GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Desulfovibrio vulgaris Hildenborough

Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate 209253 DVU0319 NAD-dependent epimerase/dehydratase family protein

Query= BRENDA::Q9WYX9
         (309 letters)



>MicrobesOnline__882:209253
          Length = 341

 Score =  181 bits (460), Expect = 2e-50
 Identities = 116/327 (35%), Positives = 178/327 (54%), Gaps = 25/327 (7%)

Query: 4   LVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNR-----------NALFYEQSI 52
           LVTG AGFIGS++++ L+  G  V+ +DN  +G   NL+            +  F E  I
Sbjct: 19  LVTGVAGFIGSNLLETLLRQGQRVVGLDNFLTGYQRNLDMVRDLVGEERWASFRFIEGDI 78

Query: 53  EDEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKF 112
            D        +    ++V H AA  SV  S+ +P    + NI G + +L  +   G K F
Sbjct: 79  RDLATCHE--ACKGVDHVLHQAALGSVPRSIDDPILSNECNITGFVNMLVAARDAGAKSF 136

Query: 113 IFSSTGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYAN 172
           +++++    YG+     P  E  I  P+SPY + KY  E+Y + FAR YG     LRY N
Sbjct: 137 VYAASSST-YGDE-PTLPKVEDIIGKPLSPYAVTKYVNELYADVFARCYGFTAIGLRYFN 194

Query: 173 VYGPRQDPYGE-AGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAM---EK 228
           V+G RQDP+G  A V+  +   +LRGE V + GDGE  RD+ Y+D+VV+AN+LA     +
Sbjct: 195 VFGQRQDPFGAYAAVIPQWFASLLRGETVFVNGDGETSRDFCYIDNVVQANILASLAPAE 254

Query: 229 GDNEVFNIGTGRGTTVNQLFKLLKEITGYDKEP------VYKPPRKGDVRKSILDYTKAK 282
             ++V+N+  G+ TT+N+LF L++E     K        V++  R GDVR S+ D T+A+
Sbjct: 255 ARDKVYNVAFGQRTTLNELFDLIREEVVRHKPEAAGATCVHRDFRAGDVRHSLADITRAQ 314

Query: 283 EKLGWEPKVSLEEGLKLTVEYFRKTLE 309
             LG+ P   + EGL+L  +++   L+
Sbjct: 315 TLLGYAPVYDVREGLRLAGDWYAANLK 341


Lambda     K      H
   0.318    0.139    0.396 

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: 251
Number of extensions: 16
Number of successful extensions: 6
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: 309
Length of database: 341
Length adjustment: 28
Effective length of query: 281
Effective length of database: 313
Effective search space:    87953
Effective search space used:    87953
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 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