GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_00221 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_00221 amino acid ABC transporter ATP-binding protein, PAAT family

Length: 259 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP hi ABC transporter for L-Arginine, putative ATPase component (characterized) 82% 100% 422.5
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 70% 99% 359 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-lysine catabolism hisP med ABC transporter for L-Lysine, ATPase component (characterized) 71% 99% 356.3 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 67% 99% 355.9 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 66% 92% 324.7 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 62% 97% 315.1 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 97% 263.1 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 50% 96% 246.1 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 90% 245 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 90% 245 ABC transporter for L-Arginine, putative ATPase component 82% 422.5
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 77% 137.1 ABC transporter for L-Arginine, putative ATPase component 82% 422.5

Sequence Analysis Tools

View H281DRAFT_00221 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNTTKQKLFVDELHKQYGDNEVLKGVTLKANAGDVISVIGSSGSGKSTMLRCINFLEQPN
AGRIFVDGEEVRTQIAKNGALRVSDPKQLQRVRTKLSMVFQHFNLWSHMNVLENIVEAPV
NVLGLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDE
PTSALDPELVGEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDE
VFRNTRSERLKQFLSGSLK

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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