GapMind for catabolism of small carbon sources

 

Alignments for a candidate for oah in Marinomonas arctica 328

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 WP_111606238.1 DK187_RS04960 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= SwissProt::Q39TV7
         (381 letters)



>NCBI__GCF_003259225.1:WP_111606238.1
          Length = 263

 Score = 82.0 bits (201), Expect = 2e-20
 Identities = 61/181 (33%), Positives = 84/181 (46%), Gaps = 4/181 (2%)

Query: 47  SVAEGIYNAWIILDNPKQYNSYTTDMVKAIILAFRRASVDRSVNAVVFTGVGDKAFCTGG 106
           SV  G+  A + L+ PK  NS+   M   +  A + A  D+ V A+V T  G + FC G 
Sbjct: 9   SVDSGV--ALLSLNRPKALNSFNEAMHLEVQQALKSALKDKQVRALVLTAEG-RGFCAGQ 65

Query: 107 NTKEY-AEYYAGNPQEYRQYMRLFNDMVSAILGCDKAVISRVNGMRIGGGQEIGMACDFS 165
           +  +   +  A +P       R +N ++  +      VI  VNG+  G G  I +ACD  
Sbjct: 66  DLSDRNVDPNAASPDLGISIERFYNPLIKQLQAFPMPVICAVNGVAAGAGANIPLACDLV 125

Query: 166 IAQDLANFGQAGPKHGSAAIGGATDFLPLMVGCEQAMVSGTLCEPFSAHKAARLGIICDV 225
           IA   A F QA  K G     G T FLP ++G  +A     L EP  A KA   G+I  V
Sbjct: 126 IAARSAKFIQAFCKIGLIPDSGGTWFLPRLIGMAKAKELALLGEPLMAEKALEWGMIYKV 185

Query: 226 V 226
           V
Sbjct: 186 V 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: 225
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: 381
Length of database: 263
Length adjustment: 27
Effective length of query: 354
Effective length of database: 236
Effective search space:    83544
Effective search space used:    83544
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 24 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