GapMind for catabolism of small carbon sources

 

Protein 6936480 in Shewanella amazonensis SB2B

Annotation: Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Length: 341 amino acids

Source: SB2B in FitnessBrowser

Candidate for 84 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 40% 95% 229.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 92% 210.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 89% 207.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 89% 207.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 98% 203.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 84% 203 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 63% 201.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 94% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 94% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 81% 196.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 83% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 83% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 83% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 83% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 34% 85% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 83% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 83% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 95% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 84% 195.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 35% 88% 195.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-sorbitol (glucitol) catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 35% 88% 195.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 86% 191.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 86% 191.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 86% 191.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 79% 189.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
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) 37% 79% 188 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 79% 186.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 82% 186.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 33% 95% 184.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 33% 95% 184.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 68% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 68% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 68% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 68% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 68% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 68% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 76% 181.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 77% 179.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 177.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 177.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 177.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 177.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 33% 77% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-mannose catabolism TT_C0211 lo 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) 37% 72% 175.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
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) 34% 76% 172.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 76% 169.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 75% 167.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 95% 158.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 38% 77% 156.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 36% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 37% 91% 152.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 83% 151.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 34% 60% 148.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
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) 34% 96% 147.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 80% 146.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 36% 99% 143.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 36% 98% 142.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 78% 141.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 141 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 141 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 90% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 90% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 35% 81% 138.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 33% 93% 136 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 33% 95% 134 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 75% 130.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 106.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 106.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 106.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 106.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 106.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 106.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 97% 105.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 98% 100.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 98% 100.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 98% 100.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 278.5

Sequence Analysis Tools

View 6936480 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

MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI
AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSVRLEEML
SLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRA
ILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGASN
YLDVRLEAGQLISTLGAFPLPQDFKAASETGRWLLRPEQLLIEARADGAGEILERRFLGN
GCHYLVRLGEQVLDIHSHLGHLACGSRVSLSAAADTPVIFA

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