GapMind for catabolism of small carbon sources

 

Protein GFF4241 in Pseudomonas stutzeri RCH2

Annotation: Psest_4314 ABC-type metal ion transport system, ATPase component

Length: 335 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 hi Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 85% 100% 564.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 304.3
L-arginine catabolism artP med Histidine transport ATP-binding protein HisP (characterized) 45% 94% 187.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 45% 94% 187.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-lysine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 45% 94% 187.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 44% 84% 184.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-glutamate catabolism gltL med Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 43% 98% 176 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 42% 96% 175.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 42% 98% 174.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 42% 98% 174.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 43% 95% 173.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 42% 92% 173.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 42% 93% 170.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 41% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 42% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 41% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 42% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 41% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 41% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 41% 92% 168.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 41% 81% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 41% 94% 167.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 40% 98% 166.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 40% 98% 166.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 37% 80% 177.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 39% 97% 172.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 38% 75% 169.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 90% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 90% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 40% 89% 160.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 39% 94% 157.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 36% 74% 149.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 74% 133.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 76% 131.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 33% 88% 125.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 85% 564.3

Sequence Analysis Tools

View GFF4241 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGG
RILVNGEDVTALDADGLRRFRQRVGMIFQHFNLLMSKTVADNVAMPLRLAGIRSRREIDA
RVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTASV
LQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFLHPKHPTTQR
FVLEDEAMDESELHDDFAHVPGRILRLTFQGDSTYKPLLGTVARETGVDYSILSGRIDRI
KDTPYGQLTLALIGGDMTAAMTRLQAADVHVEVLR

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 preprint 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