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 209495 DVU0554 NAD-dependent epimerase/dehydratase family protein

Query= BRENDA::Q9WYX9
         (309 letters)



>MicrobesOnline__882:209495
          Length = 312

 Score =  182 bits (461), Expect = 1e-50
 Identities = 107/302 (35%), Positives = 164/302 (54%), Gaps = 13/302 (4%)

Query: 5   VTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGK---VENLNRNALFYEQSIEDEEMMERI 61
           V G +GF+GSH+V  L++ G  V      S       + L  +   +     + + +ER 
Sbjct: 8   VLGASGFLGSHLVHHLLKAGCQVHAFSRDSRRNPLLTDELMSSCSIFTGDFFNTQDVER- 66

Query: 62  FSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGAI 121
            +L   +  FHL +      S  +P RD + N+ GSL LLE   + GV+K +++S+GGAI
Sbjct: 67  -ALADCDVCFHLVSTTIPKTSNDDPLRDVRENLSGSLTLLECVRRTGVRKVVYASSGGAI 125

Query: 122 YGENVKVFPTPETEIPHPISP---YGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGPRQ 178
           YG+++     P     HP  P   YGI K + E YL  +   YG+ Y  LR +N +GP Q
Sbjct: 126 YGKHLM----PRISENHPTDPLCSYGIVKLAVEKYLALYHELYGIDYAALRISNPFGPLQ 181

Query: 179 DPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAME-KGDNEVFNIG 237
               E GV+ +F  ++LR E +H++GDG  VRDY+YV+DV RA +LA     ++ VFNIG
Sbjct: 182 RTSAEQGVIGVFLGKILRNEPLHVWGDGSVVRDYIYVEDVARALVLAARLNTEHHVFNIG 241

Query: 238 TGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSLEEGL 297
           +G G ++N +  +++ +TG D    Y   R  DV  S+LD + A+ +LGW      + G+
Sbjct: 242 SGAGLSLNDIIDMMRSVTGRDVVVKYDQNRVFDVPYSVLDVSLAERELGWRALFPFKVGV 301

Query: 298 KL 299
            L
Sbjct: 302 SL 303


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: 12
Number of successful extensions: 4
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: 312
Length adjustment: 27
Effective length of query: 282
Effective length of database: 285
Effective search space:    80370
Effective search space used:    80370
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