Protein Ac3H11_1841 in Acidovorax sp. GW101-3H11
Annotation: FitnessBrowser__acidovorax_3H11:Ac3H11_1841
Length: 892 amino acids
Source: acidovorax_3H11 in FitnessBrowser
Candidate for 27 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-ribose catabolism | rbsC | hi | ABC transporter permease (characterized, see rationale) | 66% | 94% | 401.4 | | | |
| D-fructose catabolism | frcC | hi | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 41% | 97% | 206.5 | | | |
| sucrose catabolism | frcC | hi | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 41% | 97% | 206.5 | | | |
| D-ribose catabolism | rbsA | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 52% | 79% | 418.3 | Inositol transport system ATP-binding protein | 35% | 249.6 |
| D-mannose catabolism | HSERO_RS03645 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 38% | 99% | 206.5 | | | |
| xylitol catabolism | PS417_12060 | med | ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) | 38% | 100% | 204.9 | | | |
| L-fucose catabolism | HSERO_RS05255 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 33% | 99% | 199.9 | | | |
| myo-inositol catabolism | iatP | med | Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) | 37% | 98% | 186 | | | |
| D-cellobiose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| D-glucose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| lactose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| D-maltose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| sucrose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| trehalose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| D-xylose catabolism | xylH | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 33% | 96% | 179.1 | | | |
| myo-inositol catabolism | PS417_11895 | med | Inositol transport system permease protein (characterized) | 35% | 99% | 178.3 | | | |
| D-galactose catabolism | BPHYT_RS16925 | med | Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) | 33% | 96% | 172.2 | | | |
| D-mannose catabolism | frcC | med | Fructose import permease protein FrcC (characterized) | 31% | 86% | 167.2 | | | |
| D-ribose catabolism | frcC | med | Fructose import permease protein FrcC (characterized) | 31% | 86% | 167.2 | | | |
| D-fructose catabolism | fruF | med | Fructose import permease protein FruF (characterized) | 36% | 81% | 164.5 | | | |
| sucrose catabolism | fruF | med | Fructose import permease protein FruF (characterized) | 36% | 81% | 164.5 | | | |
| L-arabinose catabolism | araH | med | L-arabinose ABC transporter, permease protein AraH (characterized) | 31% | 98% | 162.9 | | | |
| D-galactose catabolism | ytfT | med | Galactofuranose transporter permease protein YtfT (characterized) | 33% | 94% | 160.6 | | | |
| L-rhamnose catabolism | rhaQ | med | RhaQ (characterized, see rationale) | 31% | 89% | 151.8 | | | |
| L-fucose catabolism | BPHYT_RS34240 | med | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 32% | 95% | 131.3 | | | |
| L-rhamnose catabolism | BPHYT_RS34240 | med | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 32% | 95% | 131.3 | | | |
| D-galactose catabolism | yjtF | lo | Inner membrane ABC transporter permease protein YjfF (characterized) | 36% | 76% | 138.7 | | | |
Sequence Analysis Tools
View Ac3H11_1841 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
Fitness BLAST: loading...
Sequence
MPSDAREQPMTPKPPTNTSPPLLAIQAIGKDYTATVLDGVNVELFAGEVLALTGENGAGK
STLSKILCGLEQPTRGGMLLAGQAYAPTSRRDAERHGVRMVMQELGLVPTLTVAENLLMG
RLPHRLGWLQRDVLHAAARAQLAKIGLDSIDPATPVSQLGIGQQQMVEIARNLQDDTRIL
VLDEPTAMLTPRETNYLFEQIAHLTARGVAIIYVSHRLEELRRIADRVAVLRDGRLVDVR
PMAGMSEDDLVQRMVGRVVSDLDHRPRRPVGPVVMSAEGLGRGTAVQGVSLELRAGEIFG
IAGLVGSGRTELVRLLFGADRADRGSVTLHPEFEQKQALPRDGQAQAAIQKIANTPNPAT
AAPRTWQRGFASPLQAIAAGVGLVTEDRKSQGLLLSQPIRINATLSDLSAVSRGGWLQRG
FENRLVQGFVRTLGIRCRSPEQPVGQLSGGNQQKGGVRPLAAPRRPRAAARRTHARRGRG
RPRRAVWRAGPHGPGRPRAAHGVVRPARTHGHGRPHRRDECGPPGGRVRARRVVRAIAAG
GCVLRARRAHQHHTFNFFSCDRMNAPTAPAAPAATPSSASVWRSQLGTYLGLLAVLAGMV
ALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAA
ILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRT
QYVGDAISWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGV
DPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGS
VVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTLRQRRAKV
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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