GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-med in Herbaspirillum seropedicae SmR1

Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate HSERO_RS16320 HSERO_RS16320 FAD-binding molybdopterin dehydrogenase

Query= metacyc::MONOMER-18072
         (282 letters)



>FitnessBrowser__HerbieS:HSERO_RS16320
          Length = 494

 Score = 83.2 bits (204), Expect = 1e-20
 Identities = 53/165 (32%), Positives = 83/165 (50%), Gaps = 2/165 (1%)

Query: 103 MQVRNLGTIGGSAANADPSADIPTVLTALNAEIILSSASGNRSVNALDFFKGAFATDLRK 162
           + VRN GT+GG+ AN  P  D    L AL A+I+L S  G R +   DF+     + L+ 
Sbjct: 296 LPVRNAGTLGGNLANGSPIGDSMPWLIALGAQIVLYSVRGQRVMPLEDFYLAYQKSALQA 355

Query: 163 GEIIS--EIVLPNLEGYRTIYKKVVRRAGDFALVSLALAIKLRQNEIEDIRLAYGGVGER 220
            E++    I LP  E    +YK   R   D + V  A A++++ + I   R+AYGG+   
Sbjct: 356 DELVQAVRIPLPRKELRFRVYKLSKRFDQDISAVCAAFALQMQGDTIVQARIAYGGMAAT 415

Query: 221 PFRALEVEKSVMGKRLNDELVEEIVSKVSSQVNPPSDTRGSSWYR 265
           P RA + E  + G   ++   +  ++ ++    P SD R S+ YR
Sbjct: 416 PKRAAQAEAVLQGGPWSEAQAQAAMAALAQDYAPLSDMRASAAYR 460


Lambda     K      H
   0.317    0.134    0.367 

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: 237
Number of extensions: 8
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: 282
Length of database: 494
Length adjustment: 30
Effective length of query: 252
Effective length of database: 464
Effective search space:   116928
Effective search space used:   116928
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 (21.6 bits)
S2: 49 (23.5 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