GapMind for catabolism of small carbon sources

 

Protein WP_083554538.1 in Bacteroides clarus YIT 12056

Annotation: NCBI__GCF_900129655.1:WP_083554538.1

Length: 804 amino acids

Source: GCF_900129655.1 in NCBI

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-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 32% 83% 161.4 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 32% 83% 161.4 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 32% 83% 161.4 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 32% 83% 161.4 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-arginine catabolism rocD lo ornithine aminotransferase; EC 2.6.1.13 (characterized) 30% 90% 157.9 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-citrulline catabolism rocD lo ornithine aminotransferase; EC 2.6.1.13 (characterized) 30% 90% 157.9 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-arginine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 93% 154.1 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-citrulline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 93% 154.1 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-lysine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 93% 154.1 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-proline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 93% 154.1 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-arginine catabolism gabT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 30% 83% 153.7 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-citrulline catabolism gabT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 30% 83% 153.7 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
putrescine catabolism gabT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 30% 83% 153.7 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-arginine catabolism astC lo Succinylornithine transaminase (EC 2.6.1.81) (characterized) 33% 75% 150.2 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2
L-citrulline catabolism astC lo Succinylornithine transaminase (EC 2.6.1.81) (characterized) 33% 75% 150.2 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 2.6.1.62 60% 524.2

Sequence Analysis Tools

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Predict transmenbrane helices: Phobius

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Sequence

MKRKQSPGHTIRFRRWSRKAYAAFASIGRCVTIGCLRKNVADSSLRKQDAVQTLPYFIHT
MTIDELKARVLAGIDISPDQAAWLANTADREALYAAAHEITVQCAQHEFDMCSIINAKSG
RCPENCKWCAQSAHYHTKADIYDLLPAEECLRQAQYNERQDVNRFSLVTSGRKPSSRQME
QLCDTARHMRRHSSIQLCASLGLLNEKELRALHDAGITRYHCNLETAPSFFPTLCSTHTQ
EDKLRTLQAARNAGMDICSGGIIGMGETMEQRIEFAFTLKELGVQSIPINLLSPIPGTPL
ENRQALTEEEVLVTIALFRFINPTAYLRFAGGRSQLSKDAVKKSLYIGINSAIVGDLLTT
LGSKISDDKKLIEEAGYEFCGSQFDREHLWHPYTSTTDPLPVYKVKRADGATITLESGQT
LIEGMSSWWCAVHGYNHPALNRAATEQLGKMSHVMFGGLTHDPAIELGKLLLPLVPPSMQ
KIFYADSGSVAVEVALKMAVQYWYAKNRGKKNNFVTIRSGYHGDTWNAMSVCDPVTGMHS
LFGSALPVRYFVPQPRSRFGGEWNPDDILPLKEIMERHADELAALILEPVVQGAGGMWFY
HPQYLREAAKLCREHGLLLIFDEIATGFGRTGKLFAWEHAGTEPDIMCIGKALTGGYMTL
SAVLAANEVADTISNHAPGAFMHGPTFMGNPLACAVACASVRLLTSPEYDWQEKVTRIEA
QLRQELEPARQLPQVADVRVLGAIGVIETKQPVDMAWMQRRFVEEGIWVRPFGRLVYLMP
PFIIEPEQLGVLTKGLIKIVEEMK

This GapMind analysis is from Sep 24 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