GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Cupriavidus basilensis 4G11

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 RR42_RS33045 RR42_RS33045 pyruvate dehydrogenase

Query= SwissProt::P9WIS3
         (367 letters)



>FitnessBrowser__Cup4G11:RR42_RS33045
          Length = 355

 Score =  238 bits (606), Expect = 2e-67
 Identities = 142/343 (41%), Positives = 183/343 (53%), Gaps = 7/343 (2%)

Query: 16  DLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTP 75
           D+E  Q + P G PT        L  E L  LY  MV+TR+ D + + LQR G++  +  
Sbjct: 8   DIEYTQFLDPQGEPTQALPAFA-LDPEALLPLYRAMVLTRQFDLKAIALQRTGQIGTFAS 66

Query: 76  CRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCC 135
             GQEA  VG A+ +R  D L P YR+      RG+      + W G   G         
Sbjct: 67  ALGQEAVGVGVASAMRAQDVLVPSYRDHAAQFQRGVSMTESLLYWGGDERGNAFAAAPHD 126

Query: 136 APMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVF 195
               VPIG Q  HA G A A +   E   TV  LGDG TS+GD +E +N A  +  P V 
Sbjct: 127 FANCVPIGNQVCHAAGIAYAMKLRREPRATVCLLGDGGTSKGDFYEGMNMAGAWHAPLVL 186

Query: 196 YVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDG 255
            V NNQWAISMP S+QTAA ++A KAI  G+PG++VDGNDV+A   V  +A  RAR G G
Sbjct: 187 VVNNNQWAISMPRSQQTAARTLAQKAIAAGIPGLQVDGNDVVAVRQVTLDALERARGGGG 246

Query: 256 PTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVT 315
            TLIEA+TYRLG HTTADD +RYR  E+V +   L+P+ R R YL   G W    E+   
Sbjct: 247 ATLIEAITYRLGDHTTADDASRYRDSEQVRQHWLLEPVARLRNYLLRLGAWDAPRED--- 303

Query: 316 ARAKHVRSELRDAV---FDAPDFDVDEVFTTVYAEITPGLQAQ 355
           A AK   +++  AV      P  +   +F  +YA +   L  Q
Sbjct: 304 ALAKDCAAQVAAAVQAYLATPLPETAAMFDCLYASLPKALAGQ 346


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: 328
Number of extensions: 15
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: 355
Length adjustment: 29
Effective length of query: 338
Effective length of database: 326
Effective search space:   110188
Effective search space used:   110188
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