GapMind for catabolism of small carbon sources

 

Protein 6939439 in Shewanella amazonensis SB2B

Annotation: Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)

Length: 370 amino acids

Source: SB2B in FitnessBrowser

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 61% 177.6 ABC-type molybdate transporter (EC 7.3.2.5) 30% 174.1
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 63% 168.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 63% 168.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 41% 59% 162.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 63% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 63% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 63% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 63% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 63% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 63% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 65% 157.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 41% 58% 156.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 32% 82% 154.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 65% 152.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 65% 152.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 37% 57% 151.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 32% 79% 151.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
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) 35% 67% 150.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 40% 60% 149.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 62% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 54% 149.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 30% 89% 146.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 30% 89% 146.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 67% 146.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 30% 89% 146.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 30% 89% 146.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 57% 144.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 66% 144.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 38% 70% 143.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 141 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 81% 132.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 40% 177.6

Sequence Analysis Tools

View 6939439 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSGSTELRVQIRQTKGIRIEADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIR
CGKRIWFDSDEGIHCSPQNRHIGFVPQHFGLFPKLSALGNIMAALDHLPSQERRPRALAA
LEKVNLHGLTDRLPSQLSGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELA
RLKAELNIPVIMVTHDLNEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMGLR
NIFNAHVVAQDCAKGVTWLKFGDRLIASDSLPRVNIGDKVRWVIPNQGIRFNSIASGRLC
RSFNILPIHIDNMLTLGESVRLEASVQDSGERLNVEIPLHLAHKLALTQGAATEVALKSD
QVHILEMIKA

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