GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF in Shewanella halifaxensis HAW-EB4

Align 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) (characterized)
to candidate WP_012277207.1 SHAL_RS11065 alpha/beta fold hydrolase

Query= BRENDA::G3KFX4
         (282 letters)



>NCBI__GCF_000019185.1:WP_012277207.1
          Length = 278

 Score =  100 bits (250), Expect = 3e-26
 Identities = 81/260 (31%), Positives = 118/260 (45%), Gaps = 22/260 (8%)

Query: 25  DQGEGFPVLLIHGSGPGVTAWANWRLVMPQLAQ-NRRVIAPDMLGFGYSDRPADGRYHQQ 83
           DQGEG  VL IHGSGPG +  +N++   P   +   R I  D+ GFG SD+P D  Y   
Sbjct: 28  DQGEGKTVLWIHGSGPGASGHSNFKGNYPVFEKAGFRNIVLDLPGFGQSDKPDDINYDLA 87

Query: 84  RWVEHAIGVLDALGIQQADIVGNSFGGGLALALAIRHPERVRRLVLMGSVGVSFPIT--- 140
            +VE     L   GI    ++GNS GG +AL  A+++P+ V +L+LM   GV    T   
Sbjct: 88  FFVETLNQFLVKTGISHCTLLGNSLGGAIALGQALKYPQSVEQLILMAPGGVEERETYFK 147

Query: 141 ----PGLDAVWGYEP-SFASMRRLMDVFAYDRS-LVTNELAELRYQASIRPGFQESFAQM 194
                 +  ++G  P     MR++M +  +D S L  N L E    A  +P  +  F+ M
Sbjct: 148 MIGIQKMVEIYGQGPMGVEEMRKVMHLQLFDTSQLDDNTLRERADVAKTQP--KNLFSTM 205

Query: 195 FPAPRQRWVDGLASDEADIRALPHETLVIHGREDQVIPLAASLTLAEWIARAQLHVFGHC 254
                      + +    +R +    L   G  D   P A      +    A+  +   C
Sbjct: 206 L----------VPNMTDQLRLIECPILGFWGTNDNFNPPAGVDKFLDNAPNARFLLLNRC 255

Query: 255 GHWTQIEHAERFARLVENFL 274
           GHW Q+EH + F R   +FL
Sbjct: 256 GHWIQVEHQDLFNRTCLDFL 275


Lambda     K      H
   0.323    0.138    0.432 

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: 208
Number of extensions: 14
Number of successful extensions: 3
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: 282
Length of database: 278
Length adjustment: 26
Effective length of query: 256
Effective length of database: 252
Effective search space:    64512
Effective search space used:    64512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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