GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pseudarthrobacter sulfonivorans Ar51

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_205630629.1 AU252_RS03450 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= SwissProt::P9WIS3
         (367 letters)



>NCBI__GCF_001484605.1:WP_205630629.1
          Length = 369

 Score =  290 bits (743), Expect = 3e-83
 Identities = 164/355 (46%), Positives = 209/355 (58%), Gaps = 4/355 (1%)

Query: 13  MSVDLEPVQLVGPDGTPTAERRYH---RDLPEETLRWLYEMMVVTRELDTEFVNLQRQGE 69
           MS D   +QLV P G   +   +    +D+ +E L  LYE + V R +D E   LQRQGE
Sbjct: 1   MSTDRNLIQLVTPAGERISHPEFDPWVKDIGDEQLCSLYEDLTVIRRIDVEATALQRQGE 60

Query: 70  LALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQ 129
           L L+ P  GQEAAQVG+   LR  D++F  YRE GV   RG+    +   WRGT   G  
Sbjct: 61  LGLWPPLLGQEAAQVGSGRALRDDDFVFSSYRENGVAYCRGVDLTDITRVWRGTASSGWD 120

Query: 130 FTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVF 189
             +   A   + IG QTLHA G AM  Q    DSV V + GDGATSEGDV+EA+ FAA F
Sbjct: 121 PYSVNMATPQIIIGAQTLHATGYAMGIQNDGADSVAVTYFGDGATSEGDVNEAMVFAASF 180

Query: 190 TTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAAR 249
             P VF+  NN WAIS PV  Q+    IA +A G+G+P +RVDGNDVLA  A    A  R
Sbjct: 181 QAPVVFFCSNNHWAISEPVRLQSHI-QIADRATGFGIPSLRVDGNDVLAVMAATRVALDR 239

Query: 250 ARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQR 309
           AR G GPT IEAVTYR+GPHTTADDPTRYR   E++ WA  DPI R +  L+ +GL + +
Sbjct: 240 ARHGGGPTFIEAVTYRMGPHTTADDPTRYRDANELEDWAAKDPILRIKALLERKGLLTDQ 299

Query: 310 LEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELA 364
           +++ V  +A+ V  E+R      PD +  ++F  VY+E    L  Q++     LA
Sbjct: 300 VQQHVHDKAESVAREIRSGCIGMPDPEPMDIFKHVYSEPNSWLDRQQDHYARYLA 354


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: 358
Number of extensions: 14
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: 369
Length adjustment: 30
Effective length of query: 337
Effective length of database: 339
Effective search space:   114243
Effective search space used:   114243
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 Apr 09 2024. 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