Protein 642683972 in Chlorobium phaeobacteroides BS1
Annotation: IMG__ChlphaBS1_FD:642683972
Length: 244 amino acids
Source: ChlphaBS1_FD in IMG
Candidate for 39 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 78% | 144.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 78% | 144.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-asparagine catabolism | aapP | med | 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) | 41% | 81% | 142.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-aspartate catabolism | aapP | med | 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) | 41% | 81% | 142.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-glutamate catabolism | aapP | med | 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) | 41% | 81% | 142.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-histidine catabolism | aapP | med | 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) | 41% | 81% | 142.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-leucine catabolism | aapP | med | 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) | 41% | 81% | 142.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-proline catabolism | aapP | med | 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) | 41% | 81% | 142.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 64% | 150.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 63% | 144.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 84% | 144.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 84% | 144.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 38% | 90% | 142.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 37% | 87% | 136.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-lysine catabolism | hisP | lo | ABC transporter for L-Lysine, ATPase component (characterized) | 37% | 89% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 38% | 92% | 136 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 89% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 89% | 135.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 132.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 132.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 132.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 60% | 132.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-arginine catabolism | artP | lo | L-Arginine ABC transporter, ATPase component (characterized) | 37% | 92% | 129 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 36% | 92% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 37% | 89% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 56% | 116.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 42% | 188.7 |
Sequence Analysis Tools
View 642683972 at IMG
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
MMDAFMEHETDSPVLRVDRVSKIYTMGEVEVHALKHVSVDFYAGELVVLLGTSGSGKSTL
LNIIGGLDVPSEGKLYFHSQEMTAASEAEMTAYRRESIGFVFQFYNLISSLTALENIQLV
TEISTQPMPAEEALRRVNLGDRMNHFPSQLSGGEQQRVAIARAVSKRPELLLCDEPTGAL
DYETGKLVLDVIRKVNEELGTTTLVITHNVSIAAMADRVIHMRSGEITEIERNERKLSPS
ELSW
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