Protein GFF3990 in Pseudomonas stutzeri RCH2
Annotation: FitnessBrowser__psRCH2:GFF3990
Length: 334 amino acids
Source: psRCH2 in FitnessBrowser
Candidate for 27 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-glucose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| lactose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-maltose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| sucrose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| trehalose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 84% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 42% | 87% | 222.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 42% | 87% | 222.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 39% | 99% | 233 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 40% | 84% | 229.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 47% | 67% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 94% | 219.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 94% | 219.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 38% | 99% | 213 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 42% | 68% | 211.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 44% | 64% | 209.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 41% | 67% | 183.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 41% | 67% | 183.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 41% | 67% | 183.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 41% | 67% | 183.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 36% | 63% | 172.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 89% | 170.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 36% | 87% | 157.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 39% | 77% | 136.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 35% | 96% | 127.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 34% | 88% | 112.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 68% | 331.3 |
Sequence Analysis Tools
View GFF3990 at FitnessBrowser
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
MSIEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIV
FHGEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHEL
LGLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLA
RLHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGDA
NRLQLDDQRSVLFRPHEVALSREAVAEHLAGEVRDIRPLGALTRVTLKVAGQAEPIEAEV
GNDHASLVGVQRGATLYFQPKGQAVRPAAAQQTG
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