GapMind for catabolism of small carbon sources

 

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

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate Ac3H11_1483 2-oxo-hepta-3-ene-1,7-dioic acid hydratase (EC 4.2.-.-)

Query= BRENDA::B0VXM8
         (267 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1483
          Length = 249

 Score =  181 bits (460), Expect = 1e-50
 Identities = 103/245 (42%), Positives = 144/245 (58%), Gaps = 8/245 (3%)

Query: 24  KREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGPKMGLTSQAKMAQMKVKEPIY 83
           + ++   + + P+++ E+ Y IQ E ++++   G  I G K+GLTS+A     ++ EP Y
Sbjct: 3   RTQLRHFSLQYPEMTIEDGYAIQREWVRLELAEGRTIKGRKIGLTSRAMQIASQITEPDY 62

Query: 84  GYLFDYMFVPSGGAIHMSELIHPKVEVEIAFILGEDLEGPHVTSTQVLSATKYVAPALEI 143
             L D MF  +GG I     I P+VEVE+AFILG+ L+GP VT   VLSAT YV PA+EI
Sbjct: 63  APLMDDMFFDAGGDIPFERFIAPRVEVELAFILGKPLKGPGVTLFDVLSATDYVVPAIEI 122

Query: 144 IDSRYQDF------TFTLPDVIADNASSSRVVIGNTMTPIHSLKTDLDLIGAALYINGEL 197
           IDSR + F         + D I+D A+++ +V+G    P+  L  DL  +GA L+ NG +
Sbjct: 123 IDSRIEQFDRETRVMRKVFDTISDFAANAGIVLGG--RPVKPLDVDLRWVGALLHKNGVI 180

Query: 198 KACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGITEAIQLSAGDTVIGQLDQ 257
           +  G  AAV NHPAN VA LAN +A  GE+L AGD++L G  T      AGD+       
Sbjct: 181 EESGLAAAVLNHPANGVAWLANKIAPYGEQLNAGDVVLAGSFTRPTAAVAGDSFHADYGP 240

Query: 258 LGDVS 262
           LG VS
Sbjct: 241 LGSVS 245


Lambda     K      H
   0.316    0.134    0.364 

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: 159
Number of extensions: 7
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: 267
Length of database: 249
Length adjustment: 24
Effective length of query: 243
Effective length of database: 225
Effective search space:    54675
Effective search space used:    54675
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 (21.6 bits)
S2: 47 (22.7 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