Protein WP_002720243.1 in Cereibacter sphaeroides ATCC 17029
Annotation: NCBI__GCF_000015985.1:WP_002720243.1
Length: 332 amino acids
Source: GCF_000015985.1 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 |
|---|
| D-mannitol catabolism | mtlK | hi | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 100% | 100% | 657.9 | ABC transporter for D-Sorbitol, ATPase component | 74% | 482.3 |
| D-sorbitol (glucitol) catabolism | mtlK | hi | ABC transporter for D-Sorbitol, ATPase component (characterized) | 74% | 99% | 482.3 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 63% | 410.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 63% | 94% | 410.2 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 63% | 94% | 410.2 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-maltose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 56% | 97% | 370.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 56% | 97% | 370.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| trehalose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 56% | 97% | 370.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 54% | 100% | 347.8 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-cellobiose catabolism | msiK | med | 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) | 50% | 94% | 310.1 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 47% | 99% | 308.1 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 45% | 98% | 304.3 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 45% | 98% | 304.3 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 45% | 98% | 304.3 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 45% | 98% | 304.3 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 45% | 98% | 304.3 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 45% | 98% | 304.3 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 49% | 95% | 302.8 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 51% | 88% | 302.4 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| trehalose catabolism | malK | med | 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) | 45% | 99% | 296.6 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 46% | 96% | 291.2 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 45% | 96% | 283.9 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 46% | 83% | 266.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 50% | 81% | 263.8 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 55% | 63% | 276.6 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 99% | 219.5 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 39% | 90% | 217.2 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 98% | 193.7 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 100% | 657.9 |
Sequence Analysis Tools
View WP_002720243.1 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
MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI
TIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI
LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH
QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN
LIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPTLTVR
TGGEFGVHHGDRVWLTPQADKIHRFGADGKAL
This GapMind analysis is from Apr 10 2024. 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