GapMind for catabolism of small carbon sources

 

Protein 5210455 in Shewanella loihica PV-4

Annotation: Shew_2896 sodium:neurotransmitter symporter (RefSeq)

Length: 503 amino acids

Source: PV4 in FitnessBrowser

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-tryptophan catabolism tnaT med High affinity tryptophan:Na+ symporter, TnaT, of 501 aas and 12 TMSs (Androutsellis-Theotokis et al., 2003). The Km for Tryptophan is 145 nM; tryptamine and serotonin weakly inhibited with Ki values of 200 and 440 μM, respectively. An evolutionarily conserved role of adjacent transmembrane segments 7 and 8 has been proposed (characterized) 41% 96% 423.3 Hypothetical Na+-dependent permease 44% 421.4
L-alanine catabolism metP med Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized) 42% 86% 382.9 High affinity tryptophan:Na+ symporter, TnaT, of 501 aas and 12 TMSs (Androutsellis-Theotokis et al., 2003). The Km for Tryptophan is 145 nM; tryptamine and serotonin weakly inhibited with Ki values of 200 and 440 μM, respectively. An evolutionarily conserved role of adjacent transmembrane segments 7 and 8 has been proposed 41% 423.3
L-proline catabolism SLC6A7 lo Sodium-dependent proline transporter (Solute carrier family 6 member 7) (characterized) 31% 83% 247.7 High affinity tryptophan:Na+ symporter, TnaT, of 501 aas and 12 TMSs (Androutsellis-Theotokis et al., 2003). The Km for Tryptophan is 145 nM; tryptamine and serotonin weakly inhibited with Ki values of 200 and 440 μM, respectively. An evolutionarily conserved role of adjacent transmembrane segments 7 and 8 has been proposed 41% 423.3
L-leucine catabolism leuT lo The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized) 32% 90% 226.5 High affinity tryptophan:Na+ symporter, TnaT, of 501 aas and 12 TMSs (Androutsellis-Theotokis et al., 2003). The Km for Tryptophan is 145 nM; tryptamine and serotonin weakly inhibited with Ki values of 200 and 440 μM, respectively. An evolutionarily conserved role of adjacent transmembrane segments 7 and 8 has been proposed 41% 423.3

Sequence Analysis Tools

View 5210455 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

MKREQWNSRVGFILAAVGSAIGLGNIWRFPYMAYDNGGGAFFIPYLFAMITAGIPFMIME
FSLGHKIKKTSPRIFAQLGHTLGFRLEWLGWFQVFIAAVIAVYYVAIIGWTLSYLGFSFS
QAWGDNPNDFFFNHYLKLGNNSPSHLGEFQIGIAIAMSIAWLMTFMAVFTGVKGGIERAN
KIMMPMLFIMVLVLIGRIMFLPGALSGLNYLFEPDFSRLLDAQVWSAAYGQIFFTLSVGF
AIMLAYSSYLPTKADINNNAFMTVLINCGFSILAGILIFGVLGYMAEEQMKPLTEVVSSG
IGLAFVTIPTAINLMPAPYILGPLFFIALVIAGLSSHISIIEAVTSAVIDKFHVRRKPAA
VLVCSLGYLVSMAFATNGGLLLLDLVDYFINNIALLLSCLLELVIITWLLKVTVIHQHAN
ENSEFRVGGWFVVCLRFISPAILATILAKNLYNTLVNGYGDYPIADQLFLGWGLVGTMLF
FAVLINFTSKSPGYPDQHPGGKT

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