Protein WP_054557366.1 in Croceitalea dokdonensis DOKDO 023
Annotation: NCBI__GCF_001306415.1:WP_054557366.1
Length: 228 amino acids
Source: GCF_001306415.1 in NCBI
Candidate for 36 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 38% | 64% | 149.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 90% | 144.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 90% | 144.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 90% | 144.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 37% | 84% | 144.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 37% | 92% | 143.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 40% | 85% | 142.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 40% | 85% | 142.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 83% | 138.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 83% | 138.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 36% | 84% | 138.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 36% | 85% | 137.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 61% | 133.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 61% | 133.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 61% | 133.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 61% | 133.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 61% | 133.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 61% | 133.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 36% | 50% | 127.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 58% | 126.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 37% | 61% | 126.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 35% | 66% | 125.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 36% | 57% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 73% | 120.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 73% | 119.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 33% | 56% | 117.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 33% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
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) | 31% | 91% | 114 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
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) | 31% | 91% | 114 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
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) | 31% | 91% | 114 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 54% | 104.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
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) | 30% | 87% | 102.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 206.8 |
Sequence Analysis Tools
View WP_054557366.1 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
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Sequence
MSKILNVTQLGKTYASGNKTLTVLEDVSFSIDTGETFAIVGPSGSGKTTLLGLCAGLDQT
DQGTVHLCGVALNELNEDERALLRNREVGFIFQNFQLLPTLTALENVAVPLELQGQKNTH
GIAAELLEKVGLQDRKHHYPSQLSGGEQQRVALARAFSSTPSILFADEPTGNLDSETGQK
VVELLFDLNKEAGTTLVIVTHDMELAQKTQRILKLKGGKVVTEENQKL
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