RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7649
(100 letters)
>gnl|CDD|239203 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate.
Length = 299
Score = 86.0 bits (214), Expect = 8e-22
Identities = 30/51 (58%), Positives = 35/51 (68%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
+EV LDGGIR GTDV KA+ LGA V +GR L+GLA G G A VL+ L
Sbjct: 228 IEVLLDGGIRRGTDVLKALALGADAVLIGRPFLYGLAAGGEAGVAHVLEIL 278
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 85.6 bits (213), Expect = 1e-21
Identities = 27/51 (52%), Positives = 33/51 (64%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
+ V +DGGIR GTDV KA+ LGA V +GR L+GLA G G A L+ L
Sbjct: 226 IPVLVDGGIRRGTDVLKALALGADAVLLGRPFLYGLAAGGEAGVAHALEIL 276
>gnl|CDD|239238 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain.
FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a
respiratory enzyme located in the intermembrane space of
fungal mitochondria which catalyzes the oxidation of
L-lactate to pyruvate. FCB2 also participates in a short
electron-transport chain involving cytochrome c and
cytochrome oxidase which ultimately directs the reducing
equivalents gained from L-lactate oxidation to oxygen,
yielding one molecule of ATP for every L-lactate
molecule consumed. FCB2 is composed of 2 domains: a
C-terminal flavin-binding domain, which includes the
active site for lacate oxidation, and an N-terminal
b2-cytochrome domain, required for efficient cytochrome
c reduction. FCB2 is a homotetramer and contains two
noncovalently bound cofactors, FMN and heme per subunit.
Length = 344
Score = 74.9 bits (185), Expect = 2e-17
Identities = 27/55 (49%), Positives = 37/55 (67%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSLVHKI 55
+EVY+DGG+R GTDV KA+ LGAK V +GR L+ L+ G G + +Q L +I
Sbjct: 272 IEVYVDGGVRRGTDVLKALCLGAKAVGLGRPFLYALSAYGEEGVEKAIQILKDEI 326
>gnl|CDD|188481 TIGR03966, actino_HemFlav, heme/flavin dehydrogenase, mycofactocin
system. Members of this protein family possess an
N-terminal heme-binding domain and C-terminal
flavodehydrogenase domain, and share homology to yeast
flavocytochrome b2, to E. coli L-lactate dehydrogenase
[cytochrome], to (S)-mandelate dehydrogenase, etc. This
enzyme appears only in the context of the mycofactocin
system. Interestingly, it is absent from the four
species detected so far with mycofactocin but without an
F420 biosynthesis system.
Length = 385
Score = 67.5 bits (165), Expect = 1e-14
Identities = 30/51 (58%), Positives = 36/51 (70%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
+EV LDGGIR G+DV KA+ LGA+ V +GRA LWGLA +G G VL L
Sbjct: 303 VEVLLDGGIRRGSDVVKALALGARAVMIGRAYLWGLAANGEAGVENVLDIL 353
>gnl|CDD|224223 COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and
related proteins) [Coenzyme transport and metabolism].
Length = 360
Score = 65.0 bits (159), Expect = 8e-14
Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 2 EVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
EV DGGIR G DV KA+ LGA V +GR L+GLA G G RVL+ +
Sbjct: 275 EVIADGGIRSGLDVAKALALGADAVGIGRPFLYGLAAGGEAGVERVLEII 324
>gnl|CDD|215294 PLN02535, PLN02535, glycolate oxidase.
Length = 364
Score = 64.1 bits (156), Expect = 2e-13
Identities = 27/49 (55%), Positives = 36/49 (73%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
V LDGG+R GTDVFKA+ LGA+ V VGR ++GLA G +G +V++ L
Sbjct: 281 VLLDGGVRRGTDVFKALALGAQAVLVGRPVIYGLAAKGEDGVRKVIEML 329
>gnl|CDD|239448 cd03332, LMO_FMN, L-Lactate 2-monooxygenase (LMO) FMN-binding
domain. LMO is a FMN-containing enzyme that catalyzes
the conversion of L-lactate and oxygen to acetate,
carbon dioxide, and water. LMO is a member of the family
of alpha-hydroxy acid oxidases. It is thought to be a
homooctamer with two- and four- fold axes in the center
of the octamer.
Length = 383
Score = 61.5 bits (150), Expect = 1e-12
Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSLV 52
V D G+R G D+ KA+ LGAK V +GR +GLA G +G VL++L+
Sbjct: 311 VLFDSGVRTGADIMKALALGAKAVLIGRPYAYGLALGGEDGVEHVLRNLL 360
>gnl|CDD|166620 PLN02979, PLN02979, glycolate oxidase.
Length = 366
Score = 60.1 bits (145), Expect = 4e-12
Identities = 27/49 (55%), Positives = 35/49 (71%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
V+LDGG+R GTDVFKA+ LGA +F+GR ++ LA G G +VLQ L
Sbjct: 281 VFLDGGVRRGTDVFKALALGASGIFIGRPVVFSLAAEGEAGVRKVLQML 329
>gnl|CDD|240087 cd04736, MDH_FMN, Mandelate dehydrogenase (MDH)-like FMN-binding
domain. MDH is part of a widespread family of
homologous FMN-dependent a-hydroxy acid oxidizing
enzymes that oxidizes (S)-mandelate to phenylglyoxalate.
MDH is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate. This family occurs in both
prokaryotes and eukaryotes. Members of this family
include flavocytochrome b2 (FCB2), glycolate oxidase
(GOX), lactate monooxygenase (LMO), mandelate
dehydrogenase (MDH), and long chain hydroxyacid oxidase
(LCHAO).
Length = 361
Score = 59.8 bits (145), Expect = 5e-12
Identities = 26/55 (47%), Positives = 35/55 (63%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSLVHKI 55
V +D GIR G+D+ KA+ LGA V +GRA L+GLA G G + VL+ L +I
Sbjct: 290 KPVLIDSGIRRGSDIVKALALGANAVLLGRATLYGLAARGEAGVSEVLRLLKEEI 344
>gnl|CDD|166134 PLN02493, PLN02493, probable peroxisomal (S)-2-hydroxy-acid
oxidase.
Length = 367
Score = 59.7 bits (144), Expect = 6e-12
Identities = 27/49 (55%), Positives = 35/49 (71%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
V+LDGG+R GTDVFKA+ LGA +F+GR ++ LA G G +VLQ L
Sbjct: 282 VFLDGGVRRGTDVFKALALGASGIFIGRPVVFSLAAEGEAGVRKVLQML 330
>gnl|CDD|240088 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain.
LOX is a member of the family of FMN-containing
alpha-hydroxyacid oxidases and catalyzes the oxidation
of l-lactate using molecular oxygen to generate pyruvate
and H2O2. This family occurs in both prokaryotes and
eukaryotes. Members of this family include
flavocytochrome b2 (FCB2), glycolate oxidase (GOX),
lactate monooxygenase (LMO), mandelate dehydrogenase
(MDH), and long chain hydroxyacid oxidase (LCHAO).
Length = 351
Score = 58.2 bits (141), Expect = 2e-11
Identities = 24/49 (48%), Positives = 30/49 (61%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
+ D G+R G VFKA+ GA V VGR L+GLA G+ G A VL+ L
Sbjct: 279 IIFDSGVRRGEHVFKALASGADAVAVGRPVLYGLALGGAQGVASVLEHL 327
>gnl|CDD|183033 PRK11197, lldD, L-lactate dehydrogenase; Provisional.
Length = 381
Score = 46.9 bits (112), Expect = 2e-07
Identities = 21/48 (43%), Positives = 29/48 (60%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVL 48
+ + D GIR G DV + I LGA V +GRA ++ LA +G G A +L
Sbjct: 301 ITILADSGIRNGLDVVRMIALGADTVLLGRAFVYALAAAGQAGVANLL 348
>gnl|CDD|131755 TIGR02708, L_lactate_ox, L-lactate oxidase. Members of this
protein oxidize L-lactate to pyruvate, reducing
molecular oxygen to hydrogen peroxide. The enzyme is
known in Aerococcus viridans, Streptococcus iniae, and
some strains of Streptococcus pyogenes where it appears
to contribute to virulence [Energy metabolism, Other].
Length = 367
Score = 46.8 bits (111), Expect = 2e-07
Identities = 22/49 (44%), Positives = 30/49 (61%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSL 51
+ D G+R G VFKA+ GA V +GR ++GLA GS GA +V + L
Sbjct: 286 IVFDSGVRRGQHVFKALASGADLVALGRPVIYGLALGGSQGARQVFEYL 334
>gnl|CDD|235465 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase;
Provisional.
Length = 352
Score = 42.1 bits (100), Expect = 7e-06
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSLVH 53
GGIR G D+ KA+ LGA V + L G +++ +
Sbjct: 268 GGIRNGLDIAKALALGADAVGMAGPFLKAALEGGEEAVIELIEQWIE 314
>gnl|CDD|223147 COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport
and metabolism].
Length = 485
Score = 40.7 bits (96), Expect = 3e-05
Identities = 17/28 (60%), Positives = 18/28 (64%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGRAAL 33
DGG+R G DV KA LGA V G AAL
Sbjct: 380 DGGLRTGADVAKAAALGADAVGFGTAAL 407
>gnl|CDD|239202 cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain.
GltS is a complex iron-sulfur flavoprotein that
catalyzes the reductive synthesis of L-glutamate from
2-oxoglutarate and L-glutamine via intramolecular
channelling of ammonia, a reaction in the plant, yeast
and bacterial pathway for ammonia assimilation. It is a
multifunctional enzyme that functions through three
distinct active centers, carrying out L-glutamine
hydrolysis, conversion of 2-oxoglutarate into
L-glutamate, and electron uptake from an electron donor.
Length = 392
Score = 39.1 bits (92), Expect = 9e-05
Identities = 16/28 (57%), Positives = 19/28 (67%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGRAAL 33
GG+R G DV KA+ LGA V +G AAL
Sbjct: 291 SGGLRTGADVAKALALGADAVGIGTAAL 318
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 38.1 bits (89), Expect = 2e-04
Identities = 17/28 (60%), Positives = 20/28 (71%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGRAAL 33
DGG+R G DV KA LGA V++G AAL
Sbjct: 279 DGGLRTGADVAKAAALGADAVYIGTAAL 306
>gnl|CDD|233750 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
type 2. Isopentenyl-diphosphate delta-isomerase (IPP
isomerase) interconverts isopentenyl diphosphate and
dimethylallyl diphosphate. This model represents the
type 2 enzyme. FMN, NADPH, and Mg2+ are required by this
form, which lacks homology to the type 1 enzyme
(TIGR02150). IPP is precursor to many compounds,
including enzyme cofactors, sterols, and isoprenoids
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 333
Score = 36.5 bits (85), Expect = 8e-04
Identities = 16/47 (34%), Positives = 22/47 (46%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAARVLQSLVH 53
GG+R G DV KAI LGA V + R L G ++ ++
Sbjct: 261 GGLRTGLDVAKAIALGADAVGMARPFLKAALDEGEEAVIEEIELIIE 307
>gnl|CDD|215936 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This
family is involved in biosynthesis of guanosine
nucleotide. Members of this family contain a TIM barrel
structure. In the inosine monophosphate dehydrogenases 2
CBS domains pfam00571 are inserted in the TIM barrel.
This family is a member of the common phosphate binding
site TIM barrel family.
Length = 467
Score = 36.1 bits (84), Expect = 0.001
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGR 30
DGGIRY D+ KA+ GA V +G
Sbjct: 332 DGGIRYSGDIAKALAAGASAVMLGS 356
>gnl|CDD|238223 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine
monophosphate dehydrogenase. IMPDH catalyzes the
NAD-dependent oxidation of inosine 5'-monophosphate
(IMP) to xanthosine 5' monophosphate (XMP). It is a
rate-limiting step in the de novo synthesis of the
guanine nucleotides. There is often a CBS domain
inserted in the middle of this domain, which is proposed
to play a regulatory role. IMPDH is a key enzyme in the
regulation of cell proliferation and differentiation. It
has been identified as an attractive target for
developing chemotherapeutic agents.
Length = 325
Score = 34.0 bits (79), Expect = 0.005
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGR 30
DGGIR D+ KA+ GA V +G
Sbjct: 203 DGGIRTSGDIVKALAAGADAVMLGS 227
>gnl|CDD|235507 PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase;
Reviewed.
Length = 486
Score = 34.0 bits (79), Expect = 0.006
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG 29
DGGIRY D+ KA+ GA V +G
Sbjct: 337 DGGIRYSGDIAKALAAGASAVMLG 360
>gnl|CDD|233350 TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase.
This model describes IMP dehydrogenase, an enzyme of GMP
biosynthesis. This form contains two CBS domains. This
model describes a rather tightly conserved cluster of
IMP dehydrogenase sequences, many of which are
characterized. The model excludes two related families
of proteins proposed also to be IMP dehydrogenases, but
without characterized members. These are related
families are the subject of separate models [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 450
Score = 33.9 bits (78), Expect = 0.007
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG 29
DGGIRY D+ KA+ GA V +G
Sbjct: 333 DGGIRYSGDIVKALAAGADAVMLG 356
>gnl|CDD|239205 cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl
diphosphate isomerase type 2 (IDI-2) FMN-binding domain.
Two types of IDIs have been characterized at present.
The long known IDI-1 is only dependent on divalent
metals for activity, whereas IDI-2 requires a metal, FMN
and NADPH. IDI-2 catalyzes the interconversion of
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP) in the mevalonate pathway.
Length = 326
Score = 32.9 bits (76), Expect = 0.013
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRAAL 33
GGIR G D+ KA+ LGA V + L
Sbjct: 262 GGIRNGLDIAKALALGADLVGMAGPFL 288
>gnl|CDD|180725 PRK06843, PRK06843, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 404
Score = 33.1 bits (75), Expect = 0.013
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG 29
DGGIR+ DV KAI GA V +G
Sbjct: 262 DGGIRFSGDVVKAIAAGADSVMIG 285
>gnl|CDD|240355 PTZ00314, PTZ00314, inosine-5'-monophosphate dehydrogenase;
Provisional.
Length = 495
Score = 31.1 bits (71), Expect = 0.058
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGR 30
DGGI+ D+ KA+ LGA V +G
Sbjct: 350 DGGIKNSGDICKALALGADCVMLGS 374
>gnl|CDD|236322 PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 368
Score = 29.4 bits (67), Expect = 0.24
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 11/44 (25%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG----RAA-------LWGLAH 38
DGGI D+ KAI GA V +G RAA WG+A
Sbjct: 262 DGGIGTSGDIAKAIACGADAVMLGSPLARAAEAPGRGWHWGMAA 305
>gnl|CDD|235479 PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase;
Provisional.
Length = 326
Score = 29.2 bits (66), Expect = 0.26
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG 29
DGGIR D+ K+I GA V +G
Sbjct: 207 DGGIRTHGDIAKSIRFGATMVMIG 230
>gnl|CDD|232779 TIGR00007, TIGR00007, phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase. This protein family
consists of HisA,
phosphoribosylformimino-5-aminoimidazole carboxamide
ribotide isomerase, the enzyme catalyzing the fourth
step in histidine biosynthesis. It is closely related to
the enzyme HisF for the sixth step. Examples of this
enzyme in Actinobacteria have been found to be
bifunctional, also possessing phosphoribosylanthranilate
isomerase activity ; the trusted cutoff here has now
been raised to 275.0 to exclude the bifunctional group,
now represented by model TIGR01919. HisA from
Lactococcus lactis was reported to be inactive
(MEDLINE:93322317) [Amino acid biosynthesis, Histidine
family].
Length = 230
Score = 28.7 bits (65), Expect = 0.35
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAALWG 35
+ V GG+ D+ LG V VG+A G
Sbjct: 190 VPVIASGGVSSIDDLIALKKLGVYGVIVGKALYEG 224
Score = 26.0 bits (58), Expect = 3.0
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRAAL 33
GGIR DV K + LG V +G AA+
Sbjct: 79 GGIRSLEDVEKLLDLGVDRVIIGTAAV 105
>gnl|CDD|130373 TIGR01306, GMP_reduct_2, guanosine monophosphate reductase,
bacterial. A deep split separates two families of GMP
reductase. The other (TIGR01305) is found in eukaryotic
and some proteobacterial lineages, including E. coli,
while this family is found in a variety of bacterial
lineages [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 321
Score = 28.8 bits (64), Expect = 0.40
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG 29
DGGIR D+ K+I GA V +G
Sbjct: 204 DGGIRTHGDIAKSIRFGASMVMIG 227
>gnl|CDD|233579 TIGR01798, cit_synth_I, citrate synthase I (hexameric type). This
model describes one of several distinct but closely
homologous classes of citrate synthase, the protein that
brings carbon (from acetyl-CoA) into the TCA cycle. This
form, class I, is known to be hexameric and
allosterically inhibited by NADH in Escherichia coli,
Acinetobacter anitratum, Azotobacter vinelandii,
Pseudomonas aeruginosa, etc. In most species with a
class I citrate synthase, a dimeric class II isozyme is
found. The class II enzyme may act primarily on
propionyl-CoA to make 2-methylcitrate or be
bifunctional, may be found among propionate utilization
enzymes, and may be constitutive or induced by
propionate. Some members of this model group as class I
enzymes, and may be hexameric, but have shown regulatory
properties more like class II enzymes [Energy
metabolism, TCA cycle].
Length = 412
Score = 28.2 bits (63), Expect = 0.59
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 29 GRAALWGLAHSGSNGAA 45
G AALWG AH G+N AA
Sbjct: 245 GIAALWGPAHGGANEAA 261
>gnl|CDD|180164 PRK05614, gltA, type II citrate synthase; Reviewed.
Length = 419
Score = 28.3 bits (64), Expect = 0.61
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 29 GRAALWGLAHSGSNGAA 45
G AALWG AH G+N A
Sbjct: 258 GIAALWGPAHGGANEAV 274
>gnl|CDD|130370 TIGR01303, IMP_DH_rel_1, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase and restricted to the
high GC Gram-positive bacteria. All species in which a
member is found so far (Corynebacterium glutamicum,
Mycobacterium tuberculosis, Streptomyces coelicolor,
etc.) also have IMP dehydrogenase as described by
TIGRFAMs entry TIGR01302 [Unknown function, General].
Length = 475
Score = 28.0 bits (62), Expect = 0.71
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVG 29
V+ DGG+R+ DV A+ GA V VG
Sbjct: 331 VWADGGVRHPRDVALALAAGASNVMVG 357
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 27.9 bits (62), Expect = 0.75
Identities = 12/28 (42%), Positives = 14/28 (50%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGR 30
V GGI D +A+ LGA V VG
Sbjct: 173 VIAGGGINDPEDAAEALALGADGVIVGS 200
>gnl|CDD|99860 cd06107, EcCS_AthCS-per_like, Escherichia coli (Ec) citrate
synthase (CS) gltA and Arabidopsis thaliana (Ath)
peroxisomal (Per) CS_like. CS catalyzes the condensation
of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to
form citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs,
including EcCS, are strongly and specifically inhibited
by NADH through an allosteric mechanism. Included in
this group is an NADH-insensitive type II Acetobacter
acetii CS which has retained many of the residues used
by EcCS for NADH binding. C. aurantiacus is a
gram-negative thermophilic green gliding bacterium; its
CS belonging to this group may be a type I CS. It is
not inhibited by NADH or 2-oxoglutarate and is inhibited
by ATP. Both gram-positive and gram-negative bacteria
are found in this group. This group also contains three
Arabidopsis peroxisomal CS proteins, CYS-1, -2, and -3
which participate in the glyoxylate cycle. AthCYS1, in
addition to a peroxisomal targeting sequence, has a
predicted secretory signal peptide; it may be targeted
to both the secretory pathway and the peroxisomes and
perhaps is located in the extracellular matrix. AthCSY1
is expressed only in siliques and specifically in
developing seeds. AthCSY2 and 3 are active during seed
germination and seedling development and are thought to
participate in the beta-oxidation of fatty acids.
Length = 382
Score = 27.8 bits (62), Expect = 0.95
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 12 GTDVFKAIGLGAKYVFVGRAALWGLAHSGSNGAA-RVLQSLVHKILPEAVADKV 64
D + AAL+G H G+N AA ++L+ + PE V +
Sbjct: 215 LADPISCMAAAI-------AALYGPLHGGANEAALKMLREIGT---PENVPAFI 258
>gnl|CDD|224329 COG1411, COG1411, Uncharacterized protein related to proFAR
isomerase (HisA) [General function prediction only].
Length = 229
Score = 27.4 bits (61), Expect = 1.0
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVGRA 31
V L GG+ D+ +G+G V V A
Sbjct: 184 VLLGGGVGGMEDLELLLGMGVSGVLVATA 212
>gnl|CDD|235274 PRK04302, PRK04302, triosephosphate isomerase; Provisional.
Length = 223
Score = 27.5 bits (62), Expect = 1.1
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 2 EVYLDGGIRYGTDVFKAIGLGA 23
+V GI G DV A+ LGA
Sbjct: 175 KVLCGAGISTGEDVKAALELGA 196
>gnl|CDD|236968 PRK11750, gltB, glutamate synthase subunit alpha; Provisional.
Length = 1485
Score = 27.1 bits (61), Expect = 1.4
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 6 DGGIRYGTDVFKAIGLGA 23
DGG++ G DV KA LGA
Sbjct: 1073 DGGLKTGLDVIKAAILGA 1090
>gnl|CDD|233351 TIGR01304, IMP_DH_rel_2, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase. Most species with a
member of this family belong to the high GC
Gram-positive bacteria, and these also have the IMP
dehydrogenase described by TIGRFAMs equivalog model
TIGR01302 [Unknown function, General].
Length = 369
Score = 27.1 bits (60), Expect = 1.4
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVG 29
V DGGI D+ KAI GA V +G
Sbjct: 258 VIADGGIETSGDLVKAIACGADAVVLG 284
>gnl|CDD|181127 PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 479
Score = 27.2 bits (61), Expect = 1.5
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 3 VYLDGGIRYGTDVFKAIGLGAKYVFVG 29
V+ DGG+R+ DV A+ GA V +G
Sbjct: 333 VWADGGVRHPRDVALALAAGASNVMIG 359
>gnl|CDD|235045 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
Length = 310
Score = 26.8 bits (60), Expect = 1.8
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRA 31
GG++ G D F+ I GA V VG A
Sbjct: 248 GGVKTGRDAFEHILCGASMVQVGTA 272
>gnl|CDD|99867 cd06114, EcCS_like, Escherichia coli (Ec) citrate synthase (CS)
GltA_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). Some type II CSs including EcCS are
strongly and specifically inhibited by NADH through an
allosteric mechanism. Included in this group is an
NADH-insensitive type II Acetobacter acetii CS which has
retained many of the residues used by EcCS for NADH
binding.
Length = 400
Score = 26.4 bits (59), Expect = 2.5
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 29 GRAALWGLAHSGSNGAA 45
G AALWG H G+N A
Sbjct: 240 GIAALWGPLHGGANEAV 256
>gnl|CDD|236235 PRK08314, PRK08314, long-chain-fatty-acid--CoA ligase; Validated.
Length = 546
Score = 26.1 bits (58), Expect = 3.8
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 10/39 (25%)
Query: 36 LAHSGSNGAARVLQSLVHKILPEAVADKVHNAYSIFFLE 74
L + G GAA +PEAVA+++ + ++E
Sbjct: 307 LRYIGGGGAA----------MPEAVAERLKELTGLDYVE 335
>gnl|CDD|180842 PRK07107, PRK07107, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 502
Score = 25.8 bits (57), Expect = 4.1
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVGR 30
DGGI Y + A+ +GA ++ +GR
Sbjct: 358 DGGIVYDYHMTLALAMGADFIMLGR 382
>gnl|CDD|234853 PRK00877, hisD, bifunctional histidinal dehydrogenase/ histidinol
dehydrogenase; Reviewed.
Length = 425
Score = 25.4 bits (57), Expect = 5.2
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 57 PEAVADKVHNAYSIF 71
P A+ D++ NA +IF
Sbjct: 333 PRALLDRIRNAGAIF 347
>gnl|CDD|130372 TIGR01305, GMP_reduct_1, guanosine monophosphate reductase,
eukaryotic. A deep split separates two families of GMP
reductase. This family includes both eukaryotic and some
proteobacterial sequences, while the other family
contains other bacterial sequences [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 343
Score = 25.3 bits (55), Expect = 6.2
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 6 DGGIRYGTDVFKAIGLGAKYVFVG 29
DGG DV KA G GA +V +G
Sbjct: 218 DGGCTCPGDVAKAFGAGADFVMLG 241
>gnl|CDD|172156 PRK13587, PRK13587,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 234
Score = 25.2 bits (55), Expect = 7.9
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRAA 32
GGIR+ D+ + L +G+AA
Sbjct: 199 GGIRHQQDIQRLASLNVHAAIIGKAA 224
>gnl|CDD|177163 MTH00101, ATP6, ATP synthase F0 subunit 6; Validated.
Length = 226
Score = 24.9 bits (55), Expect = 8.1
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 4/22 (18%)
Query: 78 LVPTLLLGSIQPPSKRLAPNRL 99
+ P+LL P RL NRL
Sbjct: 25 MFPSLLF----PTPNRLINNRL 42
>gnl|CDD|240083 cd04732, HisA, HisA. Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase catalyzes
the fourth step in histidine biosynthesis, an
isomerisation of the aminoaldose moiety of ProFAR to the
aminoketose of PRFAR
(N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-
phospho-ribosyl)-4-imidazolecarboxamide). In bacteria
and archaea, ProFAR isomerase is encoded by the HisA
gene.
Length = 234
Score = 24.7 bits (55), Expect = 8.4
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 7 GGIRYGTDVFKAIGLGAKYVFVGRAAL 33
GGIR D+ + + LG V +G AA+
Sbjct: 80 GGIRSLEDIERLLDLGVSRVIIGTAAV 106
>gnl|CDD|132848 cd07209, Pat_hypo_Ecoli_Z1214_like, Hypothetical patatin similar to
Z1214 protein of Escherichia coli. Patatin-like
phospholipase similar to Z1214 protein of Escherichia
coli. This family predominantly consists of bacterial
patatin glycoproteins and some representatives from
eukaryotes and archaea. The patatin protein accounts for
up to 40% of the total soluble protein in potato tubers.
Patatin is a storage protein, but it also has the
enzymatic activity of a lipid acyl hydrolase, catalyzing
the cleavage of fatty acids from membrane lipids.
Members of this family have also been found in
vertebrates.
Length = 215
Score = 24.9 bits (55), Expect = 9.0
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 4 YLDGGIRYGTDVFKAIGLGAKYVFV 28
Y DGG+ T + AI LGA + V
Sbjct: 138 YWDGGVVDNTPLSPAIDLGADEIIV 162
>gnl|CDD|167709 PRK04128, PRK04128,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 228
Score = 24.7 bits (54), Expect = 9.0
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 1 MEVYLDGGIRYGTDVFKAIGLGAKYVFVGRAAL 33
++V + GG+R + A +G + V +G A
Sbjct: 74 LKVQVGGGLRTYESIKDAYEIGVENVIIGTKAF 106
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
0.322 0.140 0.413
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,240,702
Number of extensions: 447917
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 439
Number of HSP's successfully gapped: 74
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
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 (21.9 bits)
S2: 53 (24.1 bits)