GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Brevibacterium jeotgali SJ5-8

Align BadH (characterized)
to candidate WP_101590136.1 BJEO58_RS14305 (S)-acetoin forming diacetyl reductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_900169175.1:WP_101590136.1
          Length = 261

 Score =  154 bits (388), Expect = 2e-42
 Identities = 97/261 (37%), Positives = 141/261 (54%), Gaps = 7/261 (2%)

Query: 1   MARLQN-KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEA 59
           MAR  N K A+I GGG GIG A   R  ++G K+AV D N   A +VA ++      A A
Sbjct: 1   MARQDNGKVALIIGGGQGIGRAAIERLHRDGFKVAVGDFNTVTANEVADSLGGKDNGAIA 60

Query: 60  VRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGAL 119
           V  +  DR SV AA+ TT + LG  D+++NNAG             +++++  +N+ G L
Sbjct: 61  VEVNATDRDSVFAAVETTASELGGFDVIINNAGIAPQTSIEDATEADFDKIFDLNVKGVL 120

Query: 120 HMHHAVLPGMVERRH-GRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGI 178
               A    + E  H G+I++ AS A   G+ G  +Y+A K  +   S+T AR+ A++GI
Sbjct: 121 WGIQAATAKLKELGHGGKIISAASQAGHKGNKGIPLYSATKFAVRGMSQTAARDLAQYGI 180

Query: 179 TVNVVCPGPTDTALL----ADVTSGAANPEKL-IEAFTKAIPLGRLGKPDDLAGAIAFFG 233
           TVN   PG   T L+     +V   A  PE+   E FT+ I L RL +P+D+A  I+F  
Sbjct: 181 TVNTYAPGIVRTPLMENLAKEVAEAAGQPEEWGWEQFTQDITLDRLSEPEDVANVISFLA 240

Query: 234 SDDAGFITGQVLSVSGGLTMN 254
             D+ +ITGQ + V GG+  N
Sbjct: 241 GSDSDYITGQSIVVDGGMVFN 261


Lambda     K      H
   0.318    0.135    0.398 

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: 155
Number of extensions: 6
Number of successful extensions: 3
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: 255
Length of database: 261
Length adjustment: 24
Effective length of query: 231
Effective length of database: 237
Effective search space:    54747
Effective search space used:    54747
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: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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