GapMind for catabolism of small carbon sources

 

Alignments for a candidate for oah in Phaeobacter inhibens BS107

Align 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized)
to candidate GFF3595 PGA1_c36500 enoyl-CoA hydratase/isomerase

Query= SwissProt::Q39TV7
         (381 letters)



>FitnessBrowser__Phaeo:GFF3595
          Length = 258

 Score = 80.5 bits (197), Expect = 5e-20
 Identities = 60/183 (32%), Positives = 87/183 (47%), Gaps = 21/183 (11%)

Query: 57  IILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGNTKE-----Y 111
           I L+ P+  N+  ++++  +  A   A     V  ++ TG  +KAF  G + KE     +
Sbjct: 17  IKLNRPEALNALNSELLSELCTALEEADASDKVRCIILTG-SEKAFAAGADIKEMSDKSF 75

Query: 112 AEYYAGNPQEYRQYMRLF---NDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQ 168
            E ++ N         LF   ND +SAI    K +I+ V G  +GGG E+ M CDF IA 
Sbjct: 76  TEVFSTN---------LFAGVNDRISAIR---KPIIAAVAGYALGGGCELAMLCDFIIAA 123

Query: 169 DLANFGQAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDVVPA 228
           D A FGQ     G  A  G T  L   VG  ++M         +A +A R G++  VVPA
Sbjct: 124 DTAKFGQPEINLGVIAGIGGTQRLTRFVGKSKSMDMNLTGRFMTAEEAERAGLVSRVVPA 183

Query: 229 LKV 231
            K+
Sbjct: 184 KKL 186


Lambda     K      H
   0.318    0.135    0.403 

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: 218
Number of extensions: 5
Number of successful extensions: 1
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: 381
Length of database: 258
Length adjustment: 27
Effective length of query: 354
Effective length of database: 231
Effective search space:    81774
Effective search space used:    81774
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 (21.7 bits)
S2: 48 (23.1 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