GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_0356 N515DRAFT_0356 pyruvate dehydrogenase E1 component alpha subunit

Query= SwissProt::P9WIS3
         (367 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0356
          Length = 361

 Score =  217 bits (552), Expect = 5e-61
 Identities = 124/314 (39%), Positives = 171/314 (54%), Gaps = 4/314 (1%)

Query: 47  LYEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVY 106
           LY++M+ TR  D + V LQR G+L  Y  C G EAA VG  + ++  D   P YRE G  
Sbjct: 39  LYKLMMSTRVFDAKSVALQRTGKLGTYASCLGHEAAHVGIGSAMKPEDVFAPSYREYGAQ 98

Query: 107 LVRGIPPGHVGVAWRGTWHGG--LQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSV 164
           L RG+ P  V + W G   G    +   +     SVPI TQ LHA G+A+A +  +E  V
Sbjct: 99  LYRGVQPREVYMYWGGDERGNDYQKEPARHDFAWSVPIATQCLHAAGSALAFKIRNEKRV 158

Query: 165 TVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGY 224
            V  +GDG +S+GD + A+N       P V  + NNQWAIS+P   Q+ AP++A K I  
Sbjct: 159 AVCTIGDGGSSKGDFYGAINITGAQNLPMVAVIVNNQWAISVPRKIQSGAPTLAQKGIAA 218

Query: 225 GMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEV 284
           G+  I+VDGND++A    M +A  RAR G G +++E VTYRL  HTTADD  RYR ++EV
Sbjct: 219 GLFSIQVDGNDIIAVRKAMEDALDRARNGQGGSVLELVTYRLSDHTTADDARRYRGEQEV 278

Query: 285 -DRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTT 343
            D WA  +P+ R R +L  + +W    EE   A          +A  +     V  +F  
Sbjct: 279 KDAWAK-EPMKRLRAWLVAKNVWDDAKEEAWKAECDEWMDNEVNAYLETKTQPVTAMFDY 337

Query: 344 VYAEITPGLQAQRE 357
            +AE+   L  QR+
Sbjct: 338 TFAEVPADLAKQRD 351


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: 299
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: 361
Length adjustment: 29
Effective length of query: 338
Effective length of database: 332
Effective search space:   112216
Effective search space used:   112216
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