Protein N515DRAFT_3134 in Dyella japonica UNC79MFTsu3.2
Annotation: FitnessBrowser__Dyella79:N515DRAFT_3134
Length: 292 amino acids
Source: Dyella79 in FitnessBrowser
Candidate for 24 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| lactose catabolism | lacF | lo | LacF, component of Lactose porter (characterized) | 37% | 94% | 186 | transmembrane permease MsmF | 35% | 193.0 |
| 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) | 36% | 93% | 179.1 | transmembrane permease MsmF | 35% | 193.0 |
| xylitol catabolism | Dshi_0548 | lo | ABC transporter for Xylitol, permease component 1 (characterized) | 35% | 97% | 177.2 | transmembrane permease MsmF | 35% | 193.0 |
| sucrose catabolism | thuF | lo | ABC transporter permease (characterized, see rationale) | 35% | 90% | 170.2 | transmembrane permease MsmF | 35% | 193.0 |
| D-maltose catabolism | thuF | lo | Trehalose/maltose transport system permease protein MalF (characterized) | 36% | 94% | 169.5 | transmembrane permease MsmF | 35% | 193.0 |
| trehalose catabolism | thuF | lo | Trehalose/maltose transport system permease protein MalF (characterized) | 36% | 94% | 169.5 | transmembrane permease MsmF | 35% | 193.0 |
| D-glucosamine (chitosamine) catabolism | SM_b21220 | lo | ABC transporter for D-Glucosamine, permease component 2 (characterized) | 35% | 96% | 161.4 | transmembrane permease MsmF | 35% | 193.0 |
| D-cellobiose catabolism | msdC1 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 31% | 97% | 148.3 | transmembrane permease MsmF | 35% | 193.0 |
| N-acetyl-D-glucosamine catabolism | ngcF | lo | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 32% | 98% | 144.1 | transmembrane permease MsmF | 35% | 193.0 |
| D-glucosamine (chitosamine) catabolism | ngcF | lo | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 32% | 98% | 144.1 | transmembrane permease MsmF | 35% | 193.0 |
| D-maltose catabolism | malF_Aa | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 33% | 92% | 137.9 | transmembrane permease MsmF | 35% | 193.0 |
| D-cellobiose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| D-glucose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| lactose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| D-maltose catabolism | aglF | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| D-maltose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| sucrose catabolism | aglF | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| sucrose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| trehalose catabolism | aglF | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| trehalose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 82% | 134.8 | transmembrane permease MsmF | 35% | 193.0 |
| L-fucose catabolism | SM_b21104 | lo | ABC transporter for L-Fucose, permease component 1 (characterized) | 32% | 93% | 133.7 | transmembrane permease MsmF | 35% | 193.0 |
| L-arabinose catabolism | xacH | lo | Xylose/arabinose import permease protein XacH (characterized, see rationale) | 31% | 87% | 126.3 | transmembrane permease MsmF | 35% | 193.0 |
| D-maltose catabolism | musF | lo | ABC-type sugar transport system, permease component, component of Maltose transporter, MusEFGKI (characterized) | 31% | 94% | 120.6 | transmembrane permease MsmF | 35% | 193.0 |
| D-cellobiose catabolism | cebG | lo | CBP protein aka CebG, 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% | 55% | 55.1 | transmembrane permease MsmF | 35% | 193.0 |
Sequence Analysis Tools
View N515DRAFT_3134 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MNPQRAAWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELL
HRPLFWSALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAV
AVIWRYLFNTKYGLANYALGGLGIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAAL
QAIPADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGP
LQSTTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLRVARRGGEA
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