GapMind for catabolism of small carbon sources

 

Alignments for a candidate for oah in Escherichia coli BW25113

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 16369 b2262 naphthoate synthase (NCBI)

Query= SwissProt::Q39TV7
         (381 letters)



>FitnessBrowser__Keio:16369
          Length = 285

 Score =  104 bits (259), Expect = 3e-27
 Identities = 60/173 (34%), Positives = 90/173 (52%), Gaps = 1/173 (0%)

Query: 55  AWIILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGGNTKEYAEY 114
           A I ++ P+  N++    VK +I A   A  D ++  ++ TG GDKAFC+GG+ K   +Y
Sbjct: 35  AKITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIILTGAGDKAFCSGGDQKVRGDY 94

Query: 115 YAGNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFSIAQDLANFG 174
                     ++ +  D    I  C K V++ V G  IGGG  + M CD +IA D A FG
Sbjct: 95  GGYKDDSGVHHLNVL-DFQRQIRTCPKPVVAMVAGYSIGGGHVLHMMCDLTIAADNAIFG 153

Query: 175 QAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDVVP 227
           Q GPK GS   G    ++  +VG ++A     LC  + A +A  +G++  VVP
Sbjct: 154 QTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAKQALDMGLVNTVVP 206


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: 283
Number of extensions: 10
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: 285
Length adjustment: 28
Effective length of query: 353
Effective length of database: 257
Effective search space:    90721
Effective search space used:    90721
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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