GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1346 in Pseudomonas fluorescens FW300-N1B4

Annotation: Urea ABC transporter, ATPase protein UrtD

Length: 289 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 38% 98% 162.2 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 38% 98% 157.9 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 38% 98% 157.9 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 37% 98% 154.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 37% 98% 154.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 37% 98% 154.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 37% 98% 154.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 37% 98% 154.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 35% 92% 145.6 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 35% 92% 145.6 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 35% 92% 145.6 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-isoleucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 35% 96% 144.8 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-leucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 35% 96% 144.8 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-proline catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 35% 96% 144.8 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-valine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 35% 96% 144.8 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 142.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 142.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 142.5 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 99% 141 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 35% 88% 139 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 35% 88% 139 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 178.7

Sequence Analysis Tools

View Pf1N1B4_1346 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

MRITATAEFMLEPAFFPVEPNKDAGSSRDAIGLGQRVGPGLNTRHGTILTLEDISVSFDG
FKALNDLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWFGETLDLTQMSEVQ
IAQAGIGRKFQKPTVFEALSVFENLELAQKTDKSVWASLRARLSGEQKDRISEVLETIRL
TASVNRPAGMLSHGQKQFLEIGMLLMQDPQLLLLDEPVAGMTDAETEFTAELFKSLAGKH
SLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQDNERVIEVYLGR

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