GapMind for catabolism of small carbon sources

 

Protein PP_1300 in Pseudomonas putida KT2440

Annotation: PP_1300 putative amino acid ABC transporter - ATP-binding subunit

Length: 254 amino acids

Source: Putida in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5405 hi ABC transporter for D-Alanine, ATPase component (characterized) 96% 100% 498.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 78% 422.5
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 80% 93% 412.5 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 79% 96% 411 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 79% 96% 411 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 79% 96% 411 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 79% 96% 411 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 79% 96% 411 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 78% 92% 394 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 78% 92% 394 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 78% 92% 394 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 67% 93% 336.3 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 63% 94% 305.8 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 63% 94% 305.8 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 62% 100% 295.4 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 62% 100% 295.4 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 55% 99% 272.7 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 55% 99% 272.7 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 99% 249.2 ABC transporter for D-Alanine, ATPase component 96% 498.8
L-asparagine catabolism glnQ med 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) 52% 97% 245 ABC transporter for D-Alanine, ATPase component 96% 498.8
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 49% 98% 245 ABC transporter for D-Alanine, ATPase component 96% 498.8

Sequence Analysis Tools

View PP_1300 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

MSEAIKQPAGPEGIIQMQGVNKWYGQFHVLKDINLNVRQGERIVLCGPSGSGKSTTIRCL
NRLEEHQQGRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLSILENCTLAPMWVRK
MPRRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSAL
DPEMVKEVLDTMVGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPDDFFDRP
RSDRTKLFLSQILH

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