GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1580 in Pseudomonas fluorescens FW300-N1B4

Annotation: Histidine transport protein (permease)

Length: 469 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism permease hi histidine permease (characterized) 95% 100% 885.2 ProY of 457 aas and 12 TMSs 62% 581.3
L-proline catabolism proY med ProY of 457 aas and 12 TMSs (characterized) 62% 96% 581.3 histidine permease 95% 885.2
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 53% 97% 518.1 histidine permease 95% 885.2
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 53% 97% 518.1 histidine permease 95% 885.2
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 46% 93% 428.7 histidine permease 95% 885.2
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 45% 96% 400.2 histidine permease 95% 885.2
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 44% 98% 398.7 histidine permease 95% 885.2
L-tryptophan catabolism aroP med Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 45% 99% 395.6 histidine permease 95% 885.2
L-tyrosine catabolism aroP med Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 45% 99% 395.6 histidine permease 95% 885.2
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 40% 97% 369.8 histidine permease 95% 885.2
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 36% 89% 327.4 histidine permease 95% 885.2
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 34% 97% 302.8 histidine permease 95% 885.2
L-serine catabolism serP lo Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) 37% 97% 296.2 histidine permease 95% 885.2
L-lysine catabolism lysP lo Lysine permease LysP (characterized) 36% 87% 290.4 histidine permease 95% 885.2
L-threonine catabolism serP1 lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 37% 96% 289.3 histidine permease 95% 885.2

Sequence Analysis Tools

View Pf1N1B4_1580 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

MQQPAKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM
RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP
EVDRWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP
GAQATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAIN
AVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSA
INSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVF
LLIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFG
VLGYFPDTQAALIVGVVWIVLLVLAYLTWVKPAAGQAALVARDPDFSHR

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