GapMind for catabolism of small carbon sources

 

Protein CA265_RS10520 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS10520 ABC transporter ATP-binding protein

Length: 568 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism TM1750 med TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 52% 77% 268.9 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-mannose catabolism TM1749 med TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 51% 83% 255.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 36% 75% 178.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 36% 81% 172.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 37% 96% 159.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-arginine catabolism artP lo Histidine transport ATP-binding protein HisP (characterized) 35% 90% 149.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 90% 149.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 90% 149.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 38% 60% 148.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 87% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 36% 79% 141.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 35% 56% 141.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 63% 139.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 63% 139.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
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) 35% 58% 138.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 95% 134.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 95% 134.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
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) 32% 81% 132.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
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) 32% 81% 132.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 92% 113.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 87% 111.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 87% 111.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 87% 111.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 87% 111.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 50% 528.9

Sequence Analysis Tools

View CA265_RS10520 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

MLNVEHLNIDFYNQEEKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDER
AAKITGEIDFEDISLLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHR
KVDQAEAKKHTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEP
TTALDVTVQKTILQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKS
IFENPQHPYTKGLLACRPSPNRQLKKLPVVADFLTGEIEDASAHLQASNQLTTAEITARR
AKLYAQEPLLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKT
TLGRTILRLIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQDPYASLNPKLSIGQSI
LEPLQVHKLYRNDSERKQKVLELLDKVGLKEEHFNRYPHEFSGGQRQRVVIARALALQPK
FIICDESVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIE
EEGFPEQIFYAPKAAYTQKLIEAIPGHQ

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, the preprint on GapMind for carbon sources, 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