Protein WP_007154870.1 in Marinobacter algicola DG893
Annotation: NCBI__GCF_000170835.1:WP_007154870.1
Length: 224 amino acids
Source: GCF_000170835.1 in NCBI
Candidate for 23 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-lysine catabolism | hisM | lo | ABC transporter for L-Lysine, permease component 2 (characterized) | 35% | 97% | 127.5 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-asparagine catabolism | natH | lo | Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) | 35% | 55% | 125.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-aspartate catabolism | natH | lo | Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) | 35% | 55% | 125.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-histidine catabolism | Ac3H11_2554 | lo | ABC transporter for L-Histidine, permease component 1 (characterized) | 34% | 92% | 123.2 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-arginine catabolism | artM | lo | Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 32% | 98% | 120.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-histidine catabolism | hisM | lo | Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 32% | 98% | 120.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-asparagine catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 32% | 80% | 118.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-aspartate catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 32% | 80% | 118.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-glutamate catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 32% | 80% | 118.6 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| D-alanine catabolism | Pf6N2E2_5404 | lo | ABC transporter for D-Alanine, permease component 1 (characterized) | 31% | 58% | 116.7 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-citrulline catabolism | AO353_03045 | lo | ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) | 33% | 91% | 114.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| 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) | 31% | 56% | 112.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| 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) | 31% | 56% | 112.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| 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) | 31% | 56% | 112.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-histidine 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) | 31% | 56% | 112.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| 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) | 31% | 56% | 112.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| 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) | 31% | 56% | 112.8 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-histidine catabolism | BPHYT_RS24010 | lo | Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) | 30% | 89% | 105.1 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-arginine catabolism | artQ | lo | ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) | 31% | 96% | 101.7 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-citrulline catabolism | AO353_03050 | lo | ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) | 31% | 96% | 101.7 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| D-glucosamine (chitosamine) catabolism | AO353_21720 | lo | ABC transporter for D-glucosamine, permease component 2 (characterized) | 32% | 85% | 100.5 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-citrulline catabolism | PS417_17600 | lo | ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) | 33% | 88% | 94 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
| L-glutamate catabolism | gluC | lo | GluC aka CGL1952, component of Glutamate porter (characterized) | 30% | 96% | 89 | Probable amino-acid permease protein YxeN | 46% | 198.0 |
Sequence Analysis Tools
View WP_007154870.1 at NCBI
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
MDVLNVEYMLGLVPVLLGYLPLTLQLAGVGMVLALILACLFAVVRVLRIPVLNQLTIVFI
SFFRGTPLLVQLFLFYYGLPQLVSALTVIDGITATIMGLTMHFSAYMAESIRAAIVGVDR
SQTEAALSIGMTNGQLMRRIVLPQATRVALPTLMNYFIDMIKATSLAFTLGVTELMGATQ
KEAAGSFLYFEAFIVAAIMYWIVVEMLSKLQHYLEIRLNKAYSR
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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