GapMind for catabolism of small carbon sources

 

Protein WP_054255670.1 in Acidovorax caeni R-24608

Annotation: NCBI__GCF_001298675.1:WP_054255670.1

Length: 1335 amino acids

Source: GCF_001298675.1 in NCBI

Candidate for 14 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) 60% 100% 1506.5
L-arginine catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-arginine catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-arginine catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710
L-citrulline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-citrulline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-citrulline catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710
L-proline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 60% 100% 1506.5
L-proline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 35% 89% 220.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 60% 1506.5
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 35% 89% 220.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 60% 1506.5
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 35% 89% 220.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 60% 1506.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 89% 196.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 60% 1506.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 89% 196.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 60% 1506.5
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 30% 98% 190.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 60% 1506.5

Sequence Analysis Tools

View WP_054255670.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSTTIGIKVDDTLRERIRNAAHNMGRTPHWLIKQAVLQYVDALERGATTIRLTGLGEPPQ
DDGAEDAPPPPPMETAQPFLVFAQSILPQTPLRAAITAAWHRPETECLPALLPLARAQDA
EQSGKVRELATRLVQGLRDAPAGSGVAALVQEFSLSSQEGVALMCLAEALLRIPDRATRD
ALIRDKISKGDWKSHVGRSPSLFVNAAAWGLVLTGKLTSTSSEKSLSAALSRVIGKGGEP
LIRQGVHRAMKLMGEQFVTGQNIAEALANSRTYEKQGFRYSYDMLGEAAATDADAQRYLQ
AYEQAIHAIGAASNGRGIFEGPGISIKLSALHPRYSRAQYDRVMAELLPRVLRLAELAKQ
YDIGMNIDAEEADRLELSLDLMEALCAAPSLKGWSGIGFVVQAYQKRCPHVIDYLVDLAR
RSRRRLMVRLVKGAYWDSEIKRAQLDGLAGYPVYTRKVYTDVSYLACARKLLEAPDAIYP
QFATHNAQTLASIYHLAQSVGGSYYSGQYEFQCLHGMGEPLYAQVTGTAADGKLARPCRI
YAPVGSHETLLAYLVRRLLENGANTSFVNRIGDASVPIAELVTDPVEDALRIANQEGRLG
APHPRIALPADLFADLGAQSRPNSHGLNLAHEQQLASLAAALLYSTRQTYLAAPPGVPLP
ADPSRTPGWQPLRNPAELSDTVGWVYEAAAHDVQAACERAAQAAPIWAGTPPATRADALQ
RAADLLEQRSQPLMGLIMREAGKTLPNAVAEIREAVDFLRYYGAQVATQFDNAAQRPLGV
VLAISPWNFPLAIFCGQVAAALAAGNTVLAKPAEQTPLTAAAMVALLHEAGVPRDALQLV
PGQGESVGAALVAHPQVAGVMFTGSTEVARLIARQLSTRLSPTGQAIPLVAETGGQNAMV
VDSSALAEQVVADVLASAFDSAGQRCSALRLLCLQDDVADRTLTMLRDALQEWTLGNPDR
LHTDVGPVIDAEARAQIEAHIARMADAGQTVTRVERTDGALNGHFVAPAIIEIDSTSRLT
REVFGPVLHVIRYPREQLDALLDGINATGYGLTFGVHSRIDETIQHLSERIHAGNLYVNR
NVIGAVVGVQPFGGMGLSGTGPKAGGPLYLHRLVHGPANTALALLPPTPSLSEHPALLLL
RRLRQTTLPLPAPEQAQAHTTCEAALTTSRLGASLLLPGPTGESNRYRLLPRGPVWALPR
TPLGLVAQVAAALASGNPCHMVLPQDDNGCAAVWQALRAAAGDAGVAWLHSAEGAALADG
AIPVAALLFEGDGDALLQACRAVAARPGPLVRVESLGSDELQAGQGYDLAALCHEQSIST
NTAAAGGNAQLMTMA

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