GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Bacteroides thetaiotaomicron VPI-5482

Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate 350587 BT1059 putative UDP-glucose 4-epimerase (NCBI ptt file)

Query= BRENDA::Q9WYX9
         (309 letters)



>FitnessBrowser__Btheta:350587
          Length = 309

 Score =  146 bits (368), Expect = 7e-40
 Identities = 99/321 (30%), Positives = 165/321 (51%), Gaps = 35/321 (10%)

Query: 3   ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLN-----------RNALFYEQS 51
           ILV+GGAGFIGSH+  +L+  G+ VI +DN  +G  +N+            R+ + Y  S
Sbjct: 4   ILVSGGAGFIGSHLCTRLVNEGHDVICLDNFFTGSKDNIKHLMGNHHFEVVRHDVTYPYS 63

Query: 52  IEDEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKK 111
            E +E             +++LA  AS      +P + AKT+++G++ +L  +++   K 
Sbjct: 64  AEVDE-------------IYNLACPASPIHYQHDPIQTAKTSVMGAINMLGLAMRLDAK- 109

Query: 112 FIFSSTGGAIYGENVKVFPTPETEIPH--PI---SPYGIAKYSTEMYLEFFAREYGLKYT 166
            I  ++   +YG+ + + P PE+   +  P+   S Y   K   E     + R+   +  
Sbjct: 110 -ILQASTSEVYGDPI-IHPQPESYWGNVNPVGYRSCYDEGKRCAETLFMDYYRQNQTRIK 167

Query: 167 VLRYANVYGPRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAM 226
           ++R  N YGPR  P  +  VV+ F  + L  E++ I+GDG+  R + Y+DD++   +  M
Sbjct: 168 IIRIFNTYGPRMLP-NDGRVVSNFIIQALNNEDITIYGDGKQTRSFQYIDDLIEGMVRMM 226

Query: 227 EKGDNEV--FNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEK 284
           +  D+     NIG      V +L + +  +TG   + V+KP    D ++   D   AKEK
Sbjct: 227 DTEDDFTGPINIGNPNEFPVLELAERVIRMTGSTSKIVFKPLPTDDPKQRQPDIKLAKEK 286

Query: 285 LGWEPKVSLEEGLKLTVEYFR 305
           LGW+P V LE+GLK  +EYF+
Sbjct: 287 LGWQPTVELEDGLKRMIEYFK 307


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: 245
Number of extensions: 16
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: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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