GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_3653 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Length: 453 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 54% 96% 514.6 Proline-specific permease (ProY) 53% 488.4
L-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 54% 96% 514.6 Proline-specific permease (ProY) 53% 488.4
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 53% 96% 488.4 L-alanine and D-alanine permease 54% 514.6
L-histidine catabolism permease med histidine permease (characterized) 53% 94% 474.9 L-alanine and D-alanine permease 54% 514.6
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 47% 95% 428.7 L-alanine and D-alanine permease 54% 514.6
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 45% 95% 416 L-alanine and D-alanine permease 54% 514.6
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% 95% 410.6 L-alanine and D-alanine permease 54% 514.6
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% 95% 410.6 L-alanine and D-alanine permease 54% 514.6
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 45% 94% 392.1 L-alanine and D-alanine permease 54% 514.6
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 41% 96% 361.7 L-alanine and D-alanine permease 54% 514.6
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 39% 87% 335.1 L-alanine and D-alanine permease 54% 514.6
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 36% 97% 308.9 L-alanine and D-alanine permease 54% 514.6
L-lysine catabolism lysP lo lysine-specific permease (characterized) 35% 94% 276.6 L-alanine and D-alanine permease 54% 514.6
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% 95% 276.2 L-alanine and D-alanine permease 54% 514.6
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) 36% 96% 273.1 L-alanine and D-alanine permease 54% 514.6
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 80% 213 L-alanine and D-alanine permease 54% 514.6
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 80% 213 L-alanine and D-alanine permease 54% 514.6
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 80% 213 L-alanine and D-alanine permease 54% 514.6
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 31% 65% 183.3 L-alanine and D-alanine permease 54% 514.6

Sequence Analysis Tools

View N515DRAFT_3653 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

MTQHLQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRAL
GEMAVHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELP
QWIWVFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPV
GLANLWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWR
ILIFYVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTT
FSGSRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMS
ILAFNTVWTWMMVLIAHYSFRRRHGATAFPLRAWPLTSVVCLLFLAFVLFMLGYSADTRV
ALYVGAGWVVLLSLAYRLLGIGARMRALEPRAI

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