Protein WP_068220191.1 in Roseivirga spongicola UST030701-084
Annotation: NCBI__GCF_001592965.1:WP_068220191.1
Length: 237 amino acids
Source: GCF_001592965.1 in NCBI
Candidate for 40 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 62% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 84% | 156.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 84% | 156.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 51% | 143.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 51% | 143.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 38% | 90% | 140.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| 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) | 38% | 53% | 140.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| 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) | 38% | 53% | 140.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 77% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 77% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| 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) | 36% | 62% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 79% | 137.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 91% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 91% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 86% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 35% | 89% | 134.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 36% | 79% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 36% | 79% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 36% | 79% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 36% | 79% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 36% | 79% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 38% | 52% | 132.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 33% | 87% | 132.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 35% | 57% | 129 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 60% | 127.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 35% | 79% | 117.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 56% | 107.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 203.0 |
Sequence Analysis Tools
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
Fitness BLAST: loading...
Sequence
MGNNKSIITTKGLKKFYYTDEIETTALNNVNLQIAEGEFVAIMGPSGCGKSTLLNIIGLL
DNPSEGEFYFYDEEVSKYSERQRAELRKRNIGFVFQSFNLIDELTVYENVELPLIYLKYP
ASERKQRVEEVLEHMQIMHRKDHFPQQLSGGQQQRVAVARAVVAKPNLILADEPTGNLDS
TNGQEVMTLLSDLNANGTTVIMVTHSATDAEYAHRVVNLFDGQVVSENINSKENSLV
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