GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Pseudomonas fluorescens GW456-L13

Align BadH (characterized)
to candidate PfGW456L13_3458 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3458
          Length = 251

 Score =  142 bits (358), Expect = 7e-39
 Identities = 92/256 (35%), Positives = 135/256 (52%), Gaps = 13/256 (5%)

Query: 3   RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62
           +L  K  ++TGG  GIG A  + F +EGA +   DL      + A    D GG A +  C
Sbjct: 2   QLAGKRIIVTGGARGIGAAVVKAFVEEGAHVVSLDLG-----EAASITGDGGGWAHSRVC 56

Query: 63  DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122
           DIAD  SVDAA A  +  L  +D+LV+ AG             EWE++ A+N  G    +
Sbjct: 57  DIADSQSVDAAFAWASEQLNGLDVLVHAAGIAPNASADSITLDEWEKVFAVNTRGTFLTN 116

Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182
            A    +++   GRI+N AS A  +G  G+A YAA KG ++A+++T+ARE    GITVN 
Sbjct: 117 RAAYE-LLKGSGGRIINFASAAGVLGQPGKAHYAASKGAVLAWTRTVAREWGPLGITVNA 175

Query: 183 VCPGPTDTALLADVTSGAANPEKLIE---AFTKAIPL-GRLGKP-DDLAGAIAFFGSDDA 237
           + P       + D T  + + E+L +        +P+ G+LG+P  DLA  + F   D +
Sbjct: 176 IAPAMWTP--MYDATRASMSAEQLQQHDAYMAGQVPIGGKLGEPARDLAPVLVFLAGDGS 233

Query: 238 GFITGQVLSVSGGLTM 253
            F+TGQ L + GG+ M
Sbjct: 234 RFVTGQTLVIDGGMMM 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: 160
Number of extensions: 11
Number of successful extensions: 5
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: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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