Protein WP_157477908.1 in Granulicella tundricola MP5ACTX9
Annotation: NCBI__GCF_000178975.2:WP_157477908.1
Length: 220 amino acids
Source: GCF_000178975.2 in NCBI
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-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 81% | 157.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 81% | 157.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 41% | 61% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 79% | 140.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 79% | 140.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 39% | 81% | 139 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 57% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 57% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 57% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 57% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 57% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 57% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-lysine catabolism | hisP | lo | ABC transporter for L-Lysine, ATPase component (characterized) | 37% | 85% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 38% | 56% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 55% | 127.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 34% | 55% | 126.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| 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) | 34% | 58% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| sucrose catabolism | thuK | 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) | 34% | 58% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 37% | 75% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 81% | 88.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 81% | 88.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 81% | 88.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 81% | 88.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 81% | 88.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 81% | 88.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 58% | 241.1 |
Sequence Analysis Tools
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MGDQQVHALRGVNLRIKHNEYVAIMGPSGSGKSTLMNLIGCLDSPSQGKYWLNGHNVSEL
NDDELARIRNKEIGFVFQTFNLLARATSLHNVELPLIYNGTPAAERTARAKEVLEQVSLG
PRMMHKPNELSGGQRQRVAIARALVNRPSIILADEPTGNLDSKTSVEIMALFAELHEKGN
TIVLVTHEPDIAEYAHRIVTIRDGVVSSDHPSARHAAQTS
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