GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Pseudomonas fluorescens FW300-N2E2

Align glutathione transferase (EC 2.5.1.18); maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate Pf6N2E2_4235 Glutathione S-transferase, unnamed subgroup (EC 2.5.1.18)

Query= BRENDA::O43708
         (216 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4235
          Length = 236

 Score = 66.2 bits (160), Expect = 5e-16
 Identities = 60/193 (31%), Positives = 86/193 (44%), Gaps = 7/193 (3%)

Query: 9   YSYFRSSCSWRVRIALALKGIDYKTVPINLIKDRGQQFSKDFQALNPMKQVPTLKIDGIT 68
           Y +  S  S RV++ L+L G+  + V ++L K  G+    DF ALN   QVP +  DG+ 
Sbjct: 35  YHFPLSGHSHRVQLMLSLLGLPVEEVFVDLAK--GEHKQADFLALNAFGQVPVIDDDGVV 92

Query: 69  IHQSLAIIEYLEEMRPTPRLLPQDPKKRASVRMISDLIAGGIQPLQNLSVLKQV-GEEMQ 127
           +  S AI+ YL       R LP DP   A V+      AG I      + L  V G    
Sbjct: 93  LADSNAILVYLAHKYGKGRWLPTDPVGAARVQRWLSAAAGPIHAGPATARLITVFGAAYN 152

Query: 128 LTWAQNAITCGFNALEQILQSTAG-IYCVGDEVTMADLCLVPQVANAERFKVDLTPYPTI 186
              A++ I    N L+ I Q  +   Y  GD  T+AD+     +A+A    V L  Y  +
Sbjct: 153 ---AEDVIARSHNVLKVIDQELSNRAYLAGDAATVADIAGYSYIAHAPEGNVSLEDYAHV 209

Query: 187 SSINKRLLVLEAF 199
            +   R+  L  F
Sbjct: 210 RAWLARIEALPGF 222


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: 78
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: 236
Length adjustment: 22
Effective length of query: 194
Effective length of database: 214
Effective search space:    41516
Effective search space used:    41516
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: 46 (22.3 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