GapMind for catabolism of small carbon sources

 

Alignments for a candidate for oah in Azospirillum brasilense Sp245

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 AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase

Query= SwissProt::Q39TV7
         (381 letters)



>FitnessBrowser__azobra:AZOBR_RS18155
          Length = 248

 Score =  100 bits (248), Expect = 6e-26
 Identities = 61/174 (35%), Positives = 82/174 (47%), Gaps = 6/174 (3%)

Query: 55  AWIILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGNTKEYAEY 114
           A I LD P++ N+ T +M   ++ A  R + D  +  VV TG G +AFC G + +E   Y
Sbjct: 6   ATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDIRELDRY 65

Query: 115 YAGNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQDLANFG 174
                 +     R   D   AI G  K  I+ VNG   GGG E  M+CD  IA + A FG
Sbjct: 66  ------DTAWNFRNREDYCDAIRGLRKPSIAAVNGYAFGGGLETAMSCDIRIASENAQFG 119

Query: 175 QAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDVVPA 228
               K G    GG   FL   +G   A +     +P  A KA   G++ +VVPA
Sbjct: 120 APEIKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPA 173


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: 220
Number of extensions: 6
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: 381
Length of database: 248
Length adjustment: 27
Effective length of query: 354
Effective length of database: 221
Effective search space:    78234
Effective search space used:    78234
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