Protein WP_038016165.1 in Tatumella morbirosei LMG 23360
Annotation: NCBI__GCF_000757425.2:WP_038016165.1
Length: 322 amino acids
Source: GCF_000757425.2 in NCBI
Candidate for 36 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 | Ribose import permease protein RbsC (characterized) | 87% | 100% | 544.7 | RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 72% | 430.3 |
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) | 48% | 94% | 279.3 | Ribose import permease protein RbsC | 87% | 544.7 |
D-mannose catabolism | HSERO_RS03645 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 42% | 97% | 240.4 | Ribose import permease protein RbsC | 87% | 544.7 |
L-fucose catabolism | HSERO_RS05255 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 45% | 88% | 237.3 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 44% | 91% | 236.5 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
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) | 42% | 98% | 231.1 | Ribose import permease protein RbsC | 87% | 544.7 |
D-fructose catabolism | frcC | med | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 45% | 90% | 229.9 | Ribose import permease protein RbsC | 87% | 544.7 |
sucrose catabolism | frcC | med | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 45% | 90% | 229.9 | Ribose import permease protein RbsC | 87% | 544.7 |
myo-inositol catabolism | PS417_11895 | med | m-Inositol ABC transporter, permease component (iatP) (characterized) | 40% | 94% | 213.8 | Ribose import permease protein RbsC | 87% | 544.7 |
D-galactose catabolism | BPHYT_RS16925 | lo | Arabinose ABC transporter permease (characterized, see rationale) | 37% | 95% | 211.1 | Ribose import permease protein RbsC | 87% | 544.7 |
D-xylose catabolism | xylF_Tm | lo | ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) | 39% | 96% | 202.6 | Ribose import permease protein RbsC | 87% | 544.7 |
D-galactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 39% | 95% | 201.1 | Ribose import permease protein RbsC | 87% | 544.7 |
D-galactose catabolism | ytfT | lo | Galactofuranose transporter permease protein YtfT (characterized) | 36% | 93% | 189.5 | Ribose import permease protein RbsC | 87% | 544.7 |
D-mannose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 35% | 84% | 183 | Ribose import permease protein RbsC | 87% | 544.7 |
D-ribose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 35% | 84% | 183 | Ribose import permease protein RbsC | 87% | 544.7 |
L-arabinose catabolism | araWsh | lo | Inner-membrane translocator (characterized, see rationale) | 35% | 75% | 181.8 | Ribose import permease protein RbsC | 87% | 544.7 |
D-fructose catabolism | fruF | lo | Fructose import permease protein FruF (characterized) | 34% | 92% | 180.3 | Ribose import permease protein RbsC | 87% | 544.7 |
sucrose catabolism | fruF | lo | Fructose import permease protein FruF (characterized) | 34% | 92% | 180.3 | Ribose import permease protein RbsC | 87% | 544.7 |
L-fucose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 35% | 91% | 177.2 | Ribose import permease protein RbsC | 87% | 544.7 |
L-rhamnose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 35% | 91% | 177.2 | Ribose import permease protein RbsC | 87% | 544.7 |
D-fructose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 33% | 97% | 176.4 | Ribose import permease protein RbsC | 87% | 544.7 |
sucrose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 33% | 97% | 176.4 | Ribose import permease protein RbsC | 87% | 544.7 |
L-rhamnose catabolism | rhaP | lo | RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) | 33% | 93% | 174.1 | Ribose import permease protein RbsC | 87% | 544.7 |
D-galactose catabolism | yjtF | lo | Inner membrane ABC transporter permease protein YjfF (characterized) | 37% | 89% | 170.6 | Ribose import permease protein RbsC | 87% | 544.7 |
L-arabinose catabolism | araZsh | lo | Inner-membrane translocator (characterized, see rationale) | 34% | 93% | 162.5 | Ribose import permease protein RbsC | 87% | 544.7 |
2'-deoxyinosine catabolism | H281DRAFT_01112 | lo | deoxynucleoside transporter, permease component 2 (characterized) | 31% | 82% | 154.5 | Ribose import permease protein RbsC | 87% | 544.7 |
L-arabinose catabolism | gguB | lo | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 31% | 87% | 144.4 | Ribose import permease protein RbsC | 87% | 544.7 |
D-galactose catabolism | gguB | lo | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 31% | 87% | 144.4 | Ribose import permease protein RbsC | 87% | 544.7 |
L-arabinose catabolism | xylHsa | lo | Xylose/arabinose import permease protein XylH (characterized, see rationale) | 30% | 83% | 140.2 | Ribose import permease protein RbsC | 87% | 544.7 |
2'-deoxyinosine catabolism | H281DRAFT_01115 | lo | deoxynucleoside transporter, permease component 1 (characterized) | 33% | 84% | 136 | Ribose import permease protein RbsC | 87% | 544.7 |
Sequence Analysis Tools
View WP_038016165.1 at NCBI
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
MSTHTIPSRRLLSKTWLLEQKSLIALLVLIAIVSGMSHNFFTLANLFNILQQTSVNAIMA
VGMTLVILTSGIDLSVGSLLALTGAVAASLVGMEVNALLAIAASLLLGAFIGGITGVIVA
KGKVQAFIATLVMMLLLRGVTMVYTNGSPISTGFSDNSDLFGWFGIGRPLGVPTPVWLMA
IIFLAAWYMLHHTRLGRYIYALGGNEAATRLSGISVNRIKIIVYALCGMLAALAGTIEVA
RLSSAQPTAGTGYELDAIAAVVLGGTSLSGGKGRIVGTLIGALILGFLNNGLNLIGVSSY
YQMIVKAVVILLAVLVDNKSSK
This GapMind analysis is from Sep 24 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:
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