GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Rhizobium etli CFN 42

Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate WP_004674373.1 RHE_RS29575 2Fe-2S iron-sulfur cluster-binding protein

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



>NCBI__GCF_000092045.1:WP_004674373.1
          Length = 94

 Score = 74.7 bits (182), Expect = 4e-19
 Identities = 41/89 (46%), Positives = 56/89 (62%), Gaps = 2/89 (2%)

Query: 71  VLAVRCEGRYIETVEGLAANGRLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLRRNPSPT 130
           +LAV+ +G  IET+   A+   L R+Q+ F +  G QC F  P   +A   LLR +P  T
Sbjct: 1   MLAVQADGSEIETMAREASI--LGRIQEAFRQHHGLQCEFVGPVSSLAIIDLLRHHPLET 58

Query: 131 DEEIRTALSGNLCRCTGYAKIVESVQAAA 159
           D++IR ALSGN+CRCTGY  IV +V+  A
Sbjct: 59  DDKIREALSGNICRCTGYENIVNAVRELA 87


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: 55
Number of extensions: 3
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: 163
Length of database: 94
Length adjustment: 14
Effective length of query: 149
Effective length of database: 80
Effective search space:    11920
Effective search space used:    11920
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: 41 (20.4 bits)

This GapMind analysis is from Apr 09 2024. 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