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:
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