GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter permease (characterized, see rationale)
to candidate Pf1N1B4_5114 Maltose/maltodextrin ABC transporter, permease protein MalG

Query= uniprot:A0A161ZE72
         (280 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5114 Maltose/maltodextrin
           ABC transporter, permease protein MalG
          Length = 280

 Score =  546 bits (1406), Expect = e-160
 Identities = 280/280 (100%), Positives = 280/280 (100%)

Query: 1   MNLRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPDFSNYA 60
           MNLRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPDFSNYA
Sbjct: 1   MNLRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPDFSNYA 60

Query: 61  AVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQ 120
           AVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQ
Sbjct: 61  AVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQ 120

Query: 121 VAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGAS 180
           VAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGAS
Sbjct: 121 VAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGAS 180

Query: 181 PWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPH 240
           PWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPH
Sbjct: 181 PWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPH 240

Query: 241 ELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG 280
           ELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG
Sbjct: 241 ELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG 280


Lambda     K      H
   0.329    0.141    0.433 

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: 398
Number of extensions: 12
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: 280
Length of database: 280
Length adjustment: 26
Effective length of query: 254
Effective length of database: 254
Effective search space:    64516
Effective search space used:    64516
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