Protein N515DRAFT_1821 in Dyella japonica UNC79MFTsu3.2
Annotation: FitnessBrowser__Dyella79:N515DRAFT_1821
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
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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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:
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