GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacB in Herbaspirillum seropedicae SmR1

Align predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate HSERO_RS05540 HSERO_RS05540 cytochrome C'

Query= reanno::Cola:Echvi_1841
         (141 letters)



>FitnessBrowser__HerbieS:HSERO_RS05540
          Length = 104

 Score = 82.8 bits (203), Expect = 1e-21
 Identities = 38/79 (48%), Positives = 57/79 (72%), Gaps = 1/79 (1%)

Query: 63  LVKESDCPSCHMVERKIVGPAYKDVAEKYESTDENIETLAKRVVDGNNGVWGQVPMPAHP 122
           L K  +C +CH V+ KIVGPA+K+VA+KY    +    L ++V++G  GVWG VPMPA+ 
Sbjct: 26  LAKSKNCMACHSVDAKIVGPAFKEVAKKYAGQKDAEAKLTQKVLNGGGGVWGAVPMPANK 85

Query: 123 G-LSEDDAKKMVKYILMLK 140
           G +SE +A+++VK++L LK
Sbjct: 86  GQVSEAEARELVKWVLTLK 104


Lambda     K      H
   0.309    0.127    0.361 

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: 39
Number of extensions: 1
Number of successful extensions: 1
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: 141
Length of database: 104
Length adjustment: 13
Effective length of query: 128
Effective length of database: 91
Effective search space:    11648
Effective search space used:    11648
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.3 bits)
S2: 41 (20.4 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