GapMind for catabolism of small carbon sources

 

Protein HSERO_RS00890 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS00890 ABC transporter ATP-binding protein

Length: 404 amino acids

Source: HerbieS 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-proline catabolism HSERO_RS00890 hi ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 100% 100% 789.3 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-isoleucine catabolism livM hi ABC transporter ATP-binding protein (characterized, see rationale) 63% 94% 461.8
L-leucine catabolism livM hi ABC transporter ATP-binding protein (characterized, see rationale) 63% 94% 461.8
L-phenylalanine catabolism livM hi ABC transporter ATP-binding protein (characterized, see rationale) 63% 94% 461.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 124.0
L-serine catabolism Ac3H11_1694 hi ABC transporter ATP-binding protein (characterized, see rationale) 63% 94% 461.8 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-tyrosine catabolism Ac3H11_1694 hi ABC transporter ATP-binding protein (characterized, see rationale) 63% 94% 461.8 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-arginine catabolism braE lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 72% 216.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-glutamate catabolism braE lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 72% 216.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-histidine catabolism braE lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 72% 216.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-valine catabolism livM lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 72% 216.9
D-alanine catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 39% 58% 204.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-proline catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 39% 58% 204.9 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-alanine catabolism braE lo High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 36% 77% 204.1 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-serine catabolism braE lo High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 36% 77% 204.1 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7
L-threonine catabolism braE lo High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 36% 77% 204.1 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 40% 235.7

Sequence Analysis Tools

View HSERO_RS00890 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

MALLTFDMKRNPQQARISLLLLLALMIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVV
VGFAGLLDLGYIAFYAIGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNG
IHLSLWLIVPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNIT
NGPQGINLIDPIKVFGVSLAGEPGSGSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRL
QDSRLGRAWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESF
SLTESIAVLAMVVLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLR
QLLYGLAMVVIMLTRPAGLWPSPRHEDRPEADHTQVGTTGEVKA

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