Finding step glt for L-aspartate catabolism in Shewanella sp. ANA-3
5 candidates for glt: aspartate:proton symporter Glt
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | Shewana3_1726 | sodium:dicarboxylate symporter (RefSeq) | Sodium:dicarboxylate symporter (characterized, see rationale) | 83% | 100% | 706.8 | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up | 32% | 244.2 |
| hi | Shewana3_3362 | sodium:dicarboxylate symporter (RefSeq) | Sodium:dicarboxylate symporter (characterized, see rationale) | 48% | 93% | 370.5 | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up | 35% | 273.9 |
| hi | Shewana3_0642 | sodium:dicarboxylate symporter (RefSeq) | Sodium:dicarboxylate symporter (characterized, see rationale) | 41% | 92% | 320.5 | | | |
| med | Shewana3_3163 | sodium:dicarboxylate symporter (RefSeq) | Sodium:dicarboxylate symporter (characterized, see rationale) | 40% | 94% | 298.1 | sodium:C4-dicarboxylate symporter (dctA) | 33% | 245.0 |
| lo | Shewana3_0142 | sodium:dicarboxylate symporter (RefSeq) | EAAT homologue, a glutamate/aspartate preferring transporter of 483 aas (characterized) | 37% | 54% | 150.6 | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up | 32% | 223.8 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Also see fitness data for the candidates
Definition of step glt
- Curated sequence P21345: Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein. Glutamate/aspartate:H+ symporter, GltP or GltT; has 8 TMSs with 2 re-entrant loops as for GltPh (TC# 2.A.23.1.5). glutamate/aspartate : H+ symporter GltP
- Curated sequence CH_014038: aerobic C4-dicarboxylate transport protein. Aerobic C4-dicarboxylate transport protein. Aerobic dicarboxylate transporter, DctA. Interacts with the DcuS sensor kinase. C4 dicarboxylate/orotate:H+ symporter. C4 dicarboxylate/orotate:H+ symporter
- UniProt sequence A0A0N9WTL5: SubName: Full=Amino acid:proton symporter {ECO:0000313|EMBL:ALI05583.1};
- UniProt sequence A0A0C4Y5S4: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:AJG18233.1};
- Curated sequence CH_088342: proton/sodium-glutamate symport protein GltT. Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein
- Curated sequence P24943: Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein. proton/sodium-glutamate symport protein GltT. Glutamate/aspartate:Na+ + H+ symporter
- Curated sequence P43003: Excitatory amino acid transporter 1; Sodium-dependent glutamate/aspartate transporter 1; GLAST-1; Solute carrier family 1 member 3. Excitatory amino acid transporter 1 (EAAT1) (Sodium-dependent glutamate/aspartate transporter 1) (GLAST-1) (Solute carrier family 1 member 3)
- Curated sequence CH_091614: excitatory amino acid transporter 1. Excitatory amino acid transporter 1; Glial glutamate transporter; Sodium-dependent glutamate/aspartate transporter 1; GLAST; GLAST-1; Solute carrier family 1 member 3. Glutamate/aspartate:Na+ symporter, GLAST or EAAT1, Structural rearrangements have been probed by Leighton et al., 2006). EAAT1 interacts directly with the Na+, K+-ATPase (TC #3.A.3.1) (Rose et al., 2009). CEAT1 couples glutamate uptake to the symport of 3 Na+ and 1 H+ followed by the antiport of 1 K+. It can function as an uncoupled anion, water and/or urea channel (Vandenberg et al., 2011). Large collective motions regulate the functional properties of EAAT1 trimers
- Curated sequence O35544: Excitatory amino acid transporter 4; High-affinity neuronal glutamate transporter; Sodium-dependent glutamate/aspartate transporter; Solute carrier family 1 member 6
- Curated sequence O35921: Excitatory amino acid transporter 4; High-affinity neuronal glutamate transporter; Sodium-dependent glutamate/aspartate transporter; Solute carrier family 1 member 6
- Curated sequence O57321: Excitatory amino acid transporter 1; SEAAT1; Sodium-dependent glutamate/aspartate transporter; GLAST
- Curated sequence O59010: Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter. Archaeal aspartate transporter, Gltph (GltPh) (3-D structure known; 3V8F and 3V8G) (Boudker et al., 2007; Yernool et al., 2004). Cotransports aspartate with 2 Na+ (Ryan et al., 2009) or 3 Na+ (Groeneveld and Slotboom, 2010) or 1Na+ plus 1 H+ plus 1 K+
- Curated sequence P24943: Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein. proton/sodium-glutamate symport protein GltT. Glutamate/aspartate:Na+ + H+ symporter
- Curated sequence P31596: Excitatory amino acid transporter 2; GLT-1; Sodium-dependent glutamate/aspartate transporter 2; GLUT-R; Solute carrier family 1 member 2. Glutamate/aspartate:Na+ symporter, GLT1; GLUT-R; EAAT2. Interacts directly with the Na+, K+-ATPase (TC #3.A.3.1) (Rose et al., 2009). Cotransports glutamic acid with three Na+ followed by countertransport of K+ (Teichman et al., 2009). The C-terminal 74aa domain regulates transport activity (Leinenweber et al., 2011). Hippocampal glutamate transporter 1 (GLT-1) levels parallel memory training (Heo et al., 2011). GLT-1 is regulated by MAGI-1
- Curated sequence P31597: Excitatory amino acid transporter 3; Excitatory amino-acid carrier 1; Sodium-dependent glutamate/aspartate transporter 3; Solute carrier family 1 member 1
- Curated sequence P43004: Excitatory amino acid transporter 2; Glutamate/aspartate transporter II; Sodium-dependent glutamate/aspartate transporter 2; Solute carrier family 1 member 2. Excitatory amino acid transporter 2, EAAT2 (Glutamate/aspartate transporter II) (Sodium-dependent glutamate/aspartate transporter 2) (Solute carrier family 1 member 2)
- Curated sequence P43005: Excitatory amino acid transporter 3; Excitatory amino-acid carrier 1; Neuronal and epithelial glutamate transporter; Sodium-dependent glutamate/aspartate transporter 3; Solute carrier family 1 member 1. Glutamate/aspartate/cysteine:Na+ symporter, EAAC1; EAAT3, SLC1A1 (Li+ can replace Na+; EAAC1 also mediates glutamate-independent anion conductance.) Cotransports glutamic acid with three Na+ followed by countertransport of K+(Teichman et al., 2009). The 50 residue 4B-4C loop (following TMS4) binds Na+ (Koch et al., 2007). (The dicarboxylic aminoaciduria protein in humans; NP_004161; Bröer, 2008a; 2008b). Neutralizing aspartate 83 modifies substrate translocation
- Curated sequence P43006: Excitatory amino acid transporter 2; GLT-1; Sodium-dependent glutamate/aspartate transporter 2; Solute carrier family 1 member 2
- Curated sequence P46411: Excitatory amino acid transporter 1; Sodium-dependent glutamate/aspartate transporter 1; GLAST-1; Solute carrier family 1 member 3
- Curated sequence P48664: Excitatory amino acid transporter 4; Sodium-dependent glutamate/aspartate transporter; Solute carrier family 1 member 6. Excitatory amino acid transporter 4, EAAT4 (Sodium-dependent glutamate/aspartate transporter) (Solute carrier family 1 member 6)
- Curated sequence P51906: Excitatory amino acid transporter 3; Excitatory amino-acid carrier 1; Sodium-dependent glutamate/aspartate transporter 3; Solute carrier family 1 member 1
- Curated sequence P51907: Excitatory amino acid transporter 3; Excitatory amino-acid carrier 1; Sodium-dependent glutamate/aspartate transporter 3; Solute carrier family 1 member 1
- Curated sequence P56564: Excitatory amino acid transporter 1; Glial high affinity glutamate transporter; High-affinity neuronal glutamate transporter; GluT-1; Sodium-dependent glutamate/aspartate transporter 1; GLAST-1; Solute carrier family 1 member 3
- Curated sequence Q9N1R2: Excitatory amino acid transporter 4; Sodium-dependent glutamate/aspartate transporter; Solute carrier family 1 member 6
- Curated sequence B0W0K4: EAAT homologue, a glutamate/aspartate preferring transporter of 483 aas
- Curated sequence Q10901: Excitatory amino acid transporter (Sodium-dependent glutamate/aspartate transporter), Gkt-1 of 503 aas and 9 - 11 TMSs
- Curated sequence Q8T0S9: Aspartate/taurine (not glutamate):Na+ symporter, dEAAT2 (mediates both uptake and heteroexchange of its two substrates, both dependent on external Na+ (with taurine outside and Asp inside)); L-glutamate is transported with low affinity and efficiency
- Curated sequence CH_088342: proton/sodium-glutamate symport protein GltT. Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein
- Ignore hits to Q9N280 when looking for 'other' hits (glucuronosyltransferase (EC 2.4.1.17))
- Curated sequence P39817: Proton/glutamate-aspartate symporter; Proton/glutamate symport protein
- UniProt sequence A1S570: SubName: Full=Sodium:dicarboxylate symporter {ECO:0000313|EMBL:ABL99526.1};
- Comment: The original cluster was entirely eukaryotic except for gltPh from Pyrococcus horikoshii. Added gltT from Bacillus caldotenax (CharProtDB::CH_088342), which is also an aspartate transporter. So, named it glt. Ignore Q9N280 which has a questionable annotation in BRENDA. But the more distantly related protein AO356_01905 (A0A0N9WTL5) also seems to be an aspartate transporter. Similarly, the related protein RR42_RS03990 (A0A0C4Y5S4) is specifically important for asparagine utilization. Asparagine is probably cleaved in the periplasm (by RR42_RS12610 or RR42_RS26140) so this is probably an aspartate transporter as well. And the related protein P24944 (CH_088342) or P24943 is an aspartate transporter. This cluster also includes the aspartate transporter DctA from E. coli; it is almost 80% identical to Pseudomonas dicarboxylate transporters whose activity on aspartate is uncertain. As these are not important for aspartate utilization (AO356_18980, AO353_02800), do not mark them as ignored. The gltP from B. subtilis (P39817) was added manually. A related aspartate/glutamate transporter was identified in Shewanella amazonensis SB2B (Sama_1319, A1S570) using fitness data.
Or cluster all characterized glt proteins
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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About GapMind
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory