Protein WP_083836758.1 in Granulicella mallensis MP5ACTX8
Annotation: NCBI__GCF_000178955.2:WP_083836758.1
Length: 230 amino acids
Source: GCF_000178955.2 in NCBI
Candidate for 34 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) | 45% | 87% | 188.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 41% | 55% | 150.2 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 41% | 55% | 150.2 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 57% | 148.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 57% | 148.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 57% | 148.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 57% | 148.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 57% | 148.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 57% | 148.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 56% | 146.4 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 41% | 55% | 146.4 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 59% | 145.2 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 59% | 145.2 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 41% | 57% | 141.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 55% | 141.4 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 59% | 140.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 41% | 61% | 140.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 59% | 140.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 41% | 61% | 140.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 59% | 140.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 41% | 61% | 140.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 35% | 62% | 139.4 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 57% | 137.9 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 54% | 134.4 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 38% | 56% | 134 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| trehalose catabolism | malK | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 38% | 56% | 134 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 51% | 134 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 54% | 133.7 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 37% | 62% | 129.8 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 58% | 128.6 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| 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) | 35% | 52% | 127.5 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 55% | 124 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 32% | 57% | 97.4 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
| D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 31% | 82% | 85.9 | Nitrate import ATP-binding protein NrtD; EC 7.3.2.4 | 45% | 194.1 |
Sequence Analysis Tools
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Sequence
MDLTIREGEFIALLGPSGCGKSTILNLVAGLDEPSTGTVTVDGLPPRQLQTKQQLGIAFQ
EHALLPWRSVEGNLELPFQIAGRKPDREHIAGLIELVGLKGFESARPSQLSGGMRQRVSI
ARALCLAPKLLLLDEPFGALDAVTRRSMNLELQRIWQEKQITTILVTHTVEEALFLADRV
LVMSGRPGRIVREVQVPFPRPRTVETMRQELFHQLVDDLTLSLEPEYKEP
This GapMind analysis is from Sep 24 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