Protein WP_011384270.1 in Magnetospirillum magneticum AMB-1
Annotation: NCBI__GCF_000009985.1:WP_011384270.1
Length: 262 amino acids
Source: GCF_000009985.1 in NCBI
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-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 44% | 89% | 185.3 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 40% | 58% | 147.1 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 78% | 146.7 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 54% | 141 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 54% | 141 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 54% | 141 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 54% | 141 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 38% | 53% | 140.6 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 66% | 137.5 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 39% | 56% | 130.6 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 34% | 68% | 129.4 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 66% | 124.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 66% | 124.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 66% | 124.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 66% | 124.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 66% | 124.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 66% | 124.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 32% | 76% | 109 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 45% | 201.4 |
Sequence Analysis Tools
View WP_011384270.1 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
MDALAPVSPPVIRLEGLAFGYPGDRSHAIVLQDLDLEVRHGDFIALVGQSGAGKSTLLRV
IAGLVPAVLGQVYVEPPKEPDSRQIGMVFQDARLLPWRRVLANVEYGLEGLVKSRHERRR
RALAALDLVGLTEFADRWPHHLSGGQRQRVGLARALAVRPALLLMDEPFGALDPATRHGL
QDQLLSIWQATGTSIIFVTHDIDEATYLADRVIVLGGSPARILRQLDVEAPRPRCRNDLA
DDPTATALRSQLYETFFYKDGI
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