Protein WP_017730867.1 in Nafulsella turpanensis ZLM-10
Annotation: NCBI__GCF_000346615.1:WP_017730867.1
Length: 225 amino acids
Source: GCF_000346615.1 in NCBI
Candidate for 23 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | lo | AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) | 37% | 87% | 140.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| 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) | 38% | 50% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 87% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 85% | 133.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| 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) | 35% | 81% | 128.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 57% | 127.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| 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) | 35% | 68% | 127.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| 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) | 36% | 51% | 123.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 53% | 123.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 34% | 54% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 34% | 56% | 115.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| 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% | 76% | 113.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 55% | 110.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 32% | 55% | 103.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
| D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 30% | 71% | 100.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 214.2 |
Sequence Analysis Tools
View WP_017730867.1 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
MIKITNLVKVYRTEEMQTTALNQLNLEVKEGEFVAVMGPSGCGKSTLLNILGLLDDPDSG
SFLFNGIEVANFNERQRSSLRKQHIGFVFQSFNLIDELSVFENVELPLIYLGVKESERRK
RVEEVLDKMQIMHRQKHFPQQLSGGQQQRVAVARAVVNKPHLILADEPTGNLDSSNGNEV
MELLTDLNEQGTTIVMVTHSEHDARYSHRIVRMLDGQTVLTDIMV
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