Protein WP_081442759.1 in Allochromatium vinosum DSM 180
Annotation: NCBI__GCF_000025485.1:WP_081442759.1
Length: 253 amino acids
Source: GCF_000025485.1 in NCBI
Candidate for 37 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) | 43% | 89% | 156.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 43% | 89% | 156.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 40% | 88% | 145.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 42% | 88% | 144.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 40% | 84% | 131.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 59% | 137.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 63% | 134.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 63% | 134.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 37% | 56% | 134 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 88% | 132.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 88% | 132.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 58% | 132.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 57% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 57% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 57% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 57% | 131 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 40% | 52% | 129.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 76% | 129 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| 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) | 33% | 68% | 129 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 61% | 124 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| 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) | 32% | 91% | 115.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 90% | 103.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 90% | 103.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 90% | 103.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 90% | 103.2 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 96.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 96.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-phenylalanine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 96.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 96.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 96.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 96.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 46% | 187.2 |
Sequence Analysis Tools
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
MSGSRGSAPRPIQGHDTESSAPVFQARGLTKIYVMGEVRVEALRGVDLDLYPGELVVLLG
PSGSGKSTLLNILGGLDSPTGGQVIAAGRDLTQAGERELTRFRRQVVGFVFQFYNLIPSL
TARENVAIVTEIAEDPMTPEAALDLVGLGARLDHFPAQLSGGEQQRVAIARAIAKRPRVL
LCDEPTGALDSTTGVRVLEVLERVNRELGTTTAVITHNAAIAAMADRVILMADGRIQSVR
TNPGRVAPREIHW
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