Protein HSERO_RS16725 in Herbaspirillum seropedicae SmR1
Annotation: HSERO_RS16725 ABC transporter permease
Length: 299 amino acids
Source: HerbieS in FitnessBrowser
Candidate for 13 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-glucosamine (chitosamine) catabolism | SM_b21220 | med | ABC transporter for D-Glucosamine, permease component 2 (characterized) | 33% | 95% | 174.9 | ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR | 35% | 171.4 |
| trehalose catabolism | thuF | lo | ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) | 35% | 92% | 171.4 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| sucrose catabolism | thuF | lo | ABC transporter permease (characterized, see rationale) | 33% | 89% | 165.6 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-maltose catabolism | thuF | lo | Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 33% | 96% | 164.5 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-maltose catabolism | malF_Aa | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 32% | 87% | 139 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-cellobiose catabolism | msdB1 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 30% | 89% | 134.8 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| L-fucose catabolism | SM_b21104 | lo | ABC transporter for L-Fucose, permease component 1 (characterized) | 32% | 92% | 132.5 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| lactose catabolism | lacF | lo | ABC transporter for Lactose, permease component 1 (characterized) | 33% | 95% | 131.7 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-cellobiose catabolism | cebF | lo | CBP protein aka CebF, 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) | 31% | 89% | 117.1 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-mannitol catabolism | mtlF | lo | SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) | 31% | 94% | 110.2 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-sorbitol (glucitol) catabolism | mtlF | lo | SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) | 31% | 94% | 110.2 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-maltose catabolism | malF | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 32% | 51% | 102.4 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
| D-maltose catabolism | malG | lo | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) | 36% | 55% | 70.5 | ABC transporter for D-Glucosamine, permease component 2 | 33% | 174.9 |
Sequence Analysis Tools
View HSERO_RS16725 at FitnessBrowser
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the SEED with FIGfam search
Fitness BLAST: loading...
Sequence
MLSRFLNNRNVLGMLFMAPAVILLVVFLTYPLGLGIWLGFTDTKIGGEGSFIGLDNFTYL
AGDSLAQLSLFNTVFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALS
ALAFWWLYDAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLA
GLQTISPSLYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRG
GPLNATHLMATLSFQRAIPGGALGEGAALATYMIPFLLAAIMFSYFGLQRRGWQQGGDK
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