Protein WP_083441151.1 in Nitriliruptor alkaliphilus DSM 45188
Annotation: NCBI__GCF_000969705.1:WP_083441151.1
Length: 303 amino acids
Source: GCF_000969705.1 in NCBI
Candidate for 19 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 | SMc02871 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) | 39% | 96% | 177.9 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-glucosamine (chitosamine) catabolism | SMc02871 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) | 39% | 96% | 177.9 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| 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) | 36% | 99% | 171.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| trehalose catabolism | thuG | lo | ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) | 34% | 99% | 169.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-maltose catabolism | malG_Bb | lo | ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) | 32% | 94% | 162.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| lactose catabolism | lacG | lo | ABC transporter for Lactose, permease component 2 (characterized) | 31% | 96% | 156.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-cellobiose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-glucose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| lactose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-maltose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-mannose catabolism | TT_C0326 | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| sucrose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| trehalose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 35% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-cellobiose catabolism | msdC2 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 34% | 91% | 146.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-maltose catabolism | thuG | lo | Trehalose/maltose transport system permease protein MalG (characterized) | 33% | 98% | 144.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-cellobiose catabolism | SMc04257 | lo | ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) | 32% | 97% | 136 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| D-maltose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 35% | 61% | 134.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| sucrose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 35% | 61% | 134.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
| trehalose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 35% | 61% | 134.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 44% | 227.6 |
Sequence Analysis Tools
View WP_083441151.1 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
MAVGQVTSAPRRTQRAGSRPSRNNGWTSTTGKRPSTGAVVRATILTAGALLTLVPIVWAV
LSSLKSPEELAQRPPTLFPRDLTLGNYTEALTSFDFPLYFFNSTFVTVVATLLTLAVNSM
AAWALAKYNFRGRDTLFVITLATIMIPLQVIFLPVYQVVASLGLVNTLWGMIIPAAATPT
GVFLLRQYMLSLPDELIEAARIDGAGEWRIFLQIILPLCRPALAVLAIFSVIWRWNDFLW
PLIVAQDESVYTLPVALARFSGQLVVPFHLVLAMSVLSIVPVVVIFLLLQRQIVAGVAQT
GLK
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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