GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Dinoroseobacter shibae DFL-12

Align BadH (characterized)
to candidate 3609684 Dshi_3067 acetoacetyl-CoA reductase (RefSeq)

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



>FitnessBrowser__Dino:3609684
          Length = 240

 Score =  164 bits (416), Expect = 1e-45
 Identities = 96/243 (39%), Positives = 137/243 (56%), Gaps = 10/243 (4%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66
           + A++TGG  GIG A  ++   +G  +A      D   + A A  +A G  +  + ++AD
Sbjct: 3   RVALVTGGSRGIGEAISKKLKADGYTVAATYAGND---EKAAAFTEATGI-KTYKWNVAD 58

Query: 67  RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126
             S  A IA     LGP++++V NAG     PF K  P +W  +I  NLTG  +  H V 
Sbjct: 59  YESSKAGIAQVEADLGPIEVVVANAGITRDAPFHKMTPEQWHEVIDTNLTGVFNTIHPVW 118

Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186
           PGM ER+ GRI+ I+S   + G   +  YAA K G +   K+LA+E AR GIT N VCPG
Sbjct: 119 PGMRERKFGRIIVISSINGQKGQFAQVNYAATKAGDLGIVKSLAQEGARAGITANAVCPG 178

Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246
              T ++       A PEK+ E+    IP+GRLG+P+++A  +AF  SDDAGFI+G  +S
Sbjct: 179 YIATEMV------MAIPEKVRESIIAGIPVGRLGEPEEIARCVAFLASDDAGFISGSTIS 232

Query: 247 VSG 249
            +G
Sbjct: 233 ANG 235


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: 152
Number of extensions: 5
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: 240
Length adjustment: 24
Effective length of query: 231
Effective length of database: 216
Effective search space:    49896
Effective search space used:    49896
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