Protein Echvi_2204 in Echinicola vietnamensis KMM 6221, DSM 17526
Annotation: FitnessBrowser__Cola:Echvi_2204
Length: 240 amino acids
Source: Cola in FitnessBrowser
Candidate for 19 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 95% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 95% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 95% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 91% | 146.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 35% | 72% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 36% | 94% | 144.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 38% | 89% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 87% | 140.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 87% | 140.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 35% | 91% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 36% | 89% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 36% | 89% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 34% | 92% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 39% | 75% | 128.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 32% | 73% | 103.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 83% | 86.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 83% | 86.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 83% | 86.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 83% | 86.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 56% | 254.6 |
Sequence Analysis Tools
View Echvi_2204 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
MGKIIETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTP
TAGNYILNNKDVSHMTENELAEIRNKEIGFVFQTFNLLPRATCLENVALPLIYAGYSKSD
REDKAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTS
YDIMNLFDELHQKGNTIIMVTHEDDIAHYAHRIVRLRDGLVETDQNNPNPTRNNFQPVSE
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