GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_3685 in Pseudomonas fluorescens FW300-N2E2

Annotation: Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

Length: 1317 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-arginine catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-arginine catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 100% 817
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-arginine catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 100% 817
L-citrulline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-citrulline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 100% 817
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-citrulline catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 100% 817
L-proline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 95% 100% 2463.3
L-proline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 100% 817

Sequence Analysis Tools

View Pf6N2E2_3685 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

MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGSPRTD
SDDAGDVQVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAQMAE
ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP
MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA
SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ
YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR
RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP
QFATHNAHTLAAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP
VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATLEGGFGLPH
PRIPLPRDLYGSDRANSSGIDLANEHRLASLSCALLATAHNDWKAVPMLGCAASEETPAP
VLNPSDHRDVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERAADLMEGEIQ
PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL
AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRLMLEAGIPEGVLQLLPGRGETVGARL
VGDERVKGVMFTGSTEVARLLQRNIAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVV
IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGNPERLSVDIGPVIDA
EAKAGIEKHIQAMRDKGRTVYQMAIADSDECKRGTFVMPTLIELESFDELQREIFGPVLH
VVRYKRKELGQLIDQINASGYGLTLGVHTRIDETIAKVIDNVHAGNVYVNRNIVGAVVGV
QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIQQSFARGDALTAPDLRLRDAMSKPLTA
LQAWADSQKLAELSALCVQFAAQSQSGITRTLTGPTGERNSYAILPREHVLCLADVEGDL
LTQLAAVLAVGGSAVWPETDTSKALFARLPKEIQARIQRVADWSKDEVLFDAVLHHGDSD
QLRGVCQQVAKRTGAIVGVHGLSQGETSVALERLVIERALSVNTAAAGGNASLMTIG

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