GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Shewanella loihica PV-4

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

Query= metacyc::MONOMER-15953
         (257 letters)



>FitnessBrowser__PV4:5210423
          Length = 708

 Score =  117 bits (294), Expect = 5e-31
 Identities = 70/164 (42%), Positives = 94/164 (57%), Gaps = 3/164 (1%)

Query: 16  LITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAERDL 75
           +I L +P  +N+L   L   L A+L  AE D    A+VL  S K F  GADI E +  D 
Sbjct: 15  VIILNQPP-VNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISEFSSDDA 73

Query: 76  VGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEINLG 135
           +     P+V     + A  K ++AAVNG  LGGGCEL +  D  IA   A+ G PE+NLG
Sbjct: 74  LAEPNLPQVC--DALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPEVNLG 131

Query: 136 IMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEV 179
           I+PGAGGTQRL R  G  LA++M+ SG+ + A     AG++  +
Sbjct: 132 ILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNL 175


Lambda     K      H
   0.320    0.134    0.374 

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: 389
Number of extensions: 20
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: 257
Length of database: 708
Length adjustment: 32
Effective length of query: 225
Effective length of database: 676
Effective search space:   152100
Effective search space used:   152100
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 (21.8 bits)
S2: 50 (23.9 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