GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_4400 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400

Length: 473 amino acids

Source: pseudo13_GW456_L13 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-tyrosine catabolism aroP hi L-tyrosine transporter (characterized) 93% 100% 887.9 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 57% 552.0
L-tryptophan catabolism aroP hi Aromatic amino acid transport protein AroP (characterized, see rationale) 72% 100% 699.5 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 57% 552.0
L-phenylalanine 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) 68% 98% 617.1 L-tyrosine transporter 93% 887.9
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 65% 99% 615.5 L-tyrosine transporter 93% 887.9
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 94% 412.9 L-tyrosine transporter 93% 887.9
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 94% 412.9 L-tyrosine transporter 93% 887.9
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 42% 95% 391.3 L-tyrosine transporter 93% 887.9
L-histidine catabolism permease med histidine permease (characterized) 42% 98% 384.8 L-tyrosine transporter 93% 887.9
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 38% 97% 351.3 L-tyrosine transporter 93% 887.9
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 38% 90% 327.4 L-tyrosine transporter 93% 887.9
L-serine catabolism serP 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) 38% 86% 290 L-tyrosine transporter 93% 887.9
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) 38% 86% 290 L-tyrosine transporter 93% 887.9
L-arginine catabolism rocE lo Amino-acid permease GAP1 (characterized) 33% 80% 248.4 L-tyrosine transporter 93% 887.9
L-lysine catabolism lysP lo Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized) 32% 81% 242.7 L-tyrosine transporter 93% 887.9
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 30% 68% 208 L-tyrosine transporter 93% 887.9

Sequence Analysis Tools

View PfGW456L13_4400 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSGQNPQSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF
MIMRQLGEMIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY
WAPDIPTWASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGNG
GPQAAVSNLWSHGGFFPNGVTGLVMAMAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ
VIYRILIFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNFV
VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLLN
YLIPHSALELLMSLVVATLVINWAMISYSHFKFRQHMNKTKQTPLFKALWYPYGNYICLA
FVLFILGVMLLIPGIQTSVYAIPVWLVFMWVCYGIKNKRSAQHALQVAGSAAK

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:

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