Protein WP_008482959.1 in Gallaecimonas xiamenensis 3-C-1
Annotation: NCBI__GCF_000299915.1:WP_008482959.1
Length: 235 amino acids
Source: GCF_000299915.1 in NCBI
Candidate for 20 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 41% | 84% | 153.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 41% | 81% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-arginine catabolism | artP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 42% | 82% | 141 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 42% | 82% | 141 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 47% | 63% | 165.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 84% | 151 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 84% | 151 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-histidine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 40% | 84% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 37% | 90% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 63% | 129 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 38% | 53% | 127.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 76% | 125.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 52% | 123.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 54% | 122.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 54% | 122.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 60% | 119.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 60% | 119.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 55% | 118.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 74% | 114.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 34% | 55% | 110.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 53% | 236.9 |
Sequence Analysis Tools
View WP_008482959.1 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
MTDVICLEAIKKAFVMAGEPFWALRGIDLTIGRNDYLAIIGPSGSGKSTLLNILGCLDVP
SEGHYWLAGEDVATLPQSQLARVRNHQIGFIFQSFNLLPRASALDNVAQPLVYQGFSLKE
RRQRALEALAKVGLADRANHRPNQLSGGQRQRVAIARALVTRPSILLADEPTGNLDSQTT
RDIMALFDELHGEGQTIVVVTHEQDIANHCRRVVRVMDGVITSDSLVAGQESRLV
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