Protein Pf1N1B4_691 in Pseudomonas fluorescens FW300-N1B4
Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691
Length: 351 amino acids
Source: pseudo1_N1B4 in FitnessBrowser
Candidate for 38 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | malK | med | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 44% | 96% | 271.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 89% | 267.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 89% | 267.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 89% | 267.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 89% | 267.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| trehalose catabolism | thuK | med | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 44% | 91% | 260.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 42% | 96% | 257.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-sorbitol, ATPase component (characterized) | 44% | 90% | 253.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 43% | 92% | 253.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 83% | 251.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 83% | 251.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 83% | 251.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 83% | 251.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 83% | 251.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 83% | 251.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 43% | 95% | 248.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 43% | 95% | 248.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-maltose catabolism | malK1 | med | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 46% | 86% | 246.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 42% | 81% | 240 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-cellobiose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 45% | 78% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-glucose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 45% | 78% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| lactose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 45% | 78% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-maltose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 45% | 78% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| sucrose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 45% | 78% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| trehalose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 45% | 78% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 40% | 81% | 238.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-maltose catabolism | malK_Sm | med | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 45% | 81% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| trehalose catabolism | malK | med | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 45% | 81% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 40% | 92% | 238.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 39% | 92% | 229.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 37% | 93% | 183.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) | 33% | 98% | 131.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) | 33% | 98% | 131.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-alanine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 100% | 130.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 100% | 130.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-serine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 100% | 130.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-threonine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 100% | 130.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 100% | 130.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 42% | 271.9 |
Sequence Analysis Tools
View Pf1N1B4_691 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
MTGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGEI
RLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL
IQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQLQ
QRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSGNIF
PATALGNGKVSLPGGDALQVPICSSIVVGEKVKMLIRPEDLQLSQPQATAGNRLLGKVTF
VRDIGATIETTVECSGVSFTALSTPCQGVGLSIGNPVSVTLPAEACRVLSA
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 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