GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Flavobacterium sp. LM5

Align BadH (characterized)
to candidate WP_024981780.1 BXU11_RS13235 3-oxoacyl-[acyl-carrier-protein] reductase

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



>NCBI__GCF_002017945.1:WP_024981780.1
          Length = 248

 Score =  139 bits (349), Expect = 7e-38
 Identities = 80/252 (31%), Positives = 134/252 (53%), Gaps = 7/252 (2%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIA-VFDLNLDAAEKVAGAIRDAGGTAEA 59
           M  L+ K A+ITG   GIG      FA+ GA IA  +  ++++A  +   +   G  A+ 
Sbjct: 1   MKLLEGKVAIITGASRGIGKGIAEVFAKHGANIAFTYSSSVESALALENELNTMGIKAKG 60

Query: 60  VRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGAL 119
            + + AD       +       G VDIL+NNAG        +    +++++I +NL    
Sbjct: 61  YQSNAADFNEAQTFVDAVLADFGSVDILINNAGITKDNLMMRMSEADFDQVIDVNLKSVF 120

Query: 120 HMHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGIT 179
           +M  A+    +++R G I+N++S     G++G+  YAA K G++ FSK++A E     I 
Sbjct: 121 NMTKAIQKTFLKQRAGSIINMSSVVGVKGNAGQTNYAASKAGVIGFSKSVALELGSRNIR 180

Query: 180 VNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGF 239
            NV+ PG  +T + A ++      + +++ + + IPL R G  DD+A A  FF SD + +
Sbjct: 181 CNVIAPGFIETEMTAKLS------DDVVKGWREGIPLKRGGSTDDVANACLFFASDMSAY 234

Query: 240 ITGQVLSVSGGL 251
           +TGQVL+V GG+
Sbjct: 235 VTGQVLNVCGGM 246


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: 154
Number of extensions: 5
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: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
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 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