GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Shewanella loihica PV-4

Align BadH (characterized)
to candidate 5211109 Shew_3525 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)

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



>FitnessBrowser__PV4:5211109
          Length = 241

 Score =  129 bits (325), Expect = 4e-35
 Identities = 83/248 (33%), Positives = 130/248 (52%), Gaps = 11/248 (4%)

Query: 6   NKTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAEAVRCDI 64
           NK  +ITG   GIG A   + A+ G  IA+ F  N  AA+     +   G     ++ D+
Sbjct: 2   NKRVLITGASRGIGKAIALKLAETGYDIALHFHSNQAAADATQTELEALGAKVSRLQFDV 61

Query: 65  ADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHM-HH 123
           ADR  V AAI       G    +V NAG      F      EW+ +I  NL G  ++ H 
Sbjct: 62  ADRAGVKAAIEADIYQHGAYYGVVLNAGITRDTAFPAMSDEEWDGVIHTNLDGFYNVIHP 121

Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183
             +P +  R+ GRI+ +AS +   G+ G+  Y+A K G++  +K L+ E A+  ITVN +
Sbjct: 122 CTMPMIQSRQGGRIITMASVSGIAGNRGQVNYSASKAGIIGATKALSLELAKRKITVNCI 181

Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243
            PG  +T ++         P+++++   + +P+ R+GK  ++AG   F  SDDA +IT Q
Sbjct: 182 APGLIETDMVESF------PQEMVK---ELVPMRRMGKASEIAGLANFLMSDDAAYITRQ 232

Query: 244 VLSVSGGL 251
           V+SV+GG+
Sbjct: 233 VISVNGGM 240


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: 137
Number of extensions: 6
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: 241
Length adjustment: 24
Effective length of query: 231
Effective length of database: 217
Effective search space:    50127
Effective search space used:    50127
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