Protein WP_012279101.1 in Shewanella halifaxensis HAW-EB4
Annotation: NCBI__GCF_000019185.1:WP_012279101.1
Length: 424 amino acids
Source: GCF_000019185.1 in NCBI
Candidate for 44 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | opuBA | med | 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) | 49% | 98% | 359 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 63% | 95% | 344.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-proline catabolism | proV | med | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 45% | 97% | 330.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 60% | 95% | 321.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 40% | 82% | 148.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 40% | 82% | 148.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-glutamate catabolism | gltL | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 40% | 82% | 148.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 42% | 68% | 181.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 35% | 62% | 174.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 35% | 79% | 167.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 85% | 163.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 85% | 163.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 39% | 97% | 162.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 38% | 95% | 159.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 75% | 158.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 39% | 86% | 157.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 69% | 157.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 100% | 157.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 34% | 75% | 156.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 94% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 94% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-asparagine catabolism | aapP | lo | 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) | 38% | 87% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-aspartate catabolism | aapP | lo | 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) | 38% | 87% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-glutamate catabolism | aapP | lo | 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) | 38% | 87% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-leucine catabolism | aapP | lo | 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) | 38% | 87% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-proline catabolism | aapP | lo | 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) | 38% | 87% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| 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) | 39% | 56% | 154.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 36% | 65% | 152.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 37% | 92% | 150.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 34% | 92% | 147.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 71% | 147.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 146.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 34% | 98% | 145.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 34% | 65% | 145.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 93% | 144.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 35% | 97% | 138.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| 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% | 77% | 137.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
| 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% | 78% | 130.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 369.8 |
Sequence Analysis Tools
View WP_012279101.1 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
MTNDAQIQPLIQIRDLFKVFGSKPNTVMPLVREGLSKDEILAKTGHTVGLKAINLDIKKG
EIFVIMGLSGSGKSTLIRHFNRLIDPTEGQILVEGLDVMKLNTKQLEQFRRSKMAMVFQR
FGLMPHRTVLENVGYGLSVQGVDKAARNAKAKQWLETVGLSGYEAQYPSQLSGGQQQRVG
LARALCTDAEILLMDEAFSALDPLIRSEMQDQLIELQKELHKTIIFITHDLDEALRIGDR
IAILKDGELVQVGEPVDILLNPADDYVEAFVKDVNRPRALTVETVMKPPAFRLTADTIGE
ALKQMKRIPANYAYYVTDEGFQGLVCQEALEDAVKADEQALMEDFEVEPLTPISQDALLE
SIIPATMESDYPLPVVDADGDLQGELSRTHLAGVLSDFYSDDADSTDKINSTDLQKSNLT
NKDK
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