GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Magnetospirillum magneticum AMB-1

Align BadH (characterized)
to candidate WP_043743408.1 AMB_RS04300 beta-ketoacyl-ACP reductase

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



>NCBI__GCF_000009985.1:WP_043743408.1
          Length = 240

 Score =  141 bits (356), Expect = 1e-38
 Identities = 91/248 (36%), Positives = 128/248 (51%), Gaps = 12/248 (4%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKI-AVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIA 65
           + A++TGG  GIG        + G K+ A +  N +AA K       A     +++ D+ 
Sbjct: 3   RLAIVTGGTRGIGREISVTLKKAGYKVVANYGGNDEAAAKFT-----AETGIPSMKWDVG 57

Query: 66  DRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAV 125
              + +AAIA      GPV+I+VNNAG        +     WE +I  NLT   +M    
Sbjct: 58  SYPACEAAIAKIVAEHGPVEIIVNNAGITRDATLHRMSYQMWEEVIHTNLTSCFNMARLA 117

Query: 126 LPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCP 185
           +  M ER  GRIVNI S   + G  G+  YAA K G+  F+K LA+E A   ITVN + P
Sbjct: 118 IDSMRERGFGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGAAKNITVNAIAP 177

Query: 186 GPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVL 245
           G  DT ++  V      P  ++E     IP+GRLG+ +D+A  + F  +D+A FITG  L
Sbjct: 178 GYVDTDMVRAV------PPAVLEKIIAKIPVGRLGRAEDIARCVMFLIADEADFITGSTL 231

Query: 246 SVSGGLTM 253
           SV+GG  M
Sbjct: 232 SVNGGQHM 239


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: 166
Number of extensions: 7
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: 240
Length adjustment: 24
Effective length of query: 231
Effective length of database: 216
Effective search space:    49896
Effective search space used:    49896
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 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