GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Rhodococcus qingshengii djl-6-2

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 WP_003942481.1 C1M55_RS30500 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= SwissProt::P9WIS3
         (367 letters)



>NCBI__GCF_002893965.1:WP_003942481.1
          Length = 375

 Score =  283 bits (725), Expect = 4e-81
 Identities = 153/345 (44%), Positives = 199/345 (57%)

Query: 20  VQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTPCRGQ 79
           VQ + P G  T     +    ++ L  +Y  M + R  D +   L +QG LA+Y   RGQ
Sbjct: 22  VQYLDPAGELTRSEARYAKPSDDRLIAMYRKMFLGRRFDQQATALTKQGRLAVYPSSRGQ 81

Query: 80  EAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCCAPMS 139
           EA Q+ AA  L  +DWLFP YR+      RG+ P  +     G WH G        AP  
Sbjct: 82  EACQIAAAMSLEPSDWLFPTYRDSMALAARGVDPVQILSMLAGDWHCGYDPVALRSAPQC 141

Query: 140 VPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQN 199
            P+ TQ LHA G A    R   ++V +A  GDGATSEGD HEALNFAAVF  P +F VQN
Sbjct: 142 TPLATQLLHAAGVAYGESRRGLNTVALALCGDGATSEGDFHEALNFAAVFKAPVIFLVQN 201

Query: 200 NQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLI 259
           N +AIS+P+SRQ+AAP++AHK +GYG+   +VDGND +A  AVM EAA   R+G+GP ++
Sbjct: 202 NGFAISVPLSRQSAAPTLAHKGVGYGIGSEQVDGNDPVAMLAVMDEAARFVRSGNGPVIV 261

Query: 260 EAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAK 319
           EA TYR+  HT ADD TRYR   EV+ W   DP+PR   YL+   L      E +TA A+
Sbjct: 262 EAHTYRIDAHTNADDATRYRDSAEVEAWLGRDPLPRLEKYLRAHDLIDDAFVESLTAEAE 321

Query: 320 HVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELA 364
              + LR  +      D  ++F  V+AE TP L+ Q+ QL  ELA
Sbjct: 322 TAAATLRAGMNVDRPHDPLDLFRYVFAEQTPQLREQQAQLETELA 366


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: 345
Number of extensions: 10
Number of successful extensions: 1
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: 375
Length adjustment: 30
Effective length of query: 337
Effective length of database: 345
Effective search space:   116265
Effective search space used:   116265
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 24 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