Protein WP_028997004.1 in Azohydromonas australica DSM 1124
Annotation: NCBI__GCF_000430725.1:WP_028997004.1
Length: 354 amino acids
Source: GCF_000430725.1 in NCBI
Candidate for 21 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 44% | 70% | 218.4 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 42% | 73% | 215.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| putrescine catabolism | potA | med | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 42% | 75% | 213 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 41% | 73% | 206.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 37% | 90% | 222.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 39% | 97% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 46% | 64% | 218 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 78% | 194.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 69% | 193 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 69% | 193 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 69% | 193 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 69% | 193 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 39% | 61% | 175.3 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 39% | 59% | 169.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 37% | 91% | 167.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 37% | 91% | 167.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 91% | 158.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 91% | 158.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 36% | 79% | 135.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 35% | 98% | 132.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 35% | 80% | 127.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 336.7 |
Sequence Analysis Tools
View WP_028997004.1 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
Fitness BLAST: loading...
Sequence
MSIEVKNLVKRFGSLAVCDNLNLTINSGELVALLGPSGSGKTTLLRIIAGLEKPDSGSVL
FHGDDATRTAVRDRNVGFVFQHYALFPQMNIFENVAFGLRVRPRATRPSEAQIRAKVMEL
LKLVQLDWLAERYPHQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLR
RLHDEMHVTSVFVTHDQEEAMEVADRIVVMNQGRIEQDGRPDEVYDHPATPFVLQFLGDV
NLFHGRTGHHGAAREGEVTMTYVRPHELQILGEARPGALPGRLQQALTVGPNTRLEFRRL
DDESYIDVELPRAEYLALREQLKLEPGSQAWLLPRRVTRFVERAEEPEDPAAMI
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