GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pseudomonas fluorescens FW300-N2E3

Align 3-methyl-2-oxobutanoate dehydrogenase subunit alpha; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit alpha; BCKADH E1-alpha; EC 1.2.4.4 (characterized)
to candidate AO353_15575 AO353_15575 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= SwissProt::P9WIS3
         (367 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15575
          Length = 365

 Score =  242 bits (617), Expect = 1e-68
 Identities = 149/354 (42%), Positives = 187/354 (52%), Gaps = 5/354 (1%)

Query: 15  VDLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYT 74
           VDL   + + PDG   +E     D     L  LY  MV+TR  D + V LQR G +  Y 
Sbjct: 6   VDLPYTRYLSPDGQALSELPAWAD-DFNLLTRLYRQMVLTRLFDQKAVALQRTGRIGTYA 64

Query: 75  PCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKC 134
           P  GQEA  V   + +   D L P YR+ GV L+RG+    + + W G   G   F    
Sbjct: 65  PTLGQEAIGVAVGSLMHPEDVLIPYYRDTGVQLMRGVRMEEILLYWGGDERGS-DFAEPA 123

Query: 135 CA---PMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTT 191
                P+ VPI TQ LHA G A A +   E  V V   GDGATS+GD  EALN A  +  
Sbjct: 124 AVEDFPICVPIATQALHACGVASAFKIRGEHRVAVTTCGDGATSKGDFLEALNVAGAWQL 183

Query: 192 PCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARAR 251
           P VF + NNQWAIS+P   Q AAP++A KAIG G  G +VDGND+LA Y  +  A  RAR
Sbjct: 184 PVVFVINNNQWAISVPRRIQCAAPTLAQKAIGAGFHGEQVDGNDILAVYDRVQIALERAR 243

Query: 252 AGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLE 311
            G GP L+E V+YRLG HTTADD TRYR  EEV +    +P+ R + YL  QG+W +  E
Sbjct: 244 HGKGPVLLECVSYRLGDHTTADDATRYRPAEEVKQAWLEEPVKRLQRYLAGQGVWDEGRE 303

Query: 312 EQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELAR 365
           + + A  + +     D    A     + V   VYA+    L  QRE L    AR
Sbjct: 304 QALIAECQALVQGAVDNFDAAGQQSAESVIDHVYAQWPAALAEQREWLLERAAR 357


Lambda     K      H
   0.320    0.134    0.413 

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: 333
Number of extensions: 10
Number of successful extensions: 2
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: 367
Length of database: 365
Length adjustment: 30
Effective length of query: 337
Effective length of database: 335
Effective search space:   112895
Effective search space used:   112895
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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