GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate AO353_03385 AO353_03385 sugar ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03385
          Length = 281

 Score =  542 bits (1397), Expect = e-159
 Identities = 271/281 (96%), Positives = 275/281 (97%)

Query: 1   MTNQLGKSGISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDG 60
           M+NQLGK  +SFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWP VIDG
Sbjct: 1   MSNQLGKPALSFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPQVIDG 60

Query: 61  IGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL 120
           IGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL
Sbjct: 61  IGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL 120

Query: 121 PFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG 180
           PFQTVLLPASFT+GK GLANTTTGLVLVH+VYGLAFTTLFFRNYYVSIPDALVKAARLDG
Sbjct: 121 PFQTVLLPASFTVGKLGLANTTTGLVLVHIVYGLAFTTLFFRNYYVSIPDALVKAARLDG 180

Query: 181 AGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTST 240
           AGFFTIF KILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTST
Sbjct: 181 AGFFTIFGKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTST 240

Query: 241 GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           G KEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG
Sbjct: 241 GVKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281


Lambda     K      H
   0.329    0.143    0.447 

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: 410
Number of extensions: 8
Number of successful extensions: 1
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: 281
Length of database: 281
Length adjustment: 26
Effective length of query: 255
Effective length of database: 255
Effective search space:    65025
Effective search space used:    65025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 bits)

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:

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