Protein WP_024329178.1 in Thioalkalivibrio halophilus HL17
Annotation: NCBI__GCF_001995255.1:WP_024329178.1
Length: 286 amino acids
Source: GCF_001995255.1 in NCBI
Candidate for 32 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 41% | 95% | 180.3 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 57% | 160.6 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 42% | 61% | 156.8 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 58% | 150.6 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 34% | 78% | 148.7 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 52% | 147.5 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 55% | 139.4 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 55% | 139.4 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 42% | 52% | 138.3 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 41% | 53% | 137.1 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 79% | 132.5 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 52% | 131 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 66% | 128.6 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 37% | 74% | 115.5 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 31% | 97% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 31% | 97% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 31% | 97% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 31% | 97% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 31% | 97% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| 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) | 31% | 97% | 100.9 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 31% | 90% | 89.7 | Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 | 41% | 196.1 |
Sequence Analysis Tools
View WP_024329178.1 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
MGAAISIDYITHHYPKQTDPTLQDIELTVSPGETIALIGQSGCGKSTLLHMLAGLLIPSE
GAVRINGHQVIKPSPRWNMMFQKPSLYPWMTVRRNASLGLIFQGRQEGMNKRVDALLETV
GLAEKAEVNVQSLSGGQQQRVALARSLATDPELLLLDEPFSALDAFTKTELQDEVVRLSR
DRGITVVFVTHDIEEAVAMADRVVVMGSNPGTLQHQLKVDLPHPRDRTSPGFTELKAELM
EFFGATRHPASRPEPTDDTSSSAEAPEADDPAASGSAPARRAIRAA
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