GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Pseudomonas fluorescens FW300-N2C3

Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate AO356_11540 AO356_11540 glutathione S-transferase

Query= curated2:P57109
         (212 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_11540
          Length = 231

 Score = 68.2 bits (165), Expect = 1e-16
 Identities = 55/196 (28%), Positives = 93/196 (47%), Gaps = 16/196 (8%)

Query: 1   MKLYTYYRSTSSYRVRIALALKGL--DYQSLPVNLIRDGGEHRQPAYLALNPQGRVPALQ 58
           MK+Y ++      RVRIALA KGL  + + +PVNL    GEH++P +LA+N  G +P L+
Sbjct: 16  MKIYDWFNGPYPARVRIALAEKGLLPNIEFVPVNLW--AGEHKKPEFLAINYSGTLPVLE 73

Query: 59  VDEGELLIQSPAIIEYLEERYPQPALLSSDPLRRARERGVAALVGCDIHPLHNASVLNLL 118
           +D+G  + +  AI +YL+     P L    P+ +     +      +     +A   +  
Sbjct: 74  LDDGTRIAECTAITQYLDSLDGHPTLTGETPVEKGIIHMMTKRAEIEFLDAVSAYFHHAT 133

Query: 119 RQWGHDEE--QVRQW---IGHWVGQGLAAVEQLIGDQGWCFGDRPGLADVYLVPQLYAAE 173
              G D E  Q  +W   +     +G+   + L+ D+ +  GD+  +AD+ ++  +  A 
Sbjct: 134 PGLGPDVELYQNAEWGARMRDKAIRGMRYFDNLLKDRPFVAGDKFSMADIAVLGGMIFAS 193

Query: 174 RFG-------VALDAW 182
                     VAL AW
Sbjct: 194 LVQLPVPEECVALRAW 209


Lambda     K      H
   0.321    0.138    0.434 

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: 133
Number of extensions: 9
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: 212
Length of database: 231
Length adjustment: 22
Effective length of query: 190
Effective length of database: 209
Effective search space:    39710
Effective search space used:    39710
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 (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