GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Rhizobium etli CFN 42

Align BadI (characterized)
to candidate WP_011423940.1 RHE_RS02885 enoyl-CoA hydratase/isomerase family protein

Query= metacyc::MONOMER-892
         (260 letters)



>NCBI__GCF_000092045.1:WP_011423940.1
          Length = 350

 Score = 62.0 bits (149), Expect = 2e-14
 Identities = 47/158 (29%), Positives = 70/158 (44%), Gaps = 4/158 (2%)

Query: 1   MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           MQ  ++I E R     I +NRP  +N+        + +AL     D +V  +V  G G+R
Sbjct: 1   MQDSEVIIERRGTAGIIRLNRPRALNSLTLAMIRTITEALDGFARDAEVATVVATGEGER 60

Query: 61  AFCTGGD-QSTHDGNYDGRGTVGLPMEE---LHTAIRDVPKPVIARVQGYAIGGGNVLAT 116
            FC GGD ++ H+    G G  G    E   L+  I   PKP +A + G  +GGG  L++
Sbjct: 61  GFCAGGDIRALHESARAGDGLAGTFWREEFRLNHMIAVYPKPYVALMDGITMGGGVGLSS 120

Query: 117 ICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGE 154
                I +E+         +G V     T  L +  GE
Sbjct: 121 HGRHRIVTERTRLAMPETGIGYVPDVGATWLLPKAPGE 158


Lambda     K      H
   0.319    0.138    0.418 

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: 191
Number of extensions: 8
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: 260
Length of database: 350
Length adjustment: 27
Effective length of query: 233
Effective length of database: 323
Effective search space:    75259
Effective search space used:    75259
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 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