Protein WP_068460177.1 in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Protein WP_068460177.1 in Hyphomicrobium sulfonivorans WDL6

Annotation: NCBI__GCF_001541235.1:WP_068460177.1

Length: 1070 amino acids

Source: GCF_001541235.1 in NCBI

Candidate for 22 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)	50%	99%	1002.3
L-arginine catabolism	putA	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-arginine catabolism	putA	hi	delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238)		99%	613.6
L-arginine catabolism	rocA	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-arginine catabolism	rocA	hi	delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238)		99%	613.6
L-citrulline catabolism	put1	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-citrulline catabolism	putA	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-citrulline catabolism	putA	hi	delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238)		99%	613.6
L-citrulline catabolism	rocA	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-citrulline catabolism	rocA	hi	delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238)		99%	613.6
L-proline catabolism	put1	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-proline catabolism	putA	hi	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)	50%	99%	1002.3
L-proline catabolism	putA	hi	delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238)		99%	613.6
L-arginine catabolism	gabD	lo	succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)	32%	95%	196.1	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-citrulline catabolism	gabD	lo	succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)	32%	95%	196.1	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
putrescine catabolism	gabD	lo	succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)	32%	95%	196.1	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-arginine catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)	34%	83%	188	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-citrulline catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)	34%	83%	188	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
4-hydroxybenzoate catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
2'-deoxyinosine catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
2-deoxy-D-ribose catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
ethanol catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-threonine catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
thymidine catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-tryptophan catabolism	adh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)	31%	83%	187.6	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-lysine catabolism	amaB	lo	Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)	31%	91%	184.9	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3
L-phenylalanine catabolism	pad-dh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	31%	83%	184.1	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)	50%	1002.3

Sequence Analysis Tools

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MVVTKPAGANDDISARLKLIPARDEIAASYLLDERQLVDRLIERAVFSEAERSRASELAL
RLAHAARSGRGKQAGVEAFMQEYGLSSEEGVILMCIAEALLRIPDSETADELIAEKLAGG
EWDKHRGHSDSMFVNASTWALMLTGRVVKMREAQGSNPINALKRLVARSGEPVIRQAVRQ
AVKLLGDQFVLGRTIREAIGNAKDYQAKGYLLSYDMLGEAARTHKDADTYFERYLAAIDA
VGQAAGPLTTLHADALYARPGISVKLSALHPRFEPGKRELLKSELLPRVLTLARAARARG
LTLTIDAEEQDRLDPTLEIFSATLVDPALDNWNGLGIAVQAYGKRAIPVLRWLRRLAERA
GKRIPVRLVKGAYWDSEIKWAQERALENYPVFTRKQNTDVSYLAAARLLISDAKAFYPQF
ATHNAYSIAATHVAAGPAAIEFQRLYGMGEGLYDEVVGKGKIIRRPVRIYAPVGSHEDLL
AYLVRRLLENGANTSFVKQLADDETTIAGIIRDPVAQAEAERSAGAKPARAIVLPRDIYM
PERKAAAGMALTEPTVRQALFTQMGNALDDVYAAGPIIGGKAITGGDMASLVTCPHDRRE
RLGTVRVTTLDQADQAIARATGASQAWNRIGGEKRAEVLCAAADLFERDHARLMAVIVRE
AGKTLEDAQGDVREAVDYLRYYAAQARRLFAGPVTQPGPTGERNTLSLNGRGVFACISPW
NFPLAIFTGQVAAALAAGNAVLAKPAEQTPITAFLATQLLHEAGVPGDVLQLLPGSGRLG
EALVKDKRVKGIAFTGSNETAWSIQRALADRRGAIVPFIAETGGINAMIADSSALPEQVV
RDAVRSAFNSAGQRCSAARVLFVQDEVADETIEMLVGAVETLAIGDPFDYATDIGPVIDD
SAQDFLDGHKVRMQRQGTQLVDLPLPDACRAGNYVTPAVFEIESLDVLDAEVFGPILHVV
RYQRGALPKVIDAINASGYGLTLGLHSRLETVADYVADHARIGNLYVNRNQIGAMVGTQP
FGGEGLSGTGPKAGGPHTLLAYATERVRSTDLTATGGNIELLTPESDAGA

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources