Protein YP_426349.1 in Rhodospirillum rubrum ATCC 11170
Annotation: NCBI__GCF_000013085.1:YP_426349.1
Length: 298 amino acids
Source: GCF_000013085.1 in NCBI
Candidate for 17 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuF | med | Trehalose/maltose transport system permease protein MalF (characterized) | 36% | 98% | 186.4 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 34% | 181.0 |
| trehalose catabolism | thuF | med | Trehalose/maltose transport system permease protein MalF (characterized) | 36% | 98% | 186.4 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 34% | 181.0 |
| D-glucosamine (chitosamine) catabolism | SM_b21220 | lo | ABC transporter for D-Glucosamine, permease component 2 (characterized) | 35% | 96% | 164.1 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| D-mannitol catabolism | mtlF | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 2 (characterized) | 35% | 93% | 163.7 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| D-sorbitol (glucitol) catabolism | mtlF | lo | MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 34% | 94% | 161.4 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| L-fucose catabolism | SM_b21104 | lo | ABC transporter for L-Fucose, permease component 1 (characterized) | 32% | 94% | 160.2 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| sucrose 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) | 36% | 92% | 159.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| glycerol catabolism | glpP | lo | ABC transporter for Glycerol, permease component 1 (characterized) | 30% | 96% | 144.4 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| xylitol catabolism | Dshi_0548 | lo | ABC transporter for Xylitol, permease component 1 (characterized) | 33% | 94% | 144.4 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| xylitol catabolism | HSERO_RS17005 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 30% | 94% | 135.2 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| D-cellobiose catabolism | gtsB | lo | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 31% | 95% | 127.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| D-glucose catabolism | gtsB | lo | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 31% | 95% | 127.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| lactose catabolism | gtsB | lo | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 31% | 95% | 127.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| D-maltose catabolism | gtsB | lo | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 31% | 95% | 127.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| sucrose catabolism | gtsB | lo | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 31% | 95% | 127.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| trehalose catabolism | gtsB | lo | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 31% | 95% | 127.5 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
| trehalose catabolism | treT | lo | TreT, component of Trehalose porter (characterized) | 31% | 93% | 110.2 | Trehalose/maltose transport system permease protein MalF | 36% | 186.4 |
Sequence Analysis Tools
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
MSGAADRPMTALERADRRFGWFLTLPGVLMLAATIAFPLLWAVATSLFDFTLIAPTYDTF
VGLDNYALALGNTEFLHASWLTVGFVVAVVLIEFAIGFLIALMLNGVRRGKPIYYAILLC
PLLINPVVVGLVWRMVLHPTLGVANYALGLIGLSPVNWLGDVTVAFWTLVGVDIWHQVSF
MIVLLLAGLSALPAEPYEAARVDGASVFQRFWHITLPLMRRVILVTLLIRMIFAVKTYDL
VYIMTRGGPGTATDLVSYSIYRTAFVGLNLGQATAMAGLLLIPVLGITAYLYRLMRKA
This GapMind analysis is from Sep 24 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