GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Paraburkholderia bryophila 376MFSha3.1

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_02585 H281DRAFT_02585 FAD/FMN-containing dehydrogenase

Query= reanno::Smeli:SMc00833
         (405 letters)



>FitnessBrowser__Burk376:H281DRAFT_02585
          Length = 461

 Score = 84.7 bits (208), Expect = 5e-21
 Identities = 64/184 (34%), Positives = 86/184 (46%), Gaps = 10/184 (5%)

Query: 7   PASEEGIASVVRSAAAERVTLAVVGGGTR-AGLGNPVRADRTLSTRRLSGIVTYDPAEMT 65
           P S E +A  +R   A    +   GG T   G  N +  +  LS  R++ IV  D    T
Sbjct: 47  PRSTEDVARALRVCHAFSQPVVTQGGLTGLVGGANALGGEVALSLERMNRIVEVDRTSAT 106

Query: 66  MSALAGTPVAEV-EAALHAKGQMLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAG 124
           M+  AG P+  V EAAL A      + P+D        G  TIGG  A N  G R    G
Sbjct: 107 MTVEAGVPLQVVQEAALDAG----FYFPLD----LGARGSCTIGGNLATNAGGNRVIKYG 158

Query: 125 AARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPP 184
             RD +LG+  V   GE      +++KN +G DL  L+ GS GTL ++T    ++ P P 
Sbjct: 159 MMRDQVLGIEAVLANGEVTSGMHKMIKNNSGYDLRHLLIGSEGTLAVITRAVLRLRPRPT 218

Query: 185 AAAT 188
           A AT
Sbjct: 219 AVAT 222


Lambda     K      H
   0.318    0.134    0.387 

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: 412
Number of extensions: 24
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 405
Length of database: 461
Length adjustment: 32
Effective length of query: 373
Effective length of database: 429
Effective search space:   160017
Effective search space used:   160017
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: 51 (24.3 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