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:
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