GapMind for catabolism of small carbon sources

 

Protein WP_022669727.1 in Hippea alviniae EP5-r

Annotation: NCBI__GCF_000420385.1:WP_022669727.1

Length: 424 amino acids

Source: GCF_000420385.1 in NCBI

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 100% 185.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
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) 36% 68% 159.1 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
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) 39% 59% 158.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
trehalose catabolism thuK 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) 39% 59% 158.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 60% 153.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 40% 84% 148.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
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) 40% 84% 148.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
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) 36% 65% 146.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
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) 36% 65% 146.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 99% 145.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 99% 145.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 99% 145.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 99% 145.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 62% 142.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 62% 142.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 62% 142.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 62% 142.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 71% 140.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 61% 139 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 53% 137.9 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 63% 137.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 74% 136.3 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 33% 71% 135.2 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 40% 57% 134.8 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 61% 134.4 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 33% 85% 133.7 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 75% 112.8 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 75% 112.8 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 35% 54% 110.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 30% 60% 107.5 Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- 41% 193.7

Sequence Analysis Tools

View WP_022669727.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

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Sequence

MEIIKLENINMIFPISKSESLTVLENISLSIEEGKIVSILGPSGCGKSTLLRIITGLLKP
TKGKVFYKGKVQSGVNDKMAMVFQNFALFPWKTVWDNIAIGIRNREIRNKDEMIKRVIDI
VGLEGFEDVYPKSLSGGMKQRVGIARALVSNPEILCMDEPFSALDVLTAENLREELMDLW
LSRKTSLKGIVIVTHNITEAVYMSDEIIIMASRPGRVQLVYKNKLSYPRDQNSADFLKIV
DAIRNYLTKNIIPDEPYTKIHEQLLPIPNATVGEVIGLLEVLEDNDGKIEMFELSERINR
RFTVAMIIATAAELMGFVQTPFRYIVLTNTGRKFLDADINERKEIFRTELLKLPIVKIFV
KFIKENNGSINSKEAKKFLRKKLPKEKPNSVLKPLLNFCMYAEILDYDSRDDEISINPDI
PIKI

This GapMind analysis is from Apr 09 2024. 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 (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:

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. 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:

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