Protein WP_106712780.1 in Phyllobacterium brassicacearum STM 196
Annotation: NCBI__GCF_003010955.1:WP_106712780.1
Length: 308 amino acids
Source: GCF_003010955.1 in NCBI
Candidate for 12 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
N-acetyl-D-glucosamine catabolism | SMc02872 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized) | 31% | 88% | 136.3 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
D-glucosamine (chitosamine) catabolism | SMc02872 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized) | 31% | 88% | 136.3 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
D-maltose catabolism | aglF | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized) | 31% | 76% | 120.2 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
sucrose catabolism | aglF | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized) | 31% | 76% | 120.2 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
trehalose catabolism | aglF | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized) | 31% | 76% | 120.2 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
D-xylose catabolism | gtsB | lo | ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) | 31% | 88% | 118.2 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
D-cellobiose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 77% | 114.4 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
D-glucose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 77% | 114.4 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
lactose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 77% | 114.4 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
D-maltose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 77% | 114.4 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
sucrose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 77% | 114.4 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
trehalose catabolism | aglF' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 77% | 114.4 | Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR | 35% | 159.5 |
Sequence Analysis Tools
View WP_106712780.1 at NCBI
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
Fitness BLAST: loading...
Sequence
MSTSHRSGESPGFFAFAREHTFVTIFGIVMPLAVFAVFVGYPILFTIYLSLFEWNGMTPD
KTFVGLENYRHMIGDSHFQIALINNFKWLAVTLAFPVLAGLLIAYALRNKILPAPALVRT
IIFFPVTMSLISVGLMFLLILNPLFGAFDTILRSVGLGFLVTEWFGNYKVAIYTLAIVSG
WAFTGMPMIFYYAGLGDVPKETFDAARIEGAGHWRMLTKVAVPQLRPVTAVVVMLTLFES
LRAFDLVAVMTKGAPFGYTNVLGYIVYLESFWNTRFGYGAAISVAILAVSALMALIILKK
LMKGAFDV
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