GapMind for catabolism of small carbon sources

 

Protein AO353_28150 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_28150 arginine aminotransferase

Length: 667 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism aruH hi arginine-pyruvate transaminase (EC 2.6.1.84) (characterized) 51% 100% 396.7
L-histidine catabolism hisP hi Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 65% 99% 340.9 ABC transporter for L-Lysine, ATPase component 64% 315.1
L-lysine catabolism hisP hi Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 65% 99% 340.9 ABC transporter for L-Arginine, putative ATPase component 64% 311.6
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 66% 98% 334.7 Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR 65% 340.9
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 54% 95% 261.2 Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR 65% 340.9
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 55% 97% 259.2 Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR 65% 340.9
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 45% 72% 186.4 Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR 65% 340.9

Sequence Analysis Tools

View AO353_28150 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

MRFSPFVERISGQGVAAWDIHNAAFDAQRRGEDVIILSVGDPDFPTPDFITDAAVDALRE
GDTHYTEIAGRLALREAIAARYSQLFGRELQASNVINVAGAQNALFITSLCLLTAGDEVL
ALDPMYVTYEATLKASGATLVRVPCAADSGFRLDAAVLAKAITPRTRAIFLSNPNNPTGV
VLNREELQAIADLAITHDLWVVVDEVYESLAFEREHLSLAALPGMAERCVVIGSLSKSHA
MTGWRIGWIVADETLVAHAETLMLSMLYGLPGFVMEAALKAVQAHEEVTHGMREIYRRRR
DLVVKGLSDCPGISVLTPDAGMFVLVDVRGTGLSSLEFAWRLLREARVSVLDAAAFGEPA
QGFVRLSFTLGEERLAQACQRIRDFIQVLKGEAPRPAITRVTSQATIEPVAAKTMIEVDG
LHKRFGNIEVLKGVSLTAREGDVISLIGASGSGKSTLLRCINMLEVPDQGRILVDGESIQ
LNFDRPGAPLVSDAKQLVRIRSSLGMVFQNFNLWPHRTVLENLIEAPTQVLRESRAEATE
RAEALLERVGLAAKRNEYPAFLSGGQQQRVAIARALAMRPKVMLFDEPTSALDPELVGEV
LRVIRSLAEEGRTMILVTHEMAFARDVSSKVAYLHQGLIEEAGSPDEVFVHPRSERCRQF
VNAHQTR

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