GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Brucella inopinata BO1

Align BadH (characterized)
to candidate WP_008511278.1 BIBO1_RS19255 SDR family oxidoreductase

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



>NCBI__GCF_000182725.1:WP_008511278.1
          Length = 252

 Score =  145 bits (367), Expect = 6e-40
 Identities = 102/253 (40%), Positives = 135/253 (53%), Gaps = 12/253 (4%)

Query: 4   LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63
           L+ K A+ITG G G G    +RFA+ GAK+ + D +   AE+VAG I   G TA AV  D
Sbjct: 3   LEGKVALITGAGSGFGEGMAKRFAKGGAKVVIVDRDKAGAERVAGEI---GDTALAVAAD 59

Query: 64  IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTK--TEPGEWERLIAINLTGALHM 121
           I+    VDAA+    +  G VDILVNNAG    KP      EP E++R++ +N+ G   M
Sbjct: 60  ISKEADVDAAVEAALSKFGKVDILVNNAGIG-HKPQNAELVEPEEFDRIVGVNVRGVYLM 118

Query: 122 HHAVLPGMVER----RHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHG 177
              ++P   E     +   I+N+AS  A       A Y A KG +V+ +K LA E A   
Sbjct: 119 TRKLIPHFKENGAKGQECVILNVASTGAGRPRPNLAWYNATKGWVVSVTKALAIELAPAK 178

Query: 178 ITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDA 237
           I V  + P   +T LL   T    + E++ + F  +IP+GRL KPDDLA A AF  S  A
Sbjct: 179 IRVVALNPVAGETPLL--TTFMGEDTEEIRKKFRDSIPMGRLLKPDDLAEAAAFLCSPQA 236

Query: 238 GFITGQVLSVSGG 250
             ITG  L V GG
Sbjct: 237 SMITGVALDVDGG 249


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: 152
Number of extensions: 6
Number of successful extensions: 4
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: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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