GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Methanospirillum lacunae Ki8-1

Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_109968284.1 DK846_RS07420 SDR family oxidoreductase

Query= curated2:Q57664
         (305 letters)



>NCBI__GCF_003173355.1:WP_109968284.1
          Length = 304

 Score =  218 bits (554), Expect = 2e-61
 Identities = 113/303 (37%), Positives = 192/303 (63%), Gaps = 7/303 (2%)

Query: 3   LVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGNKNNI-NPKAEFVNADIRDKDLDEKIN 61
           ++TGGAGFIGSH+  K +  +++V+++DNL +G   +I +   +F+   + D  L +++ 
Sbjct: 4   VITGGAGFIGSHLA-KALAMDHEVVVIDNLFSGKMEHIVHTPVKFIQGSVTDFLLLKQV- 61

Query: 62  FKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIVFASSGGAVYG 121
           F+  + + H+AA  +V  SV++P+   + N+ GT+N+L   ++ ++ K+VFASS  +VYG
Sbjct: 62  FEGSDGIFHEAAITSVPRSVKDPLPTNETNITGTLNVLLAAKEMNVRKVVFASSS-SVYG 120

Query: 122 EPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVYGERQDPKGE- 180
           +   LP  EN P NP+SPYG+SK+ GE+Y ++++ LYG++   LRY NV+G  QDPK E 
Sbjct: 121 DTPVLPKTENMPPNPMSPYGISKFAGEQYCRVFSELYGLKTVSLRYFNVFGPCQDPKSEY 180

Query: 181 AGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNWKNE-IVNIGTGKETS 239
           + VI  FI ++LK++SP+I+GDG QTRDF YV DV +AN+ A+    E + N+   ++ S
Sbjct: 181 SAVIPKFITRILKHESPVIYGDGKQTRDFTYVKDVVQANIKAMESNIEGVFNVAYNQQIS 240

Query: 240 VNELFDIIKHEIGFRGEAIYDKPREGEVYRIYLDIKKAES-LGWKPEIDLKEGIKRVVNW 298
           +  L  +I    G     I+++ R G++     DI + ++ +G+ P   +K G+   + W
Sbjct: 241 LISLASLIMELTGITAPIIFERERPGDIRDSLADISRIQNQIGYTPHYSVKSGLMETIAW 300

Query: 299 MKN 301
            +N
Sbjct: 301 YQN 303


Lambda     K      H
   0.317    0.140    0.405 

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: 265
Number of extensions: 21
Number of successful extensions: 5
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: 305
Length of database: 304
Length adjustment: 27
Effective length of query: 278
Effective length of database: 277
Effective search space:    77006
Effective search space used:    77006
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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