GapMind for catabolism of small carbon sources

 

Alignments for a candidate for oah in Pseudomonas fluorescens FW300-N2E3

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 AO353_25675 AO353_25675 enoyl-CoA hydratase

Query= SwissProt::Q39TV7
         (381 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25675
          Length = 257

 Score = 69.3 bits (168), Expect = 1e-16
 Identities = 66/219 (30%), Positives = 91/219 (41%), Gaps = 19/219 (8%)

Query: 57  IILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGNTKEYAEYYA 116
           I L+ P+  N+    +V  +  A      +  +  +V TG   KAF  G + KE AE   
Sbjct: 17  ITLNRPQALNALNAQIVSELNHALDGLEANPEIGCIVLTG-SKKAFVAGADIKEMAELTY 75

Query: 117 GNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQDLANFGQA 176
             PQ Y     LF+D    +    K VI+ V G  +GGG E+ + CDF +A D A FGQ 
Sbjct: 76  --PQIYLD--DLFSDS-DRVANRRKPVIAAVAGFALGGGCELALMCDFILAGDNAKFGQP 130

Query: 177 GPKHGSAAIGGATDFLPLMVGCEQAM---VSGTLCEPFSAHKAARLGIICDVVP------ 227
               G     G T  L   VG  +AM   +SG L +   A +A R GI+  +VP      
Sbjct: 131 EINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLID---AVEAERCGIVARIVPVDELLD 187

Query: 228 -ALKVGGKFVANPTVVTDRYLDEYGRVVHGEFKAGAAFK 265
            ALKV          +     +   R        G  F+
Sbjct: 188 EALKVAALIAKKSLPIAMMVKESVNRAFEVSLSEGVRFE 226


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: 226
Number of extensions: 7
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: 257
Length adjustment: 27
Effective length of query: 354
Effective length of database: 230
Effective search space:    81420
Effective search space used:    81420
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