GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Flavobacterium glycines Gm-149

Align BadH (characterized)
to candidate WP_066329803.1 BLR17_RS09120 SDR family oxidoreductase

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



>NCBI__GCF_900100165.1:WP_066329803.1
          Length = 254

 Score =  137 bits (344), Expect = 3e-37
 Identities = 80/252 (31%), Positives = 133/252 (52%), Gaps = 6/252 (2%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60
           M  L++K A+ITGGG GIG A    FA++GA++ + +L  ++A+     I   GG   A 
Sbjct: 1   MFSLKDKKAIITGGGSGIGKAISVLFAKQGAEVHIIELTAESAQSTVDEITAEGGKVFAH 60

Query: 61  RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120
            C++A    V A    T   +G + ILVNNAG         T   +++R++ +N+ G  +
Sbjct: 61  ACNVAKHDEVVA----TFEKIGNIHILVNNAGIAHVGKVDTTPEADFDRIMDVNVKGVYN 116

Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180
              A +P   +   G IVN+AS A+ VG S    Y+  KG +++ + ++AR++    I  
Sbjct: 117 CLFASIPQFRKSGGGSIVNMASIASWVGISDRFAYSTAKGAVMSMTLSVARDYINENIRC 176

Query: 181 NVVCPGPTDTALLAD--VTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAG 238
           N + P    T  +      +   N  ++ +  +K+ P+GR+GKP+++A    F  S++AG
Sbjct: 177 NSISPARVHTPFVDGFIAKNYPGNEAEIFDKLSKSQPIGRMGKPEEIATLALFLASEEAG 236

Query: 239 FITGQVLSVSGG 250
           FITG    + GG
Sbjct: 237 FITGSDYPIDGG 248


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: 156
Number of extensions: 4
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: 254
Length adjustment: 24
Effective length of query: 231
Effective length of database: 230
Effective search space:    53130
Effective search space used:    53130
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.

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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