GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_10285
          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.

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