GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Dyella japonica UNC79MFTsu3.2

Align BadH (characterized)
to candidate N515DRAFT_2873 N515DRAFT_2873 3-oxoacyl-[acyl-carrier-protein] reductase

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



>FitnessBrowser__Dyella79:N515DRAFT_2873
          Length = 247

 Score =  166 bits (419), Expect = 5e-46
 Identities = 97/250 (38%), Positives = 131/250 (52%), Gaps = 8/250 (3%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAVFDL--NLDAAEKVAGAIRDAGGTAEAVRCDI 64
           + A++TGG GG+G   CR+ A  G ++   DL    D        + D  G       D+
Sbjct: 3   RIAIVTGGIGGLGTEICRQLALAGRQVIAADLPARADRVAAFQAELADLDGAVRFEPVDV 62

Query: 65  ADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHA 124
           +D  S    IA      G VD+LVN AG        K +P  W+ L+ +NL G  +M   
Sbjct: 63  SDFASCSELIARVEAAHGRVDVLVNAAGITRDTTLRKMDPQHWQELMRVNLDGVFNMCRH 122

Query: 125 VLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVC 184
           V+ GM  R  GRIVN++S   + G  G+  YAA K G+  F   LARE AR G+TVN V 
Sbjct: 123 VVEGMSARGFGRIVNLSSVNGQTGQFGQTNYAAAKAGVHGFGMALARETARKGVTVNTVS 182

Query: 185 PGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQV 244
           PG  DT L+A V      P ++     + IP+GRLG P D+A A+ F  +DDAG+ITG  
Sbjct: 183 PGYCDTPLVARV------PAEIRAQILEDIPVGRLGSPADIARAVCFLAADDAGYITGAN 236

Query: 245 LSVSGGLTMN 254
           L V+GG  M+
Sbjct: 237 LPVNGGYFMS 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: 179
Number of extensions: 8
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: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
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