Protein HSERO_RS01355 in Herbaspirillum seropedicae SmR1
Annotation: FitnessBrowser__HerbieS:HSERO_RS01355
Length: 381 amino acids
Source: HerbieS in FitnessBrowser
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 53% | 98% | 381.3 | ABC transporter for D-Sorbitol, ATPase component | 54% | 379.4 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 54% | 99% | 379.4 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-mannitol catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 51% | 98% | 365.5 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 53% | 99% | 363.2 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 53% | 99% | 363.2 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 53% | 99% | 363.2 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 53% | 99% | 363.2 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 54% | 99% | 356.7 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 97% | 345.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 97% | 345.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 97% | 345.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 97% | 345.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 97% | 345.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 97% | 345.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 51% | 94% | 344 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 50% | 99% | 325.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 50% | 99% | 325.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 48% | 100% | 309.3 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| D-maltose catabolism | malK_Sm | med | 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) | 47% | 98% | 308.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| trehalose catabolism | malK | med | 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) | 47% | 98% | 308.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 44% | 99% | 293.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 44% | 96% | 270.8 | Maltose-transporting ATPase (EC 3.6.3.19) | 53% | 381.3 |
Sequence Analysis Tools
View HSERO_RS01355 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD
LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR
ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL
HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA
GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG
SQGQYGIHREVVLVERLGEQTYVHLDEPAGQPLVAKAAGDARITRGERVRVAIAPACAYL
FDQDGLALTRTQVQGGLAVAA
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