Protein Pf1N1B4_773 in Pseudomonas fluorescens FW300-N1B4
Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_773
Length: 223 amino acids
Source: pseudo1_N1B4 in FitnessBrowser
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | aatM | hi | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 (characterized) | 100% | 100% | 435.3 | Glutamine ABC transporter permease and substrate binding protein 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 | 36% | 139.8 |
| L-aspartate catabolism | aatM | hi | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 (characterized) | 100% | 100% | 435.3 | Glutamine ABC transporter permease and substrate binding protein 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 | 36% | 139.8 |
| L-glutamate catabolism | gltK | hi | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 (characterized) | 100% | 100% | 435.3 | Glutamine ABC transporter permease and substrate binding protein 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 | 36% | 139.8 |
| D-alanine catabolism | Pf6N2E2_5404 | lo | ABC transporter for D-Alanine, permease component 1 (characterized) | 33% | 56% | 131 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-glutamate catabolism | gltJ | lo | Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) | 34% | 85% | 129.4 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-asparagine catabolism | natH | lo | NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 34% | 56% | 127.5 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-aspartate catabolism | natH | lo | NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 34% | 56% | 127.5 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-asparagine catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 33% | 87% | 127.1 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-aspartate catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 33% | 87% | 127.1 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-histidine catabolism | aapM | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) | 32% | 52% | 112.5 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-asparagine catabolism | aapM | lo | AapM, 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) | 33% | 52% | 109.8 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-aspartate catabolism | aapM | lo | AapM, 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) | 33% | 52% | 109.8 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-glutamate catabolism | aapM | lo | AapM, 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) | 33% | 52% | 109.8 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-leucine catabolism | aapM | lo | AapM, 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) | 33% | 52% | 109.8 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-proline catabolism | aapM | lo | AapM, 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) | 33% | 52% | 109.8 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-glutamate catabolism | gluD | lo | GluD aka CGL1953, component of Glutamate porter (characterized) | 30% | 74% | 107.1 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-asparagine catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 35% | 93% | 105.5 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
| L-aspartate catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 35% | 93% | 105.5 | ABC transporter for L-asparagine and L-glutamate, permease subunit 2 | 100% | 435.3 |
Sequence Analysis Tools
View Pf1N1B4_773 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
Fitness BLAST: loading...
Sequence
MEFDFSGIIPSLPGLWNGMIMTLKLMALGVIGGIILGTILALMRLSHNKLLSNIAGAYVN
YFRSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQS
IPKGQMGAAQALGMEYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLN
ASRASGDIIGRSNEFLIFAGLTYFTISFAASLLVKRLQKRFAV
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:
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