GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praC in Paraburkholderia bryophila 376MFSha3.1

Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate H281DRAFT_01655 H281DRAFT_01655 4-oxalocrotonate tautomerase family enzyme

Query= BRENDA::P49172
         (63 letters)



>FitnessBrowser__Burk376:H281DRAFT_01655
          Length = 124

 Score = 57.4 bits (137), Expect = 3e-14
 Identities = 22/56 (39%), Positives = 43/56 (76%)

Query: 1  MPIAQLYIIEGRTDEQKETLIRQVSEAMANSLDAPLERVRVLITEMPKNHFGIGGE 56
          MP  ++Y+ +G +DE+K +LI+ +++A  +++ AP E VR+L++E+P +H G+GG+
Sbjct: 1  MPTLEVYLPQGHSDERKASLIQGLTQATVDAIGAPAESVRILLSELPVSHIGLGGK 56



 Score = 56.6 bits (135), Expect = 6e-14
 Identities = 26/63 (41%), Positives = 40/63 (63%)

Query: 1   MPIAQLYIIEGRTDEQKETLIRQVSEAMANSLDAPLERVRVLITEMPKNHFGIGGEPASK 60
           +P+    +I GRT+ QKE LI  +SE  A+ L+ PL+  RV+I ++P   FG+GG+ A  
Sbjct: 62  LPVIIAILIAGRTEAQKEALIAHLSETSASVLNVPLQSTRVMIKDIPSTDFGLGGKTARS 121

Query: 61  VRR 63
           + R
Sbjct: 122 LGR 124


Lambda     K      H
   0.317    0.134    0.366 

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: 36
Number of extensions: 2
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 63
Length of database: 124
Length adjustment: 9
Effective length of query: 54
Effective length of database: 115
Effective search space:     6210
Effective search space used:     6210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (20.3 bits)
S2: 38 (19.2 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