GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galE in Dyella japonica UNC79MFTsu3.2

Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate N515DRAFT_1702 N515DRAFT_1702 UDP-glucose 4-epimerase

Query= BRENDA::Q9WYX9
         (309 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1702 N515DRAFT_1702
           UDP-glucose 4-epimerase
          Length = 305

 Score =  144 bits (364), Expect = 2e-39
 Identities = 93/310 (30%), Positives = 161/310 (51%), Gaps = 12/310 (3%)

Query: 2   NILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERI 61
           +IL+ G AGFIG H+   L+++G+ V+V        + +L+  AL     +  ++    +
Sbjct: 4   SILILGAAGFIGRHLTQALLDSGHRVMVATRRPE-TLAHLSAEAL---NLVTPDDFRAAL 59

Query: 62  FSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGAI 121
              H    V H A+ ++   S  +P ++ + N+  +L LLE   +    + I+ S+GG +
Sbjct: 60  AKAHT---VIHTASSSTPGSSSGQPLKELQ-NLTPTLTLLEALHQQPSIRLIYISSGGTL 115

Query: 122 YGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGPRQDPY 181
           Y  + +   T ++ I  P S +G  K + E ++E +  +     TV+R +NVYGP Q+  
Sbjct: 116 YTNHDRTPATEKSRI-WPRSYHGAGKIAAESFIEAWCSQQAGSATVIRPSNVYGPGQELR 174

Query: 182 GEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAME---KGDNEVFNIGT 238
              GV+     ++ RGE + I+GDG   RDY+Y+DD V   L  +    K   E+FN  +
Sbjct: 175 VGFGVIPNGFAKLKRGEAMEIWGDGSATRDYLYIDDFVELCLRILSEPAKSGFEIFNASS 234

Query: 239 GRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSLEEGLK 298
           G GT++NQL + ++ + G   + VY PPR  D    ++D   A ++LGW     L++GL+
Sbjct: 235 GTGTSLNQLLQQMELVAGTALKRVYHPPRSLDAEHVVIDAMHAAQRLGWAATTPLQKGLE 294

Query: 299 LTVEYFRKTL 308
            T  + +  L
Sbjct: 295 QTWNWLKPRL 304


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: 199
Number of extensions: 9
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: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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