GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Escherichia coli BW25113

Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate 16948 b2868 xanthine dehydrogenase, Fe-S binding subunit (NCBI)

Query= metacyc::MONOMER-17403
         (163 letters)



>FitnessBrowser__Keio:16948
          Length = 159

 Score =  125 bits (313), Expect = 4e-34
 Identities = 67/126 (53%), Positives = 80/126 (63%), Gaps = 3/126 (2%)

Query: 32  LVDYLRDIAGLTGVKTGCDGGECGACTVLIDGEAAPSCLVLAVRCEGRYIETVEGLAANG 91
           L + LR+  GL  VK GC  GECGACTVL+DG A  SCL LA   EG+ I T+EG A  G
Sbjct: 28  LSELLRE-QGLLSVKQGCCVGECGACTVLVDGTAIDSCLYLAAWAEGKEIRTLEGEAKGG 86

Query: 92  RLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLR--RNPSPTDEEIRTALSGNLCRCTGYA 149
           +L  +QQ + +    QCGFCTPG+IMA   +L   R    T  EIR  L+GNLCRCTGY 
Sbjct: 87  KLSHVQQAYAKSGAVQCGFCTPGLIMATTAMLAKPREKPLTITEIRRGLAGNLCRCTGYQ 146

Query: 150 KIVESV 155
            IV +V
Sbjct: 147 MIVNTV 152


Lambda     K      H
   0.322    0.138    0.425 

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: 140
Number of extensions: 11
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: 163
Length of database: 159
Length adjustment: 17
Effective length of query: 146
Effective length of database: 142
Effective search space:    20732
Effective search space used:    20732
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 (21.9 bits)
S2: 43 (21.2 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