GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Paraburkholderia bryophila 376MFSha3.1

Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate H281DRAFT_04843 H281DRAFT_04843 UDP-glucose 4-epimerase

Query= curated2:Q57664
         (305 letters)



>FitnessBrowser__Burk376:H281DRAFT_04843
          Length = 310

 Score =  201 bits (511), Expect = 2e-56
 Identities = 114/305 (37%), Positives = 175/305 (57%), Gaps = 8/305 (2%)

Query: 2   ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGNKNNIN--PKAEFVNADIRD-KDLDE 58
           I V GG GFIGS IVD+L+ + +++ + +    G     +      ++  D+    D+ E
Sbjct: 3   ITVFGGGGFIGSTIVDRLLRDGHEICVFERARVGPYRRFDNGEDVRWMTGDLMSVHDITE 62

Query: 59  KINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIVFASSGGA 118
            I+  D+  V+H  +    ++S ++P+YD   N++ T+++L  M    + KIVF SSGG 
Sbjct: 63  AIDSTDI--VVHLVSTTLPKSSNDDPIYDVQSNLVATLHLLNAMVAKSVKKIVFISSGGT 120

Query: 119 VYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVYGERQDPK 178
           VYG+P YLPVDE HP NP   YG++K   E+Y+ LY   YGI+  ILR +N YGERQ  +
Sbjct: 121 VYGDPIYLPVDEKHPTNPKVSYGITKLAIEKYLLLYQYQYGIKANILRVANPYGERQRVE 180

Query: 179 GEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNW--KNEIVNIGTGK 236
              G I++F+DK L+ +   I+GDG  TRD++Y+GDVA+A   A+ +     + N+ +G 
Sbjct: 181 TAQGAIAVFLDKALRRRPIEIWGDGTITRDYLYIGDVAEAFARAVQYDGTESVFNVSSGY 240

Query: 237 ETSVNELFDIIKHEIGFRGEAIYDKPREGEVYRIYLDIKKAE-SLGWKPEIDLKEGIKRV 295
            TS+NE+   I+  +G   E  Y   R  +V    LD   A+  L W P++DL  GIK  
Sbjct: 241 GTSLNEIVGKIEAILGHPIERSYRPGRPFDVPASVLDNTLAKRELEWHPKVDLDAGIKMT 300

Query: 296 VNWMK 300
             W++
Sbjct: 301 AAWLR 305


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: 303
Number of extensions: 18
Number of successful extensions: 3
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: 310
Length adjustment: 27
Effective length of query: 278
Effective length of database: 283
Effective search space:    78674
Effective search space used:    78674
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