Protein HSERO_RS16725 in Herbaspirillum seropedicae SmR1
Annotation: FitnessBrowser__HerbieS:HSERO_RS16725
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
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
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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:
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