GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__PV4:5210423
          Length = 708

 Score =  119 bits (298), Expect = 2e-31
 Identities = 67/148 (45%), Positives = 91/148 (61%), Gaps = 5/148 (3%)

Query: 17  ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPA 76
           I LN+P  +N+L   L   L   + +AE+D  +  I++   GK FC GADI++F+    +
Sbjct: 16  IILNQPP-VNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISEFS----S 70

Query: 77  EAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEINL 136
           +         ++ D +EA  K  +A +NG ALGGG EL LACD RIA   A+LGLPE+NL
Sbjct: 71  DDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPEVNL 130

Query: 137 GIYPGYGGTQRLTRVIGKGRALEMMMTG 164
           GI PG GGTQRL R+ G   ALEM+ +G
Sbjct: 131 GILPGAGGTQRLPRIGGVQLALEMITSG 158


Lambda     K      H
   0.315    0.135    0.382 

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: 365
Number of extensions: 13
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: 259
Length of database: 708
Length adjustment: 32
Effective length of query: 227
Effective length of database: 676
Effective search space:   153452
Effective search space used:   153452
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: 42 (22.0 bits)
S2: 51 (24.3 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