GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Acidovorax sp. GW101-3H11

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2523
          Length = 699

 Score = 84.0 bits (206), Expect = 8e-21
 Identities = 55/156 (35%), Positives = 83/156 (53%), Gaps = 11/156 (7%)

Query: 14  VARIKIANPPVNVLDMETMKEIISAIDEVEG---VDVIVFSGEGKSFSAGAEIKEHFPDK 70
           VA I +ANPPVN L + T + I+  +        V  IV +G G +FS GA+IKE   DK
Sbjct: 11  VAVITMANPPVNGLGLATRQGIVDGLGRANADAAVKSIVITGAGGAFSGGADIKEFGTDK 70

Query: 71  A---PEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVPEI 127
           +   P ++     +I  +       VAA+   A+GGG ELA+ C + +A+    + +PE+
Sbjct: 71  SLQEPNLL----SVIAAIENSAKPVVAAMHSVAMGGGLELALGCHYRIAAPGCSIALPEV 126

Query: 128 TLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAE 162
            L   P       LPR+IG + A  LI++GE + +E
Sbjct: 127 KLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVKSE 162


Lambda     K      H
   0.318    0.136    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: 402
Number of extensions: 23
Number of successful extensions: 4
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: 252
Length of database: 699
Length adjustment: 31
Effective length of query: 221
Effective length of database: 668
Effective search space:   147628
Effective search space used:   147628
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: 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