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_042451488.1 C1M55_RS23135 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha

Query= SwissProt::P9WIS3
         (367 letters)



>NCBI__GCF_002893965.1:WP_042451488.1
          Length = 307

 Score =  115 bits (287), Expect = 2e-30
 Identities = 79/241 (32%), Positives = 115/241 (47%), Gaps = 14/241 (5%)

Query: 68  GELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGT---- 123
           G + LY+   GQEA  VG    L   D++   +R  G  + +G     +     G     
Sbjct: 22  GFIHLYS---GQEAIAVGVCENLSDADYIGSTHRGHGHCIAKGCDLNGMMAEIFGKDDGL 78

Query: 124 --WHGGLQFTTKCCAPM---SVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGD 178
               GG          M   +  +G     A+GAA++ + L    +  +F GDG +++G 
Sbjct: 79  CRGKGGSMHIADLSVGMLGANAIVGGAPSLAIGAALSGKTLRNGVIAASFTGDGGSNQGT 138

Query: 179 VHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLA 238
           V EA+N A V   P VF ++NN +  +        AP IA +A  +GMP ++VDG D  A
Sbjct: 139 VFEAMNMAVVLDLPIVFVIENNGFGEATGTDYAVGAPDIAARAASFGMPAVKVDGTDFFA 198

Query: 239 CYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRW-ATLDPIPRYR 297
            Y  MAEA+ RAR G GPT IEA  +R   H    D   YR+ E+V +   T DP+  +R
Sbjct: 199 VYDAMAEASERARIGGGPTTIEAAAFRWHGHFEG-DAQLYRTAEQVAQLRETKDPLKNFR 257

Query: 298 T 298
           +
Sbjct: 258 S 258


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: 250
Number of extensions: 13
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: 307
Length adjustment: 28
Effective length of query: 339
Effective length of database: 279
Effective search space:    94581
Effective search space used:    94581
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