GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N2E3

Align glucose transporter, ATPase component (characterized)
to candidate AO353_17105 AO353_17105 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17105
          Length = 233

 Score =  117 bits (294), Expect = 2e-31
 Identities = 63/218 (28%), Positives = 124/218 (56%), Gaps = 6/218 (2%)

Query: 15  LVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74
           +++ +++S  +G I+A+  V+V++  GE+V L+G NGAGKSTL+  L G+ Q  +G IR 
Sbjct: 1   MLQFENVSTFYGKIQALHGVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60

Query: 75  NGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECR 134
            G+++   +       +I  + +   +   L    NL +G          +    + +  
Sbjct: 61  MGEELVGQDSARIMRKSIAVVPEGRRVFARLTVEENLAMGGFFT------EKGDYQEQMD 114

Query: 135 KIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAE 194
           K++       ++F++    +SGG++Q +AI RA+    K+L++DEP+  L P   Q + +
Sbjct: 115 KVLGLFPRLKERFNQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFD 174

Query: 195 LIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232
           +I+QL+  G+ +FL++ + N  +++ DRA V++NG++V
Sbjct: 175 IIEQLRKDGVTVFLVEQNANQALKVADRAYVLENGRVV 212


Lambda     K      H
   0.317    0.135    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 130
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 233
Length adjustment: 24
Effective length of query: 236
Effective length of database: 209
Effective search space:    49324
Effective search space used:    49324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

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

Links

Downloads

Related tools

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