GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Amantichitinum ursilacus IGB-41

Align BadH (characterized)
to candidate WP_053937509.1 WG78_RS09155 3-oxoacyl-ACP reductase FabG

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



>NCBI__GCF_001294205.1:WP_053937509.1
          Length = 247

 Score =  157 bits (398), Expect = 1e-43
 Identities = 91/251 (36%), Positives = 135/251 (53%), Gaps = 6/251 (2%)

Query: 4   LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63
           L+ K A++TG   GIG A      + GA +     + + A+ +   ++ AG     +R  
Sbjct: 3   LEGKVALVTGASRGIGQAIALELGRLGATVVGTATSQEGADAITAYLQAAGLKGHGLRLQ 62

Query: 64  IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123
           + +  + +A ++      G + +LVNNAG        + +  EW+ ++A NL     +  
Sbjct: 63  VTEDGACEALVSQIEKDSGAIAVLVNNAGITRDNLLMRMKDDEWDAIMATNLKPVYQLSK 122

Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183
           AV+ GM++ R GRIVNIAS     G+ G+  Y+A K  L  F+K+LARE    GITVN V
Sbjct: 123 AVIRGMMKARWGRIVNIASVVGATGNPGQTNYSAAKAALFGFTKSLAREIGSRGITVNAV 182

Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243
            PG  DT    D+T G  + +K      ++I LGRLG   D+A A+AF  SD AG+ITG 
Sbjct: 183 APGFIDT----DMTRGLPDEQK--AKLVESIALGRLGAAQDIADAVAFLSSDKAGYITGN 236

Query: 244 VLSVSGGLTMN 254
            L V+GG+ MN
Sbjct: 237 TLHVNGGMYMN 247


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: 176
Number of extensions: 6
Number of successful extensions: 2
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 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