GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Haloglycomyces albus DSM 45210

Align BadH (characterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG

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



>NCBI__GCF_000527155.1:WP_025272362.1
          Length = 236

 Score =  130 bits (328), Expect = 2e-35
 Identities = 78/244 (31%), Positives = 127/244 (52%), Gaps = 14/244 (5%)

Query: 10  VITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIADRTS 69
           +ITGG  GIG A  +R   +G  +AV   ++  AE                + D++D  +
Sbjct: 7   LITGGTRGIGRAAAQRLKDDGFTVAVASRSIPDAENRLDV--------HHYQVDVSDGNA 58

Query: 70  VDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVLPGM 129
               I T    +G +D+L+N+AG     P       +W  +I  NL G  +M  ++   M
Sbjct: 59  CKDLITTVEDEVGDIDVLINSAGIVRDSPLLTMTGDDWNDVIRTNLDGTYNMCRSMAFSM 118

Query: 130 VERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPGPTD 189
           ++R++G I+N++S A   G+  ++ Y+A K G++ FSK L++E  R  I VNVV PG  +
Sbjct: 119 MKRKNGSIINLSSVAGIQGNPTQSNYSASKAGIIGFSKALSKELGRFNIRVNVVAPGFIE 178

Query: 190 TALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLSVSG 249
           T + AD+       E + +   + IPLGR+G  DD+A  + F  S  A ++TG V+ V G
Sbjct: 179 TDMTADLA------ESVKKKAVENIPLGRMGSVDDVAHLVGFLASPRATYMTGAVVPVDG 232

Query: 250 GLTM 253
           G+ +
Sbjct: 233 GIIL 236


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: 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: 255
Length of database: 236
Length adjustment: 24
Effective length of query: 231
Effective length of database: 212
Effective search space:    48972
Effective search space used:    48972
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: 46 (22.3 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