GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Caulobacter crescentus NA1000

Align BadH (characterized)
to candidate CCNA_00545 CCNA_00545 acetoacetyl-CoA reductase

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



>FitnessBrowser__Caulo:CCNA_00545
          Length = 240

 Score =  162 bits (409), Expect = 8e-45
 Identities = 93/248 (37%), Positives = 139/248 (56%), Gaps = 12/248 (4%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAEAVRCDIA 65
           + A +TGG  GIG A C R   +G K+A  +  N  AAE  A   ++ G     V+ ++ 
Sbjct: 3   RVAFVTGGTRGIGRAICERLIADGHKVAAGYSGNEAAAEACA---KELG--VMVVKGNVG 57

Query: 66  DRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAV 125
                 AA+      LGP+DILVNNAG        K    +W  +I +N+  A +M   V
Sbjct: 58  VFEDCQAAVKKVEAELGPIDILVNNAGITRDGMLHKMTYEQWSEVIRVNMDSAFNMTRPV 117

Query: 126 LPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCP 185
           + GM +R  GRI+NI+S   + G  G+  Y+A K GL+ F+K LA E+A+ G+TVNV+CP
Sbjct: 118 IEGMRDRSWGRIINISSINGQKGQMGQTNYSAAKAGLIGFTKALALENAKKGVTVNVICP 177

Query: 186 GPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVL 245
           G  DT ++A V      PE ++      IP+GRLG+ +++A  ++F   + AGF+TG  L
Sbjct: 178 GYIDTEMVAAV------PENVLAQIVAGIPVGRLGRGEEIADMVSFLAGERAGFVTGATL 231

Query: 246 SVSGGLTM 253
           +++GG  M
Sbjct: 232 TLNGGQYM 239


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: 170
Number of extensions: 7
Number of successful extensions: 4
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.

Links

Downloads

Related tools

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