GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Pseudomonas simiae WCS417

Align BadI (characterized)
to candidate GFF2712 PS417_13835 crotonase

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



>FitnessBrowser__WCS417:GFF2712
          Length = 367

 Score = 73.9 bits (180), Expect = 4e-18
 Identities = 49/155 (31%), Positives = 76/155 (49%), Gaps = 4/155 (2%)

Query: 4   EDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFC 63
           ++++ E+RN +  + +NRP  +NA        L   L     D  V A+VL GAG++AFC
Sbjct: 17  DEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFC 76

Query: 64  TGGD-QSTHDGNYDG---RGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICD 119
            GGD +S +D   +G        +    L  AI    KPV+A + G+ +GGG  L    D
Sbjct: 77  AGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGAD 136

Query: 120 LTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGE 154
           L + +E++        +G      G+ FL R+ GE
Sbjct: 137 LRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGE 171


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: 208
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: 260
Length of database: 367
Length adjustment: 27
Effective length of query: 233
Effective length of database: 340
Effective search space:    79220
Effective search space used:    79220
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 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