Protein WP_013645061.1 in Methanobacterium lacus AL-21
Annotation: NCBI__GCF_000191585.1:WP_013645061.1
Length: 323 amino acids
Source: GCF_000191585.1 in NCBI
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | msiK | lo | MsiK protein, 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% | 55% | 137.1 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 93% | 136.3 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 93% | 136.3 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 32% | 68% | 136.3 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-valine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 93% | 136.3 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 33% | 56% | 133.7 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| 2'-deoxyinosine catabolism | nupA | lo | RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) | 31% | 63% | 130.2 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 127.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 127.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 127.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 127.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-alanine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 92% | 124.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-isoleucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 92% | 124.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-leucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 92% | 124.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-serine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 92% | 124.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-threonine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 92% | 124.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-valine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 92% | 124.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
| L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 33% | 97% | 117.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 38% | 215.3 |
Sequence Analysis Tools
View WP_013645061.1 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
MTKYALELNNLSKKYGDFTAVDDLSLQVKEGEIFGFLGPNGAGKSTTIRMLCTLALPTSG
SAKIAGYDLSKDSGKVRENIGLVAEKLIMYDGLTAGQNLRFFGKLYGIPKKKLEKRIDEL
LELIDMKKWKDTKINTFSTGMKQRINIIRALLAEPKIIFMDEPTLGLDPQTTFSVREIIR
DINSKGVTVILTTHAMVEAEALSDRVAIIDHGKIAALDTPENLKKMLSDTDITIFKMEIT
NLTVEMIENIKSLDVVTALSKQDEHNIKISAKGPDSLEEIIDTIRFDGGKISSIANINDA
TLEDVFLTVTGKEIRDTPAANSS
This GapMind analysis is from Apr 09 2024. 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