Protein GFF4241 in Pseudomonas stutzeri RCH2
Annotation: FitnessBrowser__psRCH2:GFF4241
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
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
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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:
- 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:
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