Protein WP_011033509.1 in Methanosarcina mazei Go1
Annotation: NCBI__GCF_000007065.1:WP_011033509.1
Length: 353 amino acids
Source: GCF_000007065.1 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 |
|---|
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 95% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 95% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 95% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 95% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 33% | 82% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 79% | 169.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 79% | 169.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 79% | 169.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 79% | 169.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 31% | 94% | 168.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 32% | 95% | 166.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 32% | 95% | 166.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 31% | 98% | 165.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 87% | 158.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 36% | 98% | 157.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 30% | 95% | 115.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 30% | 95% | 115.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 30% | 95% | 115.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 30% | 95% | 115.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 33% | 220.3 |
Sequence Analysis Tools
View WP_011033509.1 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
MHIVELEEIYKNYGKLEVLKNINLQIEKGTSTALVGPTGSGKTVMLRLIDLLEKPSSGTV
YFEGADANESNNTRLEVRRQIGMVFQKPLAFKASVYDNIAYGLKIRGRKENMDGRIKELL
EMIGLPGYENRNALKLSGGETQRLALARAMITEPRLLLLDEPTANLDPISKKKLEELILK
INRESETTIIMTTHDLLQGQRLAENMVILYNGQILQSGTPDQIFRKPKNRFVADFVGIQN
LMSGIIEDSSNGLAAIKTDSITVFAVTEKEGKVHFAIRPDEITISREKVQTSARNTIQGK
VDEIIDTGSLIKLTVNTGELFTVFITRESLNELNISIGTSIWLYFKASAVHVF
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