Protein N515DRAFT_1821 in Dyella japonica UNC79MFTsu3.2
Annotation: N515DRAFT_1821 putative ABC transport system ATP-binding protein
Length: 238 amino acids
Source: Dyella79 in FitnessBrowser
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-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 42% | 92% | 169.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 86% | 154.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 86% | 154.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 87% | 154.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 87% | 154.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 39% | 70% | 154.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 37% | 90% | 153.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-asparagine catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 37% | 90% | 152.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-aspartate catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 37% | 90% | 152.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 93% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 39% | 59% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 36% | 52% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| 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) | 38% | 54% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 35% | 70% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 34% | 61% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 64% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 64% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 37% | 54% | 130.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 37% | 56% | 122.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 33% | 61% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 33% | 61% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 33% | 61% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
| 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) | 32% | 72% | 94.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 46% | 208.8 |
Sequence Analysis Tools
View N515DRAFT_1821 at FitnessBrowser
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
MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGG
EYHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQ
RIMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGV
MELLEEIHREGATIVMVTHDPELATRAQRNVHVIDGQVVDLAEDPRFHQQQARAGAPA
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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