GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsC in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate Pf1N1B4_594 Glucose ABC transport system, inner membrane component 2

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_594 Glucose ABC transport
           system, inner membrane component 2
          Length = 281

 Score =  539 bits (1389), Expect = e-158
 Identities = 272/281 (96%), Positives = 274/281 (97%)

Query: 1   MTNQLGKSGISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDG 60
           M+NQLGK GISFSRIAIYATLLLAAA+YLIPLVVMLLTSFKSPEDIRTGNLLS P VIDG
Sbjct: 1   MSNQLGKPGISFSRIAIYATLLLAAAIYLIPLVVMLLTSFKSPEDIRTGNLLSLPQVIDG 60

Query: 61  IGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL 120
           IGWIKAWD VG YFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL
Sbjct: 61  IGWIKAWDSVGSYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL 120

Query: 121 PFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG 180
           PFQTVLLPASFTLGK GLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG
Sbjct: 121 PFQTVLLPASFTLGKIGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG 180

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

Query: 241 GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG
Sbjct: 241 GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 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: 408
Number of extensions: 11
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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