Protein WP_012466358.1 in Chlorobium limicola DSM 245
Annotation: NCBI__GCF_000020465.1:WP_012466358.1
Length: 244 amino acids
Source: GCF_000020465.1 in NCBI
Candidate for 35 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-arginine catabolism | artP | med | AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) | 40% | 89% | 136.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 41% | 90% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 41% | 90% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-glutamate catabolism | gltL | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 41% | 90% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-lysine catabolism | hisP | med | ABC transporter for L-Lysine, ATPase component (characterized) | 40% | 91% | 133.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 39% | 67% | 158.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 67% | 139.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 38% | 92% | 136.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 63% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 63% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 63% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 63% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 63% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 63% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
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) | 32% | 71% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 55% | 112.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 31% | 62% | 109.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
trehalose catabolism | malK | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 31% | 62% | 109.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 36% | 91% | 107.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 36% | 91% | 107.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 31% | 97% | 105.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 31% | 97% | 105.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 31% | 97% | 105.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 94% | 97.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 94% | 97.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 94% | 97.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 31% | 55% | 94.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 31% | 91% | 91.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 189.5 |
Sequence Analysis Tools
View WP_012466358.1 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
MQDNSSGSVSHQAVLSIQDLSKTYIMGEVKVEALKHLSIEFFAGELVVLLGASGSGKSTL
LNIIGGLDLPSEGKLFFQGREITAATEAELTAYRRRSIGFVFQFYNLISSLSALENVQLV
TEIADNPMPADEALRLVGLSNRLNHFPAQLSGGEQQRVAIARAVAKKPELLLCDEPTGAL
DYQTGKLVLEVIEKVNRELGTTTIVITHNASIAGMADRVVRLGSGEVTEDRRNPERLTPA
ELVW
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