Protein N515DRAFT_2043 in Dyella japonica UNC79MFTsu3.2
Annotation: FitnessBrowser__Dyella79:N515DRAFT_2043
Length: 230 amino acids
Source: Dyella79 in FitnessBrowser
Candidate for 25 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 | med | Arginine transport ATP-binding protein ArtM (characterized) | 40% | 91% | 143.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 40% | 86% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 62% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 62% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 62% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 62% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 62% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 62% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| L-histidine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 39% | 89% | 136 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| L-lysine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 39% | 89% | 136 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| trehalose catabolism | thuK | lo | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 36% | 54% | 135.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 38% | 52% | 134.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 56% | 133.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 58% | 132.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 52% | 132.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 35% | 58% | 129.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 37% | 53% | 127.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 33% | 57% | 125.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 35% | 60% | 125.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 60% | 124.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 34% | 58% | 121.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 53% | 121.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| 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) | 33% | 55% | 116.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 31% | 55% | 115.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 88% | 110.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 200.7 |
Sequence Analysis Tools
View N515DRAFT_2043 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MSMGTLIEVRDLSKVYERGKQKVEVLHHINLNIAEGDFLALMGPSGSGKTTLLNLIGGLD
SPTGGSIGVGGQRIDQLGAGALAKWRAANVGFVFQFYNLMPMLTAQRNVELPLLLTKLSA
AQRRKNAAIALQLVGLDERSSHKPSELSGGQQQRVAIARAIVSDPTLLVCDEPTGDLDRQ
SAEDVLGLLRTLNREHGKTIVMVTHDPKAAEYANHTLHLDKGTLVEQALA
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