GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Pseudomonas fluorescens GW456-L13

Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14); 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16); (4S)-4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.42) (characterized)
to candidate PfGW456L13_1903 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)

Query= BRENDA::P0A955
         (213 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1903
          Length = 221

 Score =  199 bits (505), Expect = 4e-56
 Identities = 91/200 (45%), Positives = 138/200 (69%)

Query: 9   ESILTTGPVVPVIVVKKLEHAVPMAKALVAGGVRVLEVTLRTECAVDAIRAIAKEVPEAI 68
           +SI     ++PVI + + +  +P+A AL AGG+  LEVTLR++  + AI+ + ++ PE +
Sbjct: 18  DSICAKARILPVITIAREQDVLPLADALAAGGLTALEVTLRSQFGLKAIQILREQRPELV 77

Query: 69  VGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYG 128
            GAGTVL+   LA    AG+QF ++PG+T  LL+A+    IPL+PGIS  S +M G   G
Sbjct: 78  TGAGTVLDRHMLAAAEAAGSQFIVTPGITRDLLEASVASPIPLLPGISNASGIMEGYGLG 137

Query: 129 LKEFKFFPAEANGGVKALQAIAGPFSQVRFCPTGGISPANYRDYLALKSVLCIGGSWLVP 188
            + FK FPAE +GGV A++A+ GPF +V+FCPTGG+ PAN + Y+ALK+V+C+GGSW++ 
Sbjct: 138 YRRFKLFPAEVSGGVAAIKALGGPFGEVKFCPTGGVGPANIKSYMALKNVMCVGGSWMLD 197

Query: 189 ADALEAGDYDRITKLAREAV 208
            + ++ GD+ RI +   EA+
Sbjct: 198 PEWIKNGDWARIQECTAEAL 217


Lambda     K      H
   0.317    0.135    0.387 

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: 180
Number of extensions: 5
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: 213
Length of database: 221
Length adjustment: 22
Effective length of query: 191
Effective length of database: 199
Effective search space:    38009
Effective search space used:    38009
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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