Protein WP_009778714.1 in Leeuwenhoekiella blandensis MED217
Annotation: NCBI__GCF_000152985.1:WP_009778714.1
Length: 234 amino acids
Source: GCF_000152985.1 in NCBI
Candidate for 25 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 39% | 86% | 151.8 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 83% | 149.8 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 83% | 149.8 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-glutamate catabolism | gltL | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 83% | 149.8 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 97% | 148.7 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 147.5 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 147.5 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 147.5 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 147.5 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 147.5 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 84% | 140.2 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 84% | 140.2 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 38% | 83% | 139.8 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 35% | 91% | 138.7 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 88% | 137.5 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 78% | 136.3 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 36% | 69% | 131 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 36% | 51% | 123.6 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 78% | 116.7 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 34% | 78% | 109.4 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 61% | 107.1 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 55% | 103.2 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 32% | 79% | 97.1 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 30% | 91% | 95.9 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 71% | 94.7 | As-48G, component of The enterocin AS-48 exporter, As-48FGH | 45% | 209.9 |
Sequence Analysis Tools
View WP_009778714.1 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
MIKITDLEKYYATEEVRTIALNKLSFQVQEGEFVAVMGPSGCGKSTLLNILGLLDDPDGG
SFIFNGIEVAGFNERKRADLRKHNIGFVFQSFNLIDELTVFENVELPLIYTGVKPAERKK
RVDEVLEKMQIMHRRKHFPQQLSGGQQQRVAVARAVVNNPKLILADEPTGNLDSSNGNEV
MDLLTELNEAGTTIIMVTHSEHDAKYSHRIIRMLDGQKVTENVLTEYKSKTLEV
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