GapMind for catabolism of small carbon sources


Alignments for a candidate for DVU3032 in Pseudomonas fluorescens FW300-N2C3

Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate AO356_07560 AO356_07560 (Fe-S)-binding protein

Query= uniprot:Q726S4
         (209 letters)

          Length = 489

 Score = 52.0 bits (123), Expect = 2e-11
 Identities = 34/115 (29%), Positives = 56/115 (48%), Gaps = 12/115 (10%)

           R+ LR+     DIG + V   +AETGT ++  N    R+++ +   H+AV    K+V   

            D    L+ L    +G     Y   ISGP +  +++        GP E+HL+L++

Lambda     K      H
   0.317    0.132    0.371 

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: 193
Number of extensions: 9
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: 209
Length of database: 489
Length adjustment: 27
Effective length of query: 182
Effective length of database: 462
Effective search space:    84084
Effective search space used:    84084
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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