e-172
Identities = 161/274 (58%), Positives = 206/274 (75%)
Query: 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATSFVSPKWVPQLADAKDVMAA 159
IVEVGPRDGLQNEK +P K+ELI L ++GL +E TSFVSPKWVPQ+ADA++V+A
Sbjct: 1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADAEEVLAG 60
Query: 160 IQNVEGARFPVLTPNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVA 219
+ G R+ L PNL+G E A+AAG EVA+F SASE+FS+ NINC+I +SL R+ VA
Sbjct: 61 LPRRPGVRYSALVPNLRGAERALAAGVDEVAVFVSASETFSQKNINCSIAESLERFEPVA 120
Query: 220 LAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGTV 279
A+ + VRGY+S GCP EG VPP +VA V+++L D+GC EISLGDTIGV TP V
Sbjct: 121 ELAKAAGLRVRGYVSTAFGCPYEGEVPPERVAEVAERLLDLGCDEISLGDTIGVATPAQV 180
Query: 280 IPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASG 339
+LEAVL+ P +KLA+HFHDT GQAL+NILA+L+ G+ DSSV GLGGCP+A GA+G
Sbjct: 181 RRLLEAVLERFPDEKLALHFHDTRGQALANILAALEAGVRRFDSSVGGLGGCPFAPGATG 240
Query: 340 NVATEDVVYMLNGLGVRTNVDIRKLMIAGDFICK 373
NVATED+VYML G+G+ T +D+ KL+ A +I +
Sbjct: 241 NVATEDLVYMLEGMGIETGIDLDKLLAAARWISE 274
>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
Length = 287
Score = 479 bits (1235), Expect = e-171
Identities = 181/286 (63%), Positives = 220/286 (76%)
Query: 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATSFVSPKWVPQLADAK 154
P VKIVEVGPRDGLQNEK +P K+ LI L ++GL+ +E SFVSPKWVPQ+ADA
Sbjct: 2 PKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADAA 61
Query: 155 DVMAAIQNVEGARFPVLTPNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIR 214
+VMA IQ G + LTPNLKG EAA+AAGA EVA+FASASE+FS+ NINC+I +SL R
Sbjct: 62 EVMAGIQRRPGVTYAALTPNLKGLEAALAAGADEVAVFASASEAFSQKNINCSIAESLER 121
Query: 215 YRDVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVG 274
+ VA AA++ + VRGY+SCV+GCP EG VPP VA V+++L+ +GC EISLGDTIGVG
Sbjct: 122 FEPVAEAAKQAGVRVRGYVSCVLGCPYEGEVPPEAVADVAERLFALGCYEISLGDTIGVG 181
Query: 275 TPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYA 334
TPG V +LEAVL P ++LA HFHDTYGQAL+NI ASL+ GI+ D+SV GLGGCPYA
Sbjct: 182 TPGQVRAVLEAVLAEFPAERLAGHFHDTYGQALANIYASLEEGITVFDASVGGLGGCPYA 241
Query: 335 KGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFICKHLGRTSG 380
GASGNVATEDV+YML+GLG+ T +D+ KL+ AG FI LGR
Sbjct: 242 PGASGNVATEDVLYMLHGLGIETGIDLDKLVRAGQFIQSKLGRPLP 287
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 298 bits (767), Expect = e-100
Identities = 104/275 (37%), Positives = 152/275 (55%), Gaps = 12/275 (4%)
Query: 101 VEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATSFVSPKWVPQLADAKDVMAAI 160
+ RDGLQ+E K+E+ + L +G+ +E S SPK VPQ+ D +V+ AI
Sbjct: 1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDDWEVLRAI 60
Query: 161 -QNVEGARFPVLTPN-LKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDV 218
+ V + L N KG E A+ AG EV IF SASE+ S+ N+N + E+ L +
Sbjct: 61 RKLVPNVKLQALVRNREKGIERALEAGVDEVRIFDSASETHSRKNLNKSREEDLENAEEA 120
Query: 219 ALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGT 278
AA+E + V G L GC P V V+K L + G EISL DT+G+ TP
Sbjct: 121 IEAAKEAGLEVEGSLEDAFGCKT----DPEYVLEVAKALEEAGADEISLKDTVGLATPEE 176
Query: 279 VIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGAS 338
V +++A+ +A+P L +H H+T G A++N LA+L+ G VD SV+GLG +
Sbjct: 177 VAELVKALREALPDVPLGLHTHNTLGLAVANSLAALEAGADRVDGSVNGLG------ERA 230
Query: 339 GNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFICK 373
GN ATED+V L GLG+ T +D+ KL+ ++ +
Sbjct: 231 GNAATEDLVAALEGLGIDTGIDLEKLLEISRYVEE 265
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 215 bits (550), Expect = 4e-66
Identities = 75/283 (26%), Positives = 118/283 (41%), Gaps = 13/283 (4%)
Query: 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATSFVSPKWVPQLADAKDVM 157
V I + RDG Q K+ + K L G+ +EA V+ + A
Sbjct: 3 VIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRAIAEK 62
Query: 158 AAIQNVEGARFPVLTPNLK-GFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYR 216
A + A L +K EA + AG + IF + S+ + + T E+ L R
Sbjct: 63 AGLF--ICALIAALARAIKRDIEALLEAGVDRIHIFIATSDLHLRYKLKKTREEVLERAV 120
Query: 217 DVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTP 276
D AR+ + VR P +A V K + G I+L DT+GV TP
Sbjct: 121 DAVEYARDHGLEVRFSAEDAT------RTDPEFLAEVVKAAIEAGADRINLPDTVGVATP 174
Query: 277 GTVIPMLEAVLDAVPVD-KLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAK 335
V ++EA+ VP L+VH H+ G A++N LA+++ G V+ +V+G+G
Sbjct: 175 NEVADIIEALKANVPNKVILSVHCHNDLGMAVANSLAAVEAGADQVEGTVNGIG---ERA 231
Query: 336 GASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFICKHLGRT 378
G + + + GV T +D+ KL A + + G
Sbjct: 232 GNAALEEVVLALALRKDYGVDTGIDLEKLTEASRLVERLTGIP 274
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 182 bits (464), Expect = 1e-55
Identities = 74/251 (29%), Positives = 114/251 (45%), Gaps = 18/251 (7%)
Query: 107 DGLQNEKNIVPAVVKVELIKLLVSSGLAVVEAT-SFVSPKWVPQLADAKDVM--AAIQNV 163
DG Q K+ + + L +G+ +E F+SP + +V+ A IQ +
Sbjct: 1 DGEQALGAAFSVEEKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAIAEVLKKAKIQAL 60
Query: 164 EGARFPVLTPNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVALAAR 223
R PV EAA AGA V +F + S+ K +N E+ R AAR
Sbjct: 61 --LR-PVEHDIDAAVEAAKGAGADRVHVFIATSDLHRKYKLNKDREEVADRAVAAVEAAR 117
Query: 224 ELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGTVIPML 283
I V +GC G + + V + + G + I++ DT+GV TP ++
Sbjct: 118 SAGIDVE------LGCEDAGRTDLAFLIEVVEVAQEAGATRINIADTVGVLTPNEAADLI 171
Query: 284 EAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVAT 343
A+ D VP + VH H+ G A++N LA+++ G VD +V+GLG +GN A
Sbjct: 172 SALKDRVPPVIIEVHCHNDLGMAVANSLAAVEAGADRVDGTVNGLG------ERAGNAAL 225
Query: 344 EDVVYMLNGLG 354
E++V L LG
Sbjct: 226 EELVAALEVLG 236
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 275
Score = 64.4 bits (158), Expect = 1e-11
Identities = 38/118 (32%), Positives = 60/118 (50%), Gaps = 15/118 (12%)
Query: 252 YVS--KQLYDMGCSEISLGDTIGVGTPGTV---IPMLEAVLDAVPVDKLAVHFHDTYGQA 306
YV K+L DMG I + D G+ TP + L+ + +P+ +H HDT G A
Sbjct: 151 YVKLAKELEDMGADSICIKDMAGLLTPYAAYELVKALKKEVG-LPIH---LHTHDTSGLA 206
Query: 307 LSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKL 364
++ LA+ + G+ VD+++S L G + +TE +V L G G T +D+ KL
Sbjct: 207 VATYLAAAEAGVDIVDTAISPLSGG------TSQPSTESMVAALRGTGRDTGLDLEKL 258
>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 = 63.7 bits (156), Expect = 2e-11
Identities = 56/224 (25%), Positives = 99/224 (44%), Gaps = 42/224 (18%)
Query: 158 AAIQNVEGARFPVLTPNLKGF------EAAVAAGAKEVAIFASASESFSKSNINCTIEDS 211
AA + ++ A+ VL L G + A G V + +E+
Sbjct: 67 AAAEALKQAKLGVLL--LPGIGTVDDLKMAADLGVDVVRVATHCTEA------------- 111
Query: 212 LIRYRDVAL----AARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISL 267
DV+ AAR+L + V G+L M P ++A +K + G + +
Sbjct: 112 -----DVSEQHIGAARKLGMDVVGFLMM------SHMASPEELAEQAKLMESYGADCVYV 160
Query: 268 GDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSG 327
D+ G P V + A+ +A+ + H H+ G A++N LA+++ G + +D S++G
Sbjct: 161 TDSAGAMLPDDVRERVRALREALDPTPVGFHGHNNLGLAVANSLAAVEAGATRIDGSLAG 220
Query: 328 LGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFI 371
LG +GN E +V +L +G+ T +D+ KLM A + +
Sbjct: 221 LGAG------AGNTPLEVLVAVLERMGIETGIDLYKLMDAAEDL 258
>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 = 63.1 bits (154), Expect = 4e-11
Identities = 63/226 (27%), Positives = 103/226 (45%), Gaps = 33/226 (14%)
Query: 152 DAKDVMAAIQNVEGARFPVL-TP---NLKGFEAAVAAGAKEVAIFASASES-FSKSNINC 206
D + + AA V+ A+ VL P + +AA AGA+ V + +E+ S+ +I
Sbjct: 63 DLEYIEAAADVVKRAKVAVLLLPGIGTVHDLKAAYDAGARTVRVATHCTEADVSEQHIG- 121
Query: 207 TIEDSLIRYRDVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEIS 266
AREL + G+L + M PP K+A +K + G +
Sbjct: 122 --------------MARELGMDTVGFLM------MSHMTPPEKLAEQAKLMESYGADCVY 161
Query: 267 LGDTIGVGTPGTVIPMLEAVLDAV-PVDKLAVHFHDTYGQALSNILASLQMGISTVDSSV 325
+ D+ G P V + A+ + P ++ H H A++N +A+++ G + +D+S+
Sbjct: 162 IVDSAGAMLPDDVRDRVRALKAVLKPETQVGFHAHHNLSLAVANSIAAIEAGATRIDASL 221
Query: 326 SGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFI 371
GLG GA GN E V +L+ LG T D+ KLM A + I
Sbjct: 222 RGLGA-----GA-GNAPLEVFVAVLDRLGWNTGCDLFKLMDAAEDI 261
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 61.7 bits (151), Expect = 2e-10
Identities = 72/296 (24%), Positives = 122/296 (41%), Gaps = 74/296 (25%)
Query: 98 VKIVEVGPRDGLQNEKNIVPAVV-----KVELIKLLVSSGLAVVEATSF--VSPKWVPQL 150
++IV+ RDG Q P VV K+ + ++L G+ +EA F VS
Sbjct: 5 IEIVDTTLRDGEQ-----TPGVVFTNEEKLAIARMLDEIGVDQIEA-GFPAVS------- 51
Query: 151 ADAKDVMAAIQNVEGARFPVLT---PNLKGFEAAVAAGAKEVAIFASASESFSKSNINCT 207
D K+ + AI G +L +A++ G V IF + S+ K + T
Sbjct: 52 EDEKEAIKAIAK-LGLNASILALNRAVKSDIDASIDCGVDAVHIFIATSDIHIKHKLKKT 110
Query: 208 IEDSLIRYRDVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVS------------- 254
E+ L R + A++ G+ YVS
Sbjct: 111 REEVLERMVEAVEYAKD-----------------HGL-------YVSFSAEDASRTDLDF 146
Query: 255 -KQLY----DMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSN 309
+ + G + DT+G+ P T+ +++ +++AV + + VH H+ +G A +N
Sbjct: 147 LIEFAKAAEEAGADRVRFCDTVGILDPFTMYELVKELVEAVDIP-IEVHCHNDFGMATAN 205
Query: 310 ILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGL-GVRTNVDIRKL 364
LA ++ G V ++V+GLG +GN A E+VV L L G+ +D +L
Sbjct: 206 ALAGIEAGAKQVHTTVNGLG------ERAGNAALEEVVMALKYLYGIDLGIDTERL 255
>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 = 59.6 bits (145), Expect = 7e-10
Identities = 65/283 (22%), Positives = 114/283 (40%), Gaps = 36/283 (12%)
Query: 106 RDGLQNEKNIVPAVV-----KVELIKLLVSSGLAVVEATSFVSPKWVPQLADA-KDVMAA 159
RDG Q P V K+ + + L +G+ +E +P + + + V+ A
Sbjct: 10 RDGEQA-----PGVAFTAAEKLAIARALDEAGVDELEVG-------IPAMGEEERAVIRA 57
Query: 160 IQNVEGARFPVLT---PNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYR 216
I G ++ EAA G V I S+ ++ + L R
Sbjct: 58 IVA-LGLPARLMAWCRARDADIEAAARCGVDAVHISIPVSDLQIEAKLRKDRAWVLERLA 116
Query: 217 DVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTP 276
+ AR+ + V VG P + +++ + G DT+G+ P
Sbjct: 117 RLVSFARDRGLFV------SVGGEDASRADPDFLVELAEVAAEAGADRFRFADTVGILDP 170
Query: 277 GTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKG 336
+ ++ A+ AV + L +H H+ G A +N LA+++ G + V+++V+GLG
Sbjct: 171 FSTYELVRALRQAVDLP-LEMHAHNDLGMATANTLAAVRAGATHVNTTVNGLG------E 223
Query: 337 ASGNVATEDVVYMLNGL-GVRTNVDIRKLMIAGDFICKHLGRT 378
+GN A E+V L L G T +D +L + + GR
Sbjct: 224 RAGNAALEEVAMALKRLLGRDTGIDTSRLPALSQLVARASGRP 266
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 57.7 bits (140), Expect = 4e-09
Identities = 34/118 (28%), Positives = 61/118 (51%), Gaps = 7/118 (5%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILA 312
++K+L +MG I + D G+ TP +++A+ +PV + +H H T G A L
Sbjct: 161 LAKELLEMGVDSICIKDMAGLLTPYEAYELVKAIKKELPV-PVELHTHATSGMAEMTYLK 219
Query: 313 SLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDF 370
+++ G+ +D+++S P + G S ATE +V L G G T +D+ L ++
Sbjct: 220 AVEAGVDGIDTAIS-----PLSGGTS-QPATETMVAALRGTGYDTGLDLELLEEIAEY 271
>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 = 57.8 bits (140), Expect = 4e-09
Identities = 65/288 (22%), Positives = 124/288 (43%), Gaps = 29/288 (10%)
Query: 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATSFVSPKWVPQLADAKDVM 157
+ I + RDG Q+ + K+++ L G+ ++EA VS D + V
Sbjct: 2 IIIFDTTLRDGEQSPGASLTVEEKLQIALALERLGVDIIEAGFPVSSP-----GDFEAVQ 56
Query: 158 AAIQNVEGARFPVLTPNLKG-----FEAAVAAGAKEVAIFASASESFSKSNINCTIEDSL 212
+ V+ R L ++ EA A + F + S + + T ++ L
Sbjct: 57 RIARTVKNPRVCGLARCVEKDIDAAAEALKPAEKFRIHTFIATSPIHLEHKLKMTRDEVL 116
Query: 213 IRYRDVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIG 272
R + A+ + V C G +A + + + G + I++ DT+G
Sbjct: 117 ERAVGMVKYAKNFTDDVE------FSCEDAGRTEIPFLARIVEAAINAGATTINIPDTVG 170
Query: 273 VGTPGTVIPMLEAVLDAVP-VDK--LAVHFHDTYGQALSNILASLQMGISTVDSSVSGLG 329
P +++ + + VP +DK L+VH H+ G A++N LA++Q G V+ +++G+G
Sbjct: 171 YALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVANSLAAVQNGARQVECTINGIG 230
Query: 330 GCPYAKGASGNVATEDVVYML----NGLGVRTNVDIRKLMIAGDFICK 373
+GN A E+VV L + LGV T ++ +++ + +
Sbjct: 231 ------ERAGNAALEEVVMALKVRKDFLGVETGINTKEIYRTSRLVSQ 272
>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 = 57.5 bits (139), Expect = 5e-09
Identities = 29/118 (24%), Positives = 57/118 (48%), Gaps = 7/118 (5%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILA 312
++++L +MG I + D G+ TP ++ A+ + + +H H T G A +L
Sbjct: 154 LAEELLEMGVDSICIKDMAGILTPKAAYELVSALKKRFGL-PVHLHSHATTGMAEMALLK 212
Query: 313 SLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDF 370
+++ G +D+++S + G + + TE +V L G G T +DI L+ +
Sbjct: 213 AIEAGADGIDTAISSM------SGGTSHPPTETMVAALRGTGYDTGLDIELLLEIAAY 264
>gnl|CDD|236449 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
Length = 592
Score = 57.5 bits (140), Expect = 5e-09
Identities = 35/118 (29%), Positives = 57/118 (48%), Gaps = 13/118 (11%)
Query: 255 KQLYDMGCSEISLGDTIGVGTP---GTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNIL 311
K+L +MGC I + D G+ TP ++ L+ +D +PV +H H T G A L
Sbjct: 161 KELEEMGCDSICIKDMAGLLTPYAAYELVKALKEEVD-LPVQ---LHSHCTSGLAPMTYL 216
Query: 312 ASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGD 369
+++ G+ +D+++S P A G S TE +V L G T +D+ L +
Sbjct: 217 KAVEAGVDIIDTAIS-----PLAFGTS-QPPTESMVAALKGTPYDTGLDLELLFEIAE 268
>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 = 54.4 bits (132), Expect = 3e-08
Identities = 33/113 (29%), Positives = 61/113 (53%), Gaps = 12/113 (10%)
Query: 259 DMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDK--LAVHFHDTYGQALSNILASLQM 316
+ G + I++ DT+G TP +++ + + VP K ++VH H+ G A++N LA+++
Sbjct: 154 EAGATTINIPDTVGYLTPEEFGELIKKLKENVPNIKVPISVHCHNDLGLAVANSLAAVEA 213
Query: 317 GISTVDSSVSGLGGCPYAKGASGNVATEDVV----YMLNGLGVRTNVDIRKLM 365
G V+ +++G+G +GN A E+VV + GV T +D +L
Sbjct: 214 GARQVECTINGIG------ERAGNAALEEVVMALKTRYDYYGVETGIDTEELY 260
>gnl|CDD|183445 PRK12330, PRK12330, oxaloacetate decarboxylase; Provisional.
Length = 499
Score = 54.8 bits (132), Expect = 3e-08
Identities = 38/144 (26%), Positives = 71/144 (49%), Gaps = 14/144 (9%)
Query: 254 SKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVD-KLAVHFHDTYGQALSNILA 312
+K+L DMG I + D + P +++ + +A D ++ +H H T G L +++
Sbjct: 161 AKRLLDMGADSICIKDMAALLKPQPAYDIVKGIKEACGEDTRINLHCHSTTGVTLVSLMK 220
Query: 313 SLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFIC 372
+++ G+ VD+++S + P G+ TE +V ML G G T +D+ +L+ D
Sbjct: 221 AIEAGVDVVDTAISSMSLGP------GHNPTESLVEMLEGTGYTTKLDMDRLLKIRDHFK 274
Query: 373 KHLGR-------TSGSKTAIALSK 389
K + T+G +T I S+
Sbjct: 275 KVRPKYKEFESKTTGVETEIFKSQ 298
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 53.9 bits (130), Expect = 6e-08
Identities = 36/112 (32%), Positives = 60/112 (53%), Gaps = 7/112 (6%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILA 312
++K++ +MG I + D G+ TP +++ + +AV V L VH H T G A L
Sbjct: 159 LAKEMQEMGADSICIKDMAGILTPYVAYELVKRIKEAVTV-PLEVHTHATSGIAEMTYLK 217
Query: 313 SLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKL 364
+++ G +D+++S P+A G S ATE +V L LG T +D+ +L
Sbjct: 218 AIEAGADIIDTAIS-----PFAGGTS-QPATESMVAALQDLGYDTGLDLEEL 263
>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 = 53.1 bits (128), Expect = 7e-08
Identities = 52/205 (25%), Positives = 89/205 (43%), Gaps = 25/205 (12%)
Query: 165 GARFPVLT----PNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVAL 220
G +FP +T N + + G KE I S S+ + T E+++ +Y ++
Sbjct: 63 GYKFPEVTGWIRANKEDLKLVKEMGLKETGILMSVSDYHIFKKLKMTREEAMEKYLEIVE 122
Query: 221 AARELSIPVRGYLSCVVGCPVEGMVPP--SKVAYVSKQLYDMGCSEISLGDTIGVGTP-- 276
A + I R +L + + G V P +K+ +SK+ + I L DT+G G P
Sbjct: 123 EALDHGIKPRCHLEDITRADIYGFVLPFVNKLMKLSKE-SGIPVK-IRLCDTLGYGVPYP 180
Query: 277 GTVIP--------MLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGL 328
G +P L VP + L H H+ + +A++N +A+ G S V+ ++ G+
Sbjct: 181 GASLPRSVPKIIYGLRKDCG-VPSENLEWHGHNDFYKAVANAVAAWLYGASWVNCTLLGI 239
Query: 329 GGCPYAKGASGNVATEDVVYMLNGL 353
G +GN E +V L
Sbjct: 240 G------ERTGNCPLEAMVIEYAQL 258
>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 = 52.8 bits (127), Expect = 8e-08
Identities = 51/190 (26%), Positives = 84/190 (44%), Gaps = 20/190 (10%)
Query: 181 AVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVALAARELSIPVRGYLSCVVGCP 240
+AGAK + + S + T E+ R+V A + I V YL
Sbjct: 83 IKSAGAKVLNLLTKGSLKHCTEQLRKTPEEHFADIREVIEYAIKNGIEVNIYL------- 135
Query: 241 VE----GMV-PPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKL 295
E GM P V + L D+ I L DT+G+ +P + ++ P
Sbjct: 136 -EDWSNGMRDSPDYVFQLVDFLSDLPIKRIMLPDTLGILSPFETYTYISDMVKRYPNLHF 194
Query: 296 AVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNG-LG 354
H H+ Y A++N+LA+++ GI + ++V+GLG +GN V+ +L L
Sbjct: 195 DFHAHNDYDLAVANVLAAVKAGIKGLHTTVNGLG------ERAGNAPLASVIAVLKDKLK 248
Query: 355 VRTNVDIRKL 364
V+TN+D ++L
Sbjct: 249 VKTNIDEKRL 258
>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 = 52.5 bits (127), Expect = 1e-07
Identities = 51/192 (26%), Positives = 82/192 (42%), Gaps = 22/192 (11%)
Query: 178 FEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVALAARELSIPV---RG-YL 233
EAA+ G V I S S+I+ + L + R L + RG ++
Sbjct: 75 IEAALRCGVTAVHI------SIPVSDIH--LAHKLGKDRAWVLDQLRRLVGRAKDRGLFV 126
Query: 234 SCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVD 293
S VG P + ++ + G + DT+G+ P T ++ + A +
Sbjct: 127 S--VGAEDASRADPDFLIEFAEVAQEAGADRLRFADTVGILDPFTTYELIRRLRAATDLP 184
Query: 294 KLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGL 353
L H H+ G A +N LA+++ G + V +V+GLG +GN A E+VV L L
Sbjct: 185 -LEFHAHNDLGLATANTLAAVRAGATHVSVTVNGLG------ERAGNAALEEVVMALKHL 237
Query: 354 -GVRTNVDIRKL 364
G T +D +L
Sbjct: 238 YGRDTGIDTTRL 249
>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 = 51.6 bits (124), Expect = 2e-07
Identities = 58/243 (23%), Positives = 103/243 (42%), Gaps = 33/243 (13%)
Query: 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATS-FVSPKWVPQLADAKDV 156
KI++ R+G Q K+E+ K L + G+ +E TS SP+ ++
Sbjct: 1 FKIIDSTLREGEQFANAFFDTEDKIEIAKALDAFGVDYIELTSPAASPQ-------SRAD 53
Query: 157 MAAIQNVEGARFPVLTP---NLKGFEAAVAAGAKEVAIFASASE-----SFSKSNINCTI 208
AI + G + +LT ++ AV G V + S S KS I I
Sbjct: 54 CEAIAKL-GLKAKILTHIRCHMDDARIAVETGVDGVDLVFGTSPFLREASHGKS-ITEII 111
Query: 209 EDSLIRYRDVALAARELSIPVRGYLSC--VVGCPVEGMVPPSKVAYVSKQLYDMGCSEIS 266
E + +V + I VR S + ++ V + + +G + +
Sbjct: 112 ESA----VEVIEFVKSKGIEVR--FSSEDSFRSDLVDLLR------VYRAVDKLGVNRVG 159
Query: 267 LGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVS 326
+ DT+G+ TP V ++ + V D + H H+ G A++N A+L+ G + +D++V
Sbjct: 160 IADTVGIATPRQVYELVRTLRGVVSCD-IEFHGHNDTGCAIANAYAALEAGATHIDTTVL 218
Query: 327 GLG 329
G+G
Sbjct: 219 GIG 221
>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 = 51.3 bits (123), Expect = 4e-07
Identities = 66/277 (23%), Positives = 116/277 (41%), Gaps = 36/277 (12%)
Query: 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEATS-------FVSPKWVPQL 150
V I + RDG Q + KVE+ + L G+ V+EA F + K + Q
Sbjct: 1 VYIFDTTLRDGEQTPGVSLTVEQKVEIARKLDELGVDVIEAGFPIASEGEFEAIKKISQE 60
Query: 151 ADAKDVMAAIQNVEGARFPVLTPNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIED 210
++ + + ++ K + A+ G + F + S K + + ++
Sbjct: 61 GLNAEICSLARALK-----------KDIDKAIDCGVDSIHTFIATSPIHLKYKLKKSRDE 109
Query: 211 SLIRYRDVALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDT 270
L + + A+E + V ++ ++ V K+ + G I++ DT
Sbjct: 110 VLEKAVEAVEYAKEHGLIVEFSAEDATRTDIDFLIK------VFKRAEEAGADRINIADT 163
Query: 271 IGVGTPGTVIPMLEAVLDAVPVDKL--AVHFHDTYGQALSNILASLQMGISTVDSSVSGL 328
+GV TP M E + KL +VH H+ +G A +N +A ++ G V +V+G+
Sbjct: 164 VGVLTPQK---MEELIKKLKENVKLPISVHCHNDFGLATANSIAGVKAGAEQVHVTVNGI 220
Query: 329 GGCPYAKGASGNVATEDVVYMLNGL-GVRTNVDIRKL 364
G +GN A E+VV L L GV+T + KL
Sbjct: 221 G------ERAGNAALEEVVMALKYLYGVKTKIKTEKL 251
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 51.0 bits (123), Expect = 5e-07
Identities = 41/127 (32%), Positives = 68/127 (53%), Gaps = 7/127 (5%)
Query: 244 MVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVD-KLAVHFHDT 302
M PP K+A +K + G + + D+ G P V + A+ A+ D ++ H H+
Sbjct: 140 MAPPEKLAEQAKLMESYGAQCVYVVDSAGALLPEDVRDRVRALRAALKPDTQVGFHGHNN 199
Query: 303 YGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIR 362
G ++N LA+++ G + +D S++GLG GA GN E +V +L+ +G T VD+
Sbjct: 200 LGLGVANSLAAVEAGATRIDGSLAGLGA-----GA-GNTPLEVLVAVLDRMGWETGVDLY 253
Query: 363 KLMIAGD 369
KLM A +
Sbjct: 254 KLMDAAE 260
>gnl|CDD|178767 PLN03228, PLN03228, methylthioalkylmalate synthase; Provisional.
Length = 503
Score = 51.5 bits (123), Expect = 5e-07
Identities = 49/210 (23%), Positives = 88/210 (41%), Gaps = 24/210 (11%)
Query: 178 FEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVALAARELSIPVRGYLSCVV 237
+EA A + F S S+ K + T E+ + A+ L G+
Sbjct: 174 WEALKYAKRPRILAFTSTSDIHMKYKLKKTKEEVIEMAVSSIRYAKSL-----GFHDIQF 228
Query: 238 GCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVP-VDK-- 294
GC G + + + G + + + DT+G+ P ++ V P +D
Sbjct: 229 GCEDGGRSDKEFLCKILGEAIKAGATSVGIADTVGINMPHEFGELVTYVKANTPGIDDIV 288
Query: 295 LAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVV------- 347
+VH H+ G A +N +A + G V+ +++G+G SGN + E+VV
Sbjct: 289 FSVHCHNDLGLATANTIAGICAGARQVEVTINGIG------ERSGNASLEEVVMALKCRG 342
Query: 348 -YMLNGLGVRTNVDIRKLMIAGDFICKHLG 376
Y++N GV T +D R++M + ++ G
Sbjct: 343 AYLMN--GVYTGIDTRQIMATSKMVQEYTG 370
>gnl|CDD|237593 PRK14041, PRK14041, oxaloacetate decarboxylase; Provisional.
Length = 467
Score = 50.9 bits (122), Expect = 6e-07
Identities = 34/123 (27%), Positives = 57/123 (46%), Gaps = 11/123 (8%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLD--AVPVDKLAVHFHDTYGQALSNI 310
+++L DMG I + D G+ TP +++A+ VPV+ VH H T G A
Sbjct: 158 FARELVDMGVDSICIKDMAGLLTPKRAYELVKALKKKFGVPVE---VHSHCTTGLASLAY 214
Query: 311 LASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDF 370
LA+++ G D+++S P++ G S E + Y G T+ D + L ++
Sbjct: 215 LAAVEAGADMFDTAIS-----PFSMGTS-QPPFESMYYAFRENGKETDFDRKALKFLVEY 268
Query: 371 ICK 373
K
Sbjct: 269 FTK 271
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 50.7 bits (122), Expect = 8e-07
Identities = 39/122 (31%), Positives = 63/122 (51%), Gaps = 14/122 (11%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGT---VIPMLEAVLDAVPVDKLAVHFHDTYGQALSN 309
++KQL DMG + + D G+ P ++ ++ +D VP L +H H T G + +
Sbjct: 160 LAKQLEDMGVDSLCIKDMAGLLKPYAAYELVSRIKKRVD-VP---LHLHCHATTGLSTAT 215
Query: 310 ILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLM-IAG 368
+L +++ GI VD+++S + Y G+ ATE +V L G T +DI KL IA
Sbjct: 216 LLKAIEAGIDGVDTAISSM-SMTY-----GHSATETLVATLEGTERDTGLDILKLEEIAA 269
Query: 369 DF 370
F
Sbjct: 270 YF 271
>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 = 49.9 bits (120), Expect = 8e-07
Identities = 26/112 (23%), Positives = 56/112 (50%), Gaps = 11/112 (9%)
Query: 265 ISLGDTIGVGTPGTVIPMLEAVLDAVPVD-KLAVHFHDTYGQALSNILASLQMGISTVDS 323
+ D+ G P + ++ + + D KL H H+ AL+N L ++++G+ +D+
Sbjct: 155 FYIVDSFGSMYPEDIKRIISLLRSNLDKDIKLGFHAHNNLQLALANTLEAIELGVEIIDA 214
Query: 324 SVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDFICKHL 375
+V G+G +GA GN+ TE ++ LN ++ ++ + I +++
Sbjct: 215 TVYGMG-----RGA-GNLPTELLLDYLNNK-FGKKYNLEPVL---ELIDEYI 256
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 50.3 bits (121), Expect = 1e-06
Identities = 30/107 (28%), Positives = 55/107 (51%), Gaps = 8/107 (7%)
Query: 259 DMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGI 318
+ G I DT+G+ TP + + + + V +++H H+ +G A++N LA+L G
Sbjct: 154 EAGADRICFCDTVGILTPEKTYELFKRLSELVKG-PVSIHCHNDFGLAVANTLAALAAGA 212
Query: 319 STVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGL-GVRTNVDIRKL 364
V +++G+G +GN + E+VV L L V T + + +L
Sbjct: 213 DQVHVTINGIG------ERAGNASLEEVVMALKHLYDVETGIKLEEL 253
>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 = 44.8 bits (106), Expect = 4e-05
Identities = 47/231 (20%), Positives = 90/231 (38%), Gaps = 24/231 (10%)
Query: 106 RDGLQNEKNIVPAVVKVELIKLLVSSGLAVVEAT-------SFVSPKWVPQLADAKDVMA 158
R+G Q K+E+ K L G+ +E T S + + + L +++
Sbjct: 7 REGEQFPGANFSTEQKIEIAKALDEFGIDYIEVTHPAASKQSRIDIEIIASLGLKANIVT 66
Query: 159 AIQNVEGARFPVLTPNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDV 218
I+ L + AV G + IF S+ + + L R+
Sbjct: 67 HIRCR-----------LDDAKVAVELGVDGIDIFFGTSKLLRIAEHRSDAKSILESARET 115
Query: 219 ALAARELSIPVRGYLSCVVGCPVEGMVPPSKVAYVSKQLYDMGCSEISLGDTIGVGTPGT 278
A+ + VR S E + + + + + G + + DT+G P
Sbjct: 116 IEYAKSAGLEVR--FSAEDTFRSEL----ADLLSIYETVGVFGVDRVGIADTVGKAAPRQ 169
Query: 279 VIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGISTVDSSVSGLG 329
V ++ V+ VP + +H H+ G A++N +++ G + VD++V G+G
Sbjct: 170 VYELIRTVVRVVPGVDIELHAHNDTGCAVANAYNAIEGGATIVDTTVLGIG 220
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 43.6 bits (104), Expect = 1e-04
Identities = 39/123 (31%), Positives = 66/123 (53%), Gaps = 19/123 (15%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTP---GTVIPMLEAVLDAVP-VDK--LAVHFHDTYGQA 306
V + D G + I++ DT+G TP G +I L + VP +DK ++VH H+ G A
Sbjct: 154 VVEAAIDAGATTINIPDTVGYTTPEEFGELIKTL---RERVPNIDKAIISVHCHNDLGLA 210
Query: 307 LSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLN----GLGVRTNVDIR 362
++N LA+++ G V+ +++G+G + A GN A E+VV L GV T ++
Sbjct: 211 VANSLAAVEAGARQVECTINGIG-----ERA-GNAALEEVVMALKTRKDIYGVETGINTE 264
Query: 363 KLM 365
++
Sbjct: 265 EIY 267
>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 = 41.7 bits (99), Expect = 4e-04
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 258 YDMGCSEISLGDTIGVGT-PGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQM 316
+ G + L DT G GT P + +++ V + +P L +H H+ G A++N LA+++
Sbjct: 161 AEAGADWLVLCDTNG-GTLPHEIAEIVKEVRERLPGVPLGIHAHNDSGLAVANSLAAVEA 219
Query: 317 GISTVDSSVSGLG 329
G + V +++G G
Sbjct: 220 GATQVQGTINGYG 232
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 40.5 bits (94), Expect = 0.001
Identities = 30/106 (28%), Positives = 51/106 (48%), Gaps = 7/106 (6%)
Query: 255 KQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASL 314
K+L +MG I + D G+ TP ++ + A+ L VH H T G + LA++
Sbjct: 170 KELVEMGADSICIKDMAGILTPKAAKELVSGI-KAMTNLPLIVHTHATSGISQMTYLAAV 228
Query: 315 QMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVD 360
+ G +D+++S P+++G S ATE + L G +D
Sbjct: 229 EAGADRIDTALS-----PFSEGTS-QPATESMYLALKEAGYDITLD 268
>gnl|CDD|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 39.7 bits (92), Expect = 0.002
Identities = 32/120 (26%), Positives = 56/120 (46%), Gaps = 11/120 (9%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNI-- 310
+ K+L +MGC I++ D G+ TP + + + A L VH H L++I
Sbjct: 159 LGKKLAEMGCDSIAIKDMAGLLTPTVTVELYAGLKQAT---GLPVHLHSHSTSGLASICH 215
Query: 311 LASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDIRKLMIAGDF 370
++ G + +D+++S G GAS + TE +V L T +D+ L+ D+
Sbjct: 216 YEAVLAGCNHIDTAISSFSG-----GAS-HPPTEALVAALTDTPYDTELDLNILLEIDDY 269
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 36.2 bits (84), Expect = 0.037
Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 17/114 (14%)
Query: 253 VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDAV--PVDKLAVHFHDTYGQALSNI 310
++K+L G +++ D G+ P ++ A+ + V P+ +H HDT G ++
Sbjct: 699 LAKELEKAGAHILAIKDMAGLLKPAAAYRLISALRETVDLPIH---LHTHDTSGNGVATY 755
Query: 311 LASLQMGISTVD---SSVSGLGGCPYAKGASGNVATEDVVYMLNGLGVRTNVDI 361
LA+++ G+ VD +S+SGL P +V L G T +DI
Sbjct: 756 LAAVEAGVDIVDVAMASMSGLTSQPSLNS---------IVAALAGTERDTGLDI 800
>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 = 36.0 bits (83), Expect = 0.044
Identities = 25/128 (19%), Positives = 56/128 (43%), Gaps = 18/128 (14%)
Query: 244 MVPPSKVAY-------VSKQLYDMGCSEISLGDTIGVGTPGTVIPMLEAVLDA--VPVDK 294
++ P++ Y ++ +L G + + D G+ P +++A+ + +P+
Sbjct: 678 ILDPARPKYDLKYYTNLAVELEKAGAHILGIKDMAGLLKPAAAKLLIKALREKTDLPIH- 736
Query: 295 LAVHFHDTYGQALSNILASLQMGISTVDSSVSGLGGCPYAKGASGNVATEDVVYMLNGLG 354
H HDT G A++++LA+++ G+ VD +V + G +V L G
Sbjct: 737 --FHTHDTSGIAVASMLAAVEAGVDVVDVAVDSMSGLTSQPSLGA------IVAALEGSE 788
Query: 355 VRTNVDIR 362
+++
Sbjct: 789 RDPGLNVA 796
>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 = 35.3 bits (81), Expect = 0.064
Identities = 18/69 (26%), Positives = 35/69 (50%)
Query: 261 GCSEISLGDTIGVGTPGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQMGIST 320
G + L DT G P + + V ++ +L +H H+ G A++N L +++ G +
Sbjct: 167 GADWLVLCDTNGGTLPHEISEITTKVKRSLKQPQLGIHAHNDSGTAVANSLLAVEAGATM 226
Query: 321 VDSSVSGLG 329
V +++G G
Sbjct: 227 VQGTINGYG 235
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 34.3 bits (80), Expect = 0.11
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 14/75 (18%)
Query: 295 LAVHFH--DTYGQALSNILASLQMGISTVD---SSVSGLGGCPYAKGASGNVATEDVVYM 349
L +H H DT G L+ LA+ + G+ VD +S+SGL P S N +V
Sbjct: 735 LPIHLHTHDTSGNGLATYLAAAEAGVDIVDVAVASMSGLTSQP-----SLNS----IVAA 785
Query: 350 LNGLGVRTNVDIRKL 364
L G T +D+ +
Sbjct: 786 LEGTERDTGLDLDAI 800
>gnl|CDD|236166 PRK08149, PRK08149, ATP synthase SpaL; Validated.
Length = 428
Score = 31.1 bits (71), Expect = 1.0
Identities = 17/28 (60%), Positives = 18/28 (64%), Gaps = 7/28 (25%)
Query: 210 DSLIRY----RDVALAARELSIPVR-GY 232
DS+ RY RDVALAA EL P R GY
Sbjct: 248 DSMTRYARALRDVALAAGEL--PARRGY 273
>gnl|CDD|193565 cd08018, M20_Acy1_amhX_like, M20 Peptidase Aminoacylase 1 amhX_like
subfamily. Peptidase M20 family, Uncharacterized
subfamily of uncharacterized proteins predicted as
putative amidohydrolases, including the amhX gene
product from Bacillus subtilis. These are a class of
zinc binding homodimeric enzymes involved in hydrolysis
of N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic
N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate into
L-amino acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 365
Score = 30.7 bits (70), Expect = 1.3
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 7/47 (14%)
Query: 251 AYVSKQLYDMGCSEISLGDTIGV------GTPGTVIPMLEAVLDAVP 291
Y++K+L ++G + GD GV G PG V+ L A +DA+
Sbjct: 28 EYLAKKLEELGFEVRTFGDCTGVVAEIGSGKPGPVV-ALRADMDALW 73
>gnl|CDD|152354 pfam11919, DUF3437, Domain of unknown function (DUF3437). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 142 to 163 amino acids in length.
Length = 89
Score = 28.7 bits (65), Expect = 1.3
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 132 GL-AVVEATSFVSPKWVPQL 150
GL A+V A + P W+P++
Sbjct: 12 GLGALVLAFPYEVPPWIPKV 31
>gnl|CDD|129562 TIGR00470, sepS, O-phosphoserine--tRNA ligase. This family of
archaeal proteins resembles known phenylalanyl-tRNA
synthetase alpha chains. Recently, it was shown to act
in a proposed pathway of tRNA(Cys) indirect
aminoacylation, resulting in Cys biosynthesis from
O-phosphoserine, in certain archaea. It charges
tRNA(Cys) with O-phosphoserine. The pscS gene product
converts the phosphoserine to Cys [Amino acid
biosynthesis, Serine family, Protein synthesis, tRNA
aminoacylation].
Length = 533
Score = 30.6 bits (69), Expect = 1.8
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 179 EAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVALAARELSIPVRGYLSCVVG 238
E A+ + +EV + S S +IN I++ +RY + + I VRG L
Sbjct: 476 EEALVSNVEEVKVRVPIVRSLS--DINLKIDELALRY----IMGKNKVIDVRGPLFLTAK 529
Query: 239 CPVE 242
++
Sbjct: 530 VEIK 533
>gnl|CDD|237068 PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate
synthase family transferase; Provisional.
Length = 524
Score = 29.7 bits (68), Expect = 2.8
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 258 YDMGCSEISLGDTIGVGT-PGTVIPMLEAVLDAVPVDKLAVHFHDTYGQALSNILASLQM 316
+ G + L DT G GT P V ++ V A V L +H H+ G A++N LA+++
Sbjct: 168 AEAGADWVVLCDTNG-GTLPHEVAEIVAEVRAAPGV-PLGIHAHNDSGCAVANSLAAVEA 225
Query: 317 GISTVDSSVSGLG 329
G V +++G G
Sbjct: 226 GARQVQGTINGYG 238
>gnl|CDD|181274 PRK08184, PRK08184, benzoyl-CoA-dihydrodiol lyase; Provisional.
Length = 550
Score = 29.6 bits (67), Expect = 3.7
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 13/64 (20%)
Query: 178 FEAAVAAGAKEVAIFASAS------ESFSKSNINCTIEDSLIRYRDVAL----AARELSI 227
F+A VA A E A+AS + + + + TI+ +RYR V + AAR +I
Sbjct: 219 FDAKVAERAAE---LAAASDRPADAKGVALTPLERTIDADGLRYRHVDVEIDRAARTATI 275
Query: 228 PVRG 231
V+
Sbjct: 276 TVKA 279
>gnl|CDD|214614 smart00317, SET, SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)
domain. Putative methyl transferase, based on outlier
plant homologues.
Length = 124
Score = 28.1 bits (63), Expect = 3.8
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 352 GLGVRTNVDIRKLMIAGDFICKHLG 376
G GVR DI K G+FI +++G
Sbjct: 12 GWGVRATEDIPK----GEFIGEYVG 32
>gnl|CDD|214707 smart00518, AP2Ec, AP endonuclease family 2. These endonucleases
play a role in DNA repair. Cleave phosphodiester bonds
at apurinic or apyrimidinic sites.
Length = 273
Score = 28.4 bits (64), Expect = 6.1
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 165 GARFPVLTPNLKGFEAAVAAGAKEVAIFASASESFSKSNINCTIEDSLIRYRDVALAARE 224
GA K F AV GA+ +F S+ ++ E++ ++++ A +E
Sbjct: 3 GAHVSAAGGLYKAFIEAVDIGARSFQLFLGNPRSWKGVRLS---EETAEKFKE---ALKE 56
Query: 225 LSIPV 229
+I V
Sbjct: 57 NNIDV 61
>gnl|CDD|171527 PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional.
Length = 612
Score = 28.9 bits (65), Expect = 6.2
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 156 VMAAIQNV--EGARFPVLTPN----LKGFEAAVAAGAKEVAIFA 193
V A +Q V G R +L P + GF AA+ AG V +FA
Sbjct: 81 VGARLQQVAGPGDRVAILAPQGIDYVAGFFAAIKAGTIAVPLFA 124
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
0.315 0.131 0.365
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,227,682
Number of extensions: 1849648
Number of successful extensions: 1774
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1728
Number of HSP's successfully gapped: 58
Length of query: 398
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 299
Effective length of database: 6,546,556
Effective search space: 1957420244
Effective search space used: 1957420244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.9 bits)