GapMind for catabolism of small carbon sources

 

Protein HSERO_RS05325 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS05325 ribose ABC transporter permease

Length: 328 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 33 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) 50% 92% 282.7 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) 47% 266.2
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) 43% 98% 273.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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) 40% 97% 246.1 Ribose import permease protein RbsC 49% 282.7
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% 87% 231.1 Ribose import permease protein RbsC 49% 282.7
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 40% 96% 231.5 Ribose import permease protein RbsC 49% 282.7
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 96% 227.6 Ribose import permease protein RbsC 49% 282.7
myo-inositol catabolism PS417_11895 lo m-Inositol ABC transporter, permease component (iatP) (characterized) 39% 93% 217.6 Ribose import permease protein RbsC 49% 282.7
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 39% 96% 217.2 Ribose import permease protein RbsC 49% 282.7
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 39% 96% 217.2 Ribose import permease protein RbsC 49% 282.7
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) 37% 92% 215.3 Ribose import permease protein RbsC 49% 282.7
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 88% 207.2 Ribose import permease protein RbsC 49% 282.7
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 88% 207.2 Ribose import permease protein RbsC 49% 282.7
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 35% 88% 202.2 Ribose import permease protein RbsC 49% 282.7
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 37% 90% 194.5 Ribose import permease protein RbsC 49% 282.7
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 34% 91% 188.7 Ribose import permease protein RbsC 49% 282.7
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) 37% 89% 179.9 Ribose import permease protein RbsC 49% 282.7
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 34% 89% 175.6 Ribose import permease protein RbsC 49% 282.7
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 37% 92% 171.4 Ribose import permease protein RbsC 49% 282.7
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 33% 74% 163.3 Ribose import permease protein RbsC 49% 282.7
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 33% 95% 162.5 Ribose import permease protein RbsC 49% 282.7
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 34% 87% 157.5 Ribose import permease protein RbsC 49% 282.7
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 33% 83% 154.8 Ribose import permease protein RbsC 49% 282.7
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 33% 92% 151 Ribose import permease protein RbsC 49% 282.7
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 33% 92% 151 Ribose import permease protein RbsC 49% 282.7
myo-inositol catabolism PGA1_c07310 lo Inositol transport system permease protein (characterized) 30% 95% 141 Ribose import permease protein RbsC 49% 282.7
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% 64% 137.1 Ribose import permease protein RbsC 49% 282.7
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% 64% 137.1 Ribose import permease protein RbsC 49% 282.7

Sequence Analysis Tools

View HSERO_RS05325 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MPHDANALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLSNWFNVL
RQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLAT
CIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMVP
VPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGL
AAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLN
LMGINPYLQDIIRGVIILLAIYIAREWR

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, 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