GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Stutzerimonas stutzeri A1501

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_011911348.1 PST_RS00510 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::O87873
         (258 letters)



>NCBI__GCF_000013785.1:WP_011911348.1
          Length = 701

 Score = 75.5 bits (184), Expect = 3e-18
 Identities = 56/173 (32%), Positives = 83/173 (47%), Gaps = 6/173 (3%)

Query: 12  LERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVD 71
           LER G +  + +  P  N +  A+   +  A  +  +AP + AV+L  EGP F  GA + 
Sbjct: 7   LERRGDIALILVNNPPVNALGHAVRKGLLDAFRQADEAPEVTAVVLVCEGPTFMAGADIK 66

Query: 72  EH-MPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFG 130
           E   P Q      SL  ++  +     P +  + G  LGGGLEVA   +   A  DAK G
Sbjct: 67  EFGKPPQAP----SLPEVIEVIEGCRKPSVAVIHGSALGGGLEVALGCHYRIARSDAKVG 122

Query: 131 QPEIRLGVFAPAASCLLPPRV-GQACAEDLLWSGRSIDGAEGHRIGLIDVLAE 182
            PE++LG+   A      PR+ G   A +++ SG+ I  AE     ++D L E
Sbjct: 123 LPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPIGAAEALEHHIVDELFE 175


Lambda     K      H
   0.321    0.135    0.402 

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: 420
Number of extensions: 28
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: 258
Length of database: 701
Length adjustment: 32
Effective length of query: 226
Effective length of database: 669
Effective search space:   151194
Effective search space used:   151194
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

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