Protein 3608624 in Dinoroseobacter shibae DFL-12
Annotation: FitnessBrowser__Dino:3608624
Length: 333 amino acids
Source: Dino in FitnessBrowser
Candidate for 35 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 52% | 100% | 342 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 52% | 100% | 342 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 53% | 97% | 329.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| trehalose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 53% | 97% | 329.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-cellobiose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-glucose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| lactose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-maltose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| sucrose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| trehalose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 95% | 315.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-maltose catabolism | malK1 | med | 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) | 53% | 86% | 312.4 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-mannose catabolism | TT_C0211 | med | 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) | 57% | 76% | 311.6 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 54% | 87% | 309.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 49% | 85% | 299.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 47% | 95% | 294.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 47% | 99% | 289.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 47% | 87% | 258.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 46% | 75% | 250 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| L-arabinose catabolism | araV | med | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 78% | 205.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-fructose catabolism | araV | med | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 78% | 205.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| sucrose catabolism | araV | med | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 78% | 205.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-xylose catabolism | araV | med | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 78% | 205.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-cellobiose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-galactose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-glucose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| lactose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-maltose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| D-mannose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| sucrose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| trehalose catabolism | glcV | med | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 40% | 80% | 200.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 99% | 208.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 38% | 96% | 154.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 98% | 153.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 98% | 153.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 56% | 342.4 |
Sequence Analysis Tools
View 3608624 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
MATLTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEV
RIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKL
LQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQ
RELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPPTN
FLPADMVRAGPAGQQVGIRPEHLRVAPQGRLEAHVAYAEALGAETLLHLRASQGTTLTVR
QDAAAPMPAEGATVQLDWDDSDTMLFADNGRRV
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