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Information on EC 5.1.2.1 - lactate racemase
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EC Tree
5.1.2.1 lactate racemaseIUBMB Comments
The enzyme has been characterized from the bacterium Lactobacillus plantarum and appears to be restricted to lactic acid bacteria. It contains a unique nickel-containing cofactor, pyridinium-3-thioamide-5-thiocarboxylate mononucleotide Ni pincer complex.
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Word Map
- 5.1.2.1
- lactobacillus
- plantarum
-
racemization
-
pincer
-
hydride
-
organometallic
-
nickel-containing
-
proton-coupled
- nife-hydrogenase
-
sacrificial
-
insertase
-
ni-dependent
- sakei
-
pyridinium
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
lactate racemase, lactic acid racemase, nickel-dependent lactate racemase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Hydroxyacid racemase
-
-
-
-
Lactic acid racemase
-
-
-
-
Lacticoracemase
-
-
-
-
LARa
nickel-dependent lactate racemase
Racemase, lactate
-
-
-
-
nickel-dependent lactate racemase
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(S)-Lactate = (R)-lactate
direct internal hydride transfer mechanism, symmetrical alpha-carbon intermediate
-
(S)-Lactate = (R)-lactate
transient carbonyl intermediate, carbonyl is in the alpha-position of the enzyme-bound lactic acid
-
(S)-Lactate = (R)-lactate
the enzyme does not follow a proton-coupled electron transfer mechanism, but a proton-coupled hydride transfer (PCHT) mechanism. The nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization
(S)-Lactate = (R)-lactate
the Ni-tethered pincer cofactor in enzyme LarA increases reaction barriers and destabilizes NADH-like pyruvate intermediates, due to the less electrophilic Ni cofactor and to the ring strain in the pyruvate intermediates, reaction mechanism, active and transition state structure, modeling
(S)-Lactate = (R)-lactate
the enzyme does not follow a proton-coupled electron transfer mechanism, but a proton-coupled hydride transfer (PCHT) mechanism. The nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
-
(S)-Lactate = (R)-lactate
the Ni-tethered pincer cofactor in enzyme LarA increases reaction barriers and destabilizes NADH-like pyruvate intermediates, due to the less electrophilic Ni cofactor and to the ring strain in the pyruvate intermediates, reaction mechanism, active and transition state structure, modeling
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
-
(S)-Lactate = (R)-lactate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
lactate racemase
The enzyme has been characterized from the bacterium Lactobacillus plantarum and appears to be restricted to lactic acid bacteria. It contains a unique nickel-containing cofactor, pyridinium-3-thioamide-5-thiocarboxylate mononucleotide Ni pincer complex.
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CAS REGISTRY NUMBER
COMMENTARY
9024-05-9
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
no exchange reaction between lactate and water
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
the enzyme contains an organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide. The nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization
-
additional information
-
the enzyme contains an organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide. The nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ni2+
additional information
Ni2+
absolutely required. Lactobacillus plantarum possesses an organometallic nickel-containing prosthetic group. A nicotinic acid mononucleotide derivative is tethered to Lys184 and forms a tridentate pincer complex that coordinates nickel through one metal-carbon and two metal-sulfur bonds, with His200 as another ligand. Nickel-binding site structure and the role of three accessory proteins required for its activation, overview
Ni2+
dependent on, nickel is an essential cofactor, the enzyme contains 19-21% nickel, measured by PAR assays and ICP-AES. The LarA Ni center is coordinated by His residues, a four coordinate square planar nickel center or a five coordinate square pyramidal site
Ni2+
required, the Ni-tethered pincer cofactor in enzyme LarA increases reaction barriers and destabilizes NADH-like pyruvate intermediates, due to the less electrophilic Ni cofactor and to the ring strain in the pyruvate intermediates, the Ni ion decreases the electron affinity of cofactor
additional information
model of the assembly of the lactate racemase metallocenter, overview. Enzyme LarA receives Ni2+ from the pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase, LarE (EC 4.4.1.37)
additional information
-
model of the assembly of the lactate racemase metallocenter, overview. Enzyme LarA receives Ni2+ from the pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase, LarE (EC 4.4.1.37)
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
LacR
hypothetical model of PlarA regulation by LarR: in the presence of L-lactate, activated LarR binds to the Lar box motif and multimerizes on the half-Lar boxes. This will promote direct interaction of one LarR dimer with the RNA polymerase, resulting in transcriptional activation of the PlarA (productive binding). In the presence of D-lactate, D-lactatet can block LarR activation, for instance, by impairing L-lactate recognition, which will result in limited LarR binding and multimerization and absence of transcriptional activation (unproductive binding)
-
additional information
-
yeast extract (0.1% (w/v)), MgSO4 (2 mM), MnSO4 (2 mM) and ascorbic acid (2 mM) enhance lactate racemase activity in vitro
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additional information
lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Effect of accessory Lar proteins and cofactors on the in vitro activation of LarANiDELTABCE (apo-LarA) by LarENiBC, overview. Necessity of the Lar accessory proteins (larBCE), for LarA activation. Ni-loaded LarE acts as a maturation protein responsible for the activation of apo-LarA, and indicate that LarB and LarC are involved in the activation of LarE prior to apo-LarA activation
-
additional information
-
lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Effect of accessory Lar proteins and cofactors on the in vitro activation of LarANiDELTABCE (apo-LarA) by LarENiBC, overview. Necessity of the Lar accessory proteins (larBCE), for LarA activation. Ni-loaded LarE acts as a maturation protein responsible for the activation of apo-LarA, and indicate that LarB and LarC are involved in the activation of LarE prior to apo-LarA activation
-
additional information
nickel-binding site structure and the role of three accessory proteins required for its activation, overview
-
additional information
-
nickel-binding site structure and the role of three accessory proteins required for its activation, overview
-
additional information
the lactate racemase is a nickel-dependent enzyme requiring activation by the accessory protein LarE, which itself requires activation by the accessory proteins LarB and LarC and nickel
-
additional information
-
the lactate racemase is a nickel-dependent enzyme requiring activation by the accessory protein LarE, which itself requires activation by the accessory proteins LarB and LarC and nickel
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
11
(R)-lactate
pH and temperature not specified in the publication
46
(S)-lactate
pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1333
(R)-lactate
pH and temperature not specified in the publication
4745
(S)-lactate
pH and temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
15 - 50
-
15°C: about 40% of maximal activity, 50°C: about 60% of maximal activity
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
analysis of the lar gene cluster and its encoded Lar proteins, phylogenetic tree. 92% of the genomes bearing a larA homologue (102 out of 111 genomes) also contain the genes for the Lar accessory proteins (larBCE), further reinforcing the necessity of these proteins for LarA activation
evolution
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
analysis of the lar gene cluster and its encoded Lar proteins, phylogenetic tree. 92% of the genomes bearing a larA homologue (102 out of 111 genomes) also contain the genes for the Lar accessory proteins (larBCE), further reinforcing the necessity of these proteins for LarA activation
-
malfunction
disruption of the operon encoding lactate racemase (larA-E), which catalyzes the interconversion between D- and L-latate, completely abolishes D-lactate production. An engineered Lactobacillus plantarum strain lacking the enzyme is useful in the production of L-lactate from starchy materials
malfunction
mutations in the Lar box strongly affect LarR binding and completely abolish transcription from the larA promoter (PlarA)
malfunction
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
disruption of the operon encoding lactate racemase (larA-E), which catalyzes the interconversion between D- and L-latate, completely abolishes D-lactate production. An engineered Lactobacillus plantarum strain lacking the enzyme is useful in the production of L-lactate from starchy materials
-
malfunction
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
mutations in the Lar box strongly affect LarR binding and completely abolish transcription from the larA promoter (PlarA)
-
physiological function
lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Four proteins and Ni are required for in vivo Lar activity. Necessity of the Lar accessory proteins (larBCE), for LarA activation. Ni-loaded LarE acts as a maturation protein responsible for the activation of apo-LarA, and indicate that LarB and LarC are involved in the activation of LarE prior to apo-LarA activation
physiological function
lactic acid racemization is involved in lactate metabolism and cell wall assembly of many microorganisms
physiological function
the lactate racemase is a nickel-dependent enzyme requiring activation by the accessory protein LarE, which itself requires activation by the accessory proteins LarB and LarC and nickel. The interconversion of lactate isomers is performed by a lactate racemase (Lar) that is transcriptionally controlled by the L-/D-lactate ratio and maximally induced in the presence of L-lactate. The Lar activity depends on the expression of two divergently oriented operons: (i) the larABCDE operon encodes the nickel-dependent lactate racemase (LarA), its maturases (LarBCE), and a lactic acid channel (LarD), and (ii) the larR(MN)QO operon encodes a transcriptional regulator (LarR) and a four-component ABC-type nickel transporter [Lar(MN), in which the M and N components are fused, LarQ, and LarO]. LarR is a regulator of the Crp-Fnr family (PrfA group). L-Lactate has a positive effect on the binding and multimerization of LarR, while D-lactate antagonizes the positive effect of L-lactate. A possible mechanism of LarR regulation by lactate enantiomers is proposed. Hypothetical model of PlarA regulation by LarR: in the presence of L-lactate, activated LarR binds to the Lar box motif and multimerizes on the half-Lar boxes. This will promote direct interaction of one LarR dimer with the RNA polymerase, resulting in transcriptional activation of the PlarA (productive binding). In the presence of D-lactate, D-lactatet can block LarR activation, for instance, by impairing L-lactate recognition, which will result in limited LarR binding and multimerization and absence of transcriptional activation (unproductive binding). Role of LarR in vivo and in vitro
physiological function
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Four proteins and Ni are required for in vivo Lar activity. Necessity of the Lar accessory proteins (larBCE), for LarA activation. Ni-loaded LarE acts as a maturation protein responsible for the activation of apo-LarA, and indicate that LarB and LarC are involved in the activation of LarE prior to apo-LarA activation
-
physiological function
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
the lactate racemase is a nickel-dependent enzyme requiring activation by the accessory protein LarE, which itself requires activation by the accessory proteins LarB and LarC and nickel. The interconversion of lactate isomers is performed by a lactate racemase (Lar) that is transcriptionally controlled by the L-/D-lactate ratio and maximally induced in the presence of L-lactate. The Lar activity depends on the expression of two divergently oriented operons: (i) the larABCDE operon encodes the nickel-dependent lactate racemase (LarA), its maturases (LarBCE), and a lactic acid channel (LarD), and (ii) the larR(MN)QO operon encodes a transcriptional regulator (LarR) and a four-component ABC-type nickel transporter [Lar(MN), in which the M and N components are fused, LarQ, and LarO]. LarR is a regulator of the Crp-Fnr family (PrfA group). L-Lactate has a positive effect on the binding and multimerization of LarR, while D-lactate antagonizes the positive effect of L-lactate. A possible mechanism of LarR regulation by lactate enantiomers is proposed. Hypothetical model of PlarA regulation by LarR: in the presence of L-lactate, activated LarR binds to the Lar box motif and multimerizes on the half-Lar boxes. This will promote direct interaction of one LarR dimer with the RNA polymerase, resulting in transcriptional activation of the PlarA (productive binding). In the presence of D-lactate, D-lactatet can block LarR activation, for instance, by impairing L-lactate recognition, which will result in limited LarR binding and multimerization and absence of transcriptional activation (unproductive binding). Role of LarR in vivo and in vitro
-
physiological function
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
lactic acid racemization is involved in lactate metabolism and cell wall assembly of many microorganisms
-
additional information
electron paramagnetic resonance spectroscopy of LarA in the absence or presence of substrate revealing a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand
additional information
-
electron paramagnetic resonance spectroscopy of LarA in the absence or presence of substrate revealing a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand
additional information
LarA catalytic site structure analysis in subunits one and two, overview. Structure comparisons to LarA from Thermus thermophilus
additional information
-
LarA catalytic site structure analysis in subunits one and two, overview. Structure comparisons to LarA from Thermus thermophilus
additional information
the active-site structure is constructed from chain B of the recent crystal structure of Lactobacillus plantarum LarA, PDB ID 5HUQ
additional information
the wide distribution of the accessory proteins without Lar
additional information
-
the wide distribution of the accessory proteins without Lar
additional information
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
LarA catalytic site structure analysis in subunits one and two, overview. Structure comparisons to LarA from Thermus thermophilus
-
additional information
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
electron paramagnetic resonance spectroscopy of LarA in the absence or presence of substrate revealing a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand
-
additional information
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
the active-site structure is constructed from chain B of the recent crystal structure of Lactobacillus plantarum LarA, PDB ID 5HUQ
-
additional information
Lactiplantibacillus plantarum ATCC BAA-793 / NCIMB 8826 / WCFS1
-
the wide distribution of the accessory proteins without Lar
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). LARA_LACPL
Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
424
0
46239
Swiss-Prot
-
LARA_THETC
Thermoanaerobacterium thermosaccharolyticum (strain ATCC 7956 / DSM 571 / NCIMB 9385 / NCA 3814 / NCTC 13789 / WDCM 00135 / 2032)
426
0
46879
Swiss-Prot
-
A0A644XVK8_9ZZZZ
418
0
45430
TrEMBL
other Location (Reliability: 1)
A0A644T9Q4_9ZZZZ
437
0
47976
TrEMBL
other Location (Reliability: 2)
A0A644XL16_9ZZZZ
415
0
46087
TrEMBL
other Location (Reliability: 1)
A0A645AFR8_9ZZZZ
449
0
48875
TrEMBL
other Location (Reliability: 1)
A0A644UHV6_9ZZZZ
426
0
47760
TrEMBL
other Location (Reliability: 1)
A0A644X2N2_9ZZZZ
422
0
46063
TrEMBL
other Location (Reliability: 2)
A0A8A0RM69_9FIRM
431
0
47547
TrEMBL
-
A0A645GNJ5_9ZZZZ
201
0
22035
TrEMBL
Secretory Pathway (Reliability: 5)
A0A645AFT0_9ZZZZ
425
0
46923
TrEMBL
other Location (Reliability: 2)
A0A645EAR7_9ZZZZ
293
0
32046
TrEMBL
other Location (Reliability: 1)
A0A644VBJ0_9ZZZZ
433
0
47210
TrEMBL
other Location (Reliability: 1)
A0A644XT32_9ZZZZ
434
0
47754
TrEMBL
other Location (Reliability: 4)
A0A645BED8_9ZZZZ
362
0
39902
TrEMBL
other Location (Reliability: 4)
A0A645G361_9ZZZZ
206
0
22828
TrEMBL
other Location (Reliability: 2)
A0A645GRP2_9ZZZZ
148
0
16154
TrEMBL
other Location (Reliability: 1)
A0A644U8V8_9ZZZZ
425
0
46537
TrEMBL
other Location (Reliability: 2)
A0A644UDN2_9ZZZZ
420
0
46286
TrEMBL
other Location (Reliability: 2)
A0A644VCW3_9ZZZZ
425
0
47188
TrEMBL
other Location (Reliability: 2)
A0A645DWQ8_9ZZZZ
83
0
9105
TrEMBL
other Location (Reliability: 2)
A0A2U3KCZ4_9FIRM
427
0
46178
TrEMBL
-
A0A644W8W5_9ZZZZ
430
0
45732
TrEMBL
other Location (Reliability: 1)
A0A645CDX4_9ZZZZ
101
0
11254
TrEMBL
other Location (Reliability: 1)
A0A644TMR9_9ZZZZ
432
0
47703
TrEMBL
other Location (Reliability: 1)
A0A644TLZ5_9ZZZZ
431
0
47674
TrEMBL
other Location (Reliability: 2)
A0A644Y8P7_9ZZZZ
423
0
45244
TrEMBL
other Location (Reliability: 3)
A0A645B2E5_9ZZZZ
161
0
17070
TrEMBL
other Location (Reliability: 1)
A0A644UID1_9ZZZZ
432
0
47268
TrEMBL
other Location (Reliability: 2)
A0A6S6XLX8_9FIRM
426
0
45790
TrEMBL
-
A0A645AHF6_9ZZZZ
312
0
34097
TrEMBL
other Location (Reliability: 2)
A0A644ZJ36_9ZZZZ
405
0
43354
TrEMBL
other Location (Reliability: 2)
A0A644VKL3_9ZZZZ
427
0
45470
TrEMBL
Mitochondrion (Reliability: 4)
A0A644TRB7_9ZZZZ
428
0
46020
TrEMBL
other Location (Reliability: 2)
A0A2U3K395_9FIRM
420
0
46798
TrEMBL
-
A0A644VZY3_9ZZZZ
418
0
44494
TrEMBL
other Location (Reliability: 2)
A0A645GD25_9ZZZZ
206
0
22916
TrEMBL
other Location (Reliability: 1)
A0A645HF15_9ZZZZ
198
0
22016
TrEMBL
other Location (Reliability: 1)
A0A644VWZ0_9ZZZZ
435
0
47159
TrEMBL
other Location (Reliability: 2)
A0A644YFA2_9ZZZZ
425
0
46156
TrEMBL
other Location (Reliability: 2)
A0A645DXV1_9ZZZZ
223
0
24068
TrEMBL
other Location (Reliability: 3)
A0A644Y6L7_9ZZZZ
414
0
45947
TrEMBL
other Location (Reliability: 2)
A0A644TAG8_9ZZZZ
430
0
46723
TrEMBL
other Location (Reliability: 1)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY