GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1020 Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)

Query= SwissProt::P9WIS3
         (367 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1020
          Length = 332

 Score =  227 bits (578), Expect = 4e-64
 Identities = 136/323 (42%), Positives = 175/323 (54%), Gaps = 6/323 (1%)

Query: 47  LYEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVY 106
           LY  MV+TR  D + V LQR G +  Y P  GQEA  V   + +   D L P YR+  V 
Sbjct: 4   LYRQMVLTRLFDQKAVALQRTGRIGTYAPTLGQEAIGVAVGSLMHAEDVLIPYYRDTAVQ 63

Query: 107 LVRGIPPGHVGVAWRGTWHGGLQFTTKCCA---PMSVPIGTQTLHAVGAAMAAQRLDEDS 163
           L+RG+    + + W G   G   F     A   P+ VPI TQ LHA G A A +   E  
Sbjct: 64  LMRGVRMEEILLYWGGDERGS-DFADPAVAQDFPICVPIATQALHACGVASAFKIRGEHR 122

Query: 164 VTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIG 223
           V V   GDG TS+GD  EALN A  +  P VF V NNQWAIS+P   Q  AP++A KAIG
Sbjct: 123 VAVTTCGDGGTSKGDFLEALNVAGAWQLPVVFMVNNNQWAISVPRRIQCGAPTLAQKAIG 182

Query: 224 YGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEE 283
            G  G +VDGND+LA Y  +  A  R R G GP L+E ++YRLG HTTADD TRYRS +E
Sbjct: 183 AGFHGEQVDGNDMLAVYDRVQAALERTRHGKGPVLLECLSYRLGDHTTADDATRYRSADE 242

Query: 284 VDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDE-VFT 342
           V +    +PI R + ++  QG+W +  E+ + +  + +     D  F+A      E V  
Sbjct: 243 VKQAWLEEPIKRLQRFMAGQGVWDEGREQALISECQGLVQRAVDN-FEAAGLQAPESVMD 301

Query: 343 TVYAEITPGLQAQREQLRAELAR 365
            VYA+    L  QRE     +AR
Sbjct: 302 HVYAQWPQALAEQREDFLERVAR 324


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: 286
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: 332
Length adjustment: 29
Effective length of query: 338
Effective length of database: 303
Effective search space:   102414
Effective search space used:   102414
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