GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutC in Dechlorosoma suillum PS

Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate Dsui_1584 Dsui_1584 hypothetical protein

Query= uniprot:A0A0C4YFN9
         (234 letters)



>FitnessBrowser__PS:Dsui_1584
          Length = 217

 Score = 69.3 bits (168), Expect = 6e-17
 Identities = 55/146 (37%), Positives = 74/146 (50%), Gaps = 16/146 (10%)

Query: 91  PAAEQGAALMRALPA------SVAPLSYARP---IEAWKAELFDTVDAGFTVARSGIAAT 141
           PAA     + R LP       S+A  ++A     +EA  +   D V  G T     +A T
Sbjct: 75  PAAAAAYLIARELPTRAVCWPSLADQAWAGAGLQVEARPSRGDDLV--GITSTFCAVADT 132

Query: 142 GTLVLAPDAQTPRTVSLVPPLHIALVYAETLHP---DLHCAARAERWSAGMPTNLVLVSG 198
           GTL+L   A T    SL+P  HIA+V  E + P   D     RAE+  A    N V  SG
Sbjct: 133 GTLMLLSGADTHAATSLLPETHIAVVPVERVVPLMEDGFALLRAEKGEAPRAVNFV--SG 190

Query: 199 PSKTSDIQQTLAYGAHGPRELWVIIV 224
           PS+T+DI+QT+  GAHGP  + +I+V
Sbjct: 191 PSRTADIEQTVTLGAHGPYRVHLILV 216


Lambda     K      H
   0.317    0.127    0.375 

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: 164
Number of extensions: 8
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: 234
Length of database: 217
Length adjustment: 22
Effective length of query: 212
Effective length of database: 195
Effective search space:    41340
Effective search space used:    41340
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: 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