Protein GFF3910 in Phaeobacter inhibens BS107
Annotation: FitnessBrowser__Phaeo:GFF3910
Length: 251 amino acids
Source: Phaeo in FitnessBrowser
Candidate for 26 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 48% | 97% | 227.3 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 48% | 99% | 225.7 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-asparagine catabolism | glnQ | med | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 48% | 96% | 223.8 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-glutamate catabolism | gltL | med | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 48% | 96% | 223.8 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 48% | 97% | 219.2 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 48% | 97% | 219.2 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-histidine catabolism | hisP | med | histidine transport ATP-binding protein hisP (characterized) | 46% | 96% | 218.8 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 46% | 96% | 218.4 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 47% | 92% | 216.1 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 47% | 92% | 216.1 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 46% | 95% | 212.6 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-citrulline catabolism | PS417_17605 | med | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 46% | 92% | 211.1 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-asparagine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 210.7 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-aspartate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 210.7 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-glutamate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 210.7 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-leucine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 210.7 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-proline catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 210.7 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 44% | 97% | 207.6 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 46% | 94% | 207.2 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 46% | 91% | 206.1 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 46% | 91% | 206.1 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 45% | 98% | 204.9 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 45% | 98% | 204.9 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 42% | 99% | 195.3 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 42% | 99% | 195.3 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 45% | 65% | 176.8 | Probable amino-acid import ATP-binding protein YxeO; EC 7.4.2.- | 55% | 274.6 |
Sequence Analysis Tools
View GFF3910 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MKDTTQGPAISITGLRKTFGDSVVLDGIDLTIQPGERIVIIGPSGTGKSTLLRCLNFLDA
PDAGLVRIGDLDVDAARASKAEILALRRRTAFVFQNYALFANKTAAENIMEALITVQKQP
RAEAEARAREILAETGLADKADAYPASLSGGQQQRVGIGRAMALGAELMLFDEPTSALDP
EWVGEVLALMHKVAEERQTMLIVTHEMQFAREIADRVVFMEGGRIVEQGPPTQIFDAPQD
PRTRAFLRRVG
This GapMind analysis is from Sep 17 2021. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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