GapMind for catabolism of small carbon sources

 

Aligments for a candidate for maiA in Pseudomonas fluorescens FW300-N2E3

Align glutathione transferase (EC 2.5.1.18); maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate AO353_10285 AO353_10285 glutathione S-transferase

Query= BRENDA::O43708
         (216 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_10285 AO353_10285
           glutathione S-transferase
          Length = 207

 Score = 67.4 bits (163), Expect = 2e-16
 Identities = 57/193 (29%), Positives = 88/193 (45%), Gaps = 5/193 (2%)

Query: 8   LYSYFRSSCSWRVRIALALKGIDYKTVPINLIKDRGQQFSKDFQALNPMKQVPTLKIDGI 67
           LY++ RS  + RV + L+L  +  + + ++L K   +Q   DF ALN   QVP +   G+
Sbjct: 6   LYNFPRSGHAHRVELMLSLLELPTELIFVDLAKGAHKQ--PDFLALNAFGQVPVIDDQGV 63

Query: 68  TIHQSLAIIEYLEEMRPTPRLLPQDPKKRASVRMISDLIAGGIQPLQNLSVLKQVGEEMQ 127
            +  S AI+ YL +     R LP DP   A V+    + AG I      ++ + +     
Sbjct: 64  VLADSNAILVYLAQKYGKGRWLPADPVGAARVQRWLSIAAGPI--AFGPAIARLITVFGA 121

Query: 128 LTWAQNAITCGFNALEQILQS-TAGIYCVGDEVTMADLCLVPQVANAERFKVDLTPYPTI 186
              A   IT   N L+ I Q  +   Y  GDE T+AD+     +A+A    V L  Y  +
Sbjct: 122 PNNADEVITRSHNLLKVIDQELSKSTYLAGDEPTIADVAAYSYIAHAPEGNVSLADYANV 181

Query: 187 SSINKRLLVLEAF 199
            +   R+  L  F
Sbjct: 182 RAWLARIEALPGF 194


Lambda     K      H
   0.321    0.136    0.400 

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: 71
Number of extensions: 2
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: 216
Length of database: 207
Length adjustment: 21
Effective length of query: 195
Effective length of database: 186
Effective search space:    36270
Effective search space used:    36270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 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