Protein YP_004141675.1 in Mesorhizobium ciceri WSM1271
Annotation: NCBI__GCF_000185905.1:YP_004141675.1
Length: 311 amino acids
Source: GCF_000185905.1 in NCBI
Candidate for 13 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 | ngcF | med | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 32% | 99% | 180.3 | TogM, component of Saturated and unsaturated oligogalacturonide transporter, TogMNAB (transports di- to tetrasaccharide pectin degradation products which consist of D-galacuronate, sometimes with 4-deoxy-L-threo-5-hexosulose uronate at the reducing end of the oligosaccharide) (Hugouvieux-Cotte-Pattat et al. 2001). Regulated by pectin utilization regulator KdgR | 38% | 169.5 |
| D-glucosamine (chitosamine) catabolism | ngcF | med | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 32% | 99% | 180.3 | TogM, component of Saturated and unsaturated oligogalacturonide transporter, TogMNAB (transports di- to tetrasaccharide pectin degradation products which consist of D-galacuronate, sometimes with 4-deoxy-L-threo-5-hexosulose uronate at the reducing end of the oligosaccharide) (Hugouvieux-Cotte-Pattat et al. 2001). Regulated by pectin utilization regulator KdgR | 38% | 169.5 |
| sucrose catabolism | thuF | lo | ABC transporter permease (characterized, see rationale) | 34% | 91% | 171.8 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| lactose catabolism | lacF | lo | ABC transporter for Lactose, permease component 1 (characterized) | 35% | 100% | 167.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| 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) | 33% | 99% | 159.8 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| D-cellobiose catabolism | gtsB | lo | ABC transporter permease (characterized, see rationale) | 32% | 90% | 140.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| D-glucose catabolism | gtsB | lo | ABC transporter permease (characterized, see rationale) | 32% | 90% | 140.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| lactose catabolism | gtsB | lo | ABC transporter permease (characterized, see rationale) | 32% | 90% | 140.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| D-maltose catabolism | gtsB | lo | ABC transporter permease (characterized, see rationale) | 32% | 90% | 140.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| sucrose catabolism | gtsB | lo | ABC transporter permease (characterized, see rationale) | 32% | 90% | 140.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| trehalose catabolism | gtsB | lo | ABC transporter permease (characterized, see rationale) | 32% | 90% | 140.2 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| D-cellobiose catabolism | msdB1 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 30% | 87% | 139.8 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
| D-maltose catabolism | musF | lo | ABC-type sugar transport system, permease component, component of Maltose transporter, MusEFGKI (characterized) | 31% | 91% | 134 | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 180.3 |
Sequence Analysis Tools
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
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Sequence
MSTRPQEAAPVSSRSGTWRFDAGDGATAFVMILPAAILFGLFYLWPFVNGFWLSLHNWDG
FSDPTWAGFSNYMRLAHDRTFLGALRNNLIFVVAVVVLKNALGLGLALLLNRALLGRAFF
RAAAFIPVTMSFVAVGLLWSWIYNPVFGLLNSGLDLIGLAGLKRSWLGDADIALYSIIVV
DVWKWLGFHAVIYLAGLQTIPSELYESAKMDGAGPLQRFRHVTVPMMTPIIFINTILGLS
GAFVRNFDIVYVLTKGGPNHATEVVLTYMMSKAFQDGAMSYAAAIGYVLFMIVGLASVGL
LALMRRQRLDV
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