GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-small in Pseudomonas fluorescens FW300-N2E2

Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate Pf6N2E2_5938 Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16)

Query= metacyc::MONOMER-18073
         (163 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5938
          Length = 156

 Score =  117 bits (294), Expect = 7e-32
 Identities = 59/151 (39%), Positives = 87/151 (57%)

Query: 12  IKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLF 71
           I +K+NG  ++  V+  + L+  +R+  G  GTK GC    CGACT+ ++G   +SC   
Sbjct: 2   ITLKLNGKDHQLDVTEDMPLLWAIRDVAGYNGTKFGCGMGLCGACTIHIDGAPARSCITP 61

Query: 72  AVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEE 131
                G +I+TI+GL  D     +Q+A+ +    QCG+C  G IM A  LLK NPNPS+E
Sbjct: 62  IGSVKGLDISTIDGLHADPVGQIVQKAWLDTAVAQCGYCQGGQIMSATALLKTNPNPSDE 121

Query: 132 EVRDGLHGNICRCTGYQNIVKAVLDASRRLR 162
           ++ + + GNICRC  Y  I  A+  AS  L+
Sbjct: 122 QIEEAMVGNICRCGTYNRIKTAIRQASTHLK 152


Lambda     K      H
   0.322    0.138    0.409 

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: 101
Number of extensions: 3
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: 163
Length of database: 156
Length adjustment: 17
Effective length of query: 146
Effective length of database: 139
Effective search space:    20294
Effective search space used:    20294
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 43 (21.2 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