GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF3429
          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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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