Aligments for a candidate for bkdA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for bkdA in Pseudomonas simiae WCS417

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF3429 PS417_17545 2-oxoisovalerate dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_26635
         (411 letters)



>lcl|FitnessBrowser__WCS417:GFF3429 PS417_17545 2-oxoisovalerate
           dehydrogenase
          Length = 411

 Score =  805 bits (2078), Expect = 0.0
 Identities = 395/411 (96%), Positives = 404/411 (98%)

Query: 1   MNQAYEPLRLHVPEPSGRPGCKTDFSYLRLTDAGTVRKPPIDVEPADTADLAKGLIRVLD 60
           M Q YEPLRLHVPEPSGRPGCKTDF+YLRLTDAGTVRKP IDVEPADTADLAKGLIRVLD
Sbjct: 1   MTQQYEPLRLHVPEPSGRPGCKTDFTYLRLTDAGTVRKPAIDVEPADTADLAKGLIRVLD 60

Query: 61  DQGNALGPWAEGVPVEILRKGMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQ 120
           DQG ALGPWAEGV VEI+R+GMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQ
Sbjct: 61  DQGQALGPWAEGVSVEIMRRGMRAMLKTRIFDNRMVVAQRQKKMSFYMQSLGEEAIGSAQ 120

Query: 121 ALALNIDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180
           ALALNIDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFT
Sbjct: 121 ALALNIDDMCFPTYRQQSILMAREVPLVDLICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180

Query: 181 ISGNLATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240
           ISGNLATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV
Sbjct: 181 ISGNLATQFVQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240

Query: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFVAVYAASAWAAERARRNLGP 300
           VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDF+AVYAASAWAAERARRNLGP
Sbjct: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFIAVYAASAWAAERARRNLGP 300

Query: 301 TMIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLVKIGQWSEEEHVALSA 360
           T+IEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHL+KIGQWSEEEH A+SA
Sbjct: 301 TLIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIGQWSEEEHAAVSA 360

Query: 361 ELEAEIIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI 411
           ELEAE++ AQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI
Sbjct: 361 ELEAEVVKAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQELGI 411


Lambda     K      H
   0.319    0.134    0.403 

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: 685
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: 411
Length of database: 411
Length adjustment: 31
Effective length of query: 380
Effective length of database: 380
Effective search space:   144400
Effective search space used:   144400
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources