GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pseudomonas fluorescens FW300-N2E2

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate Pf6N2E2_481 Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)

Query= reanno::pseudo6_N2E2:Pf6N2E2_481
         (411 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_481
          Length = 411

 Score =  832 bits (2148), Expect = 0.0
 Identities = 411/411 (100%), Positives = 411/411 (100%)

Query: 1   MNPAYEPLRLHVPEPSGRPGCKTDFSYLHLSDAGTVRKPSIDVEPADTADLARSLIRVLD 60
           MNPAYEPLRLHVPEPSGRPGCKTDFSYLHLSDAGTVRKPSIDVEPADTADLARSLIRVLD
Sbjct: 1   MNPAYEPLRLHVPEPSGRPGCKTDFSYLHLSDAGTVRKPSIDVEPADTADLARSLIRVLD 60

Query: 61  DQGNAHGPWAEDVPLDILRKGMRAMLKTRIYDNRMVVAQRQKKMSFYMQSLGEEAIGSGQ 120
           DQGNAHGPWAEDVPLDILRKGMRAMLKTRIYDNRMVVAQRQKKMSFYMQSLGEEAIGSGQ
Sbjct: 61  DQGNAHGPWAEDVPLDILRKGMRAMLKTRIYDNRMVVAQRQKKMSFYMQSLGEEAIGSGQ 120

Query: 121 ALALNIDDMCFPTYRQQSILMAREVPLVGMICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180
           ALALNIDDMCFPTYRQQSILMAREVPLVGMICQLLSNERDPLKGRQLPIMYSVKDAGFFT
Sbjct: 121 ALALNIDDMCFPTYRQQSILMAREVPLVGMICQLLSNERDPLKGRQLPIMYSVKDAGFFT 180

Query: 181 ISGNLATQFIQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240
           ISGNLATQFIQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV
Sbjct: 181 ISGNLATQFIQGVGWGMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNV 240

Query: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFMAVYAASRWAAERARRNLGP 300
           VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFMAVYAASRWAAERARRNLGP
Sbjct: 241 VNNQWAISTFQAIAGGEATTFAGRGVGCGIASLRVDGNDFMAVYAASRWAAERARRNLGP 300

Query: 301 ALIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHMVKIGQWSEEEHAAVTA 360
           ALIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHMVKIGQWSEEEHAAVTA
Sbjct: 301 ALIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHMVKIGQWSEEEHAAVTA 360

Query: 361 ELEAEVIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQQLGI 411
           ELEAEVIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQQLGI
Sbjct: 361 ELEAEVIAAQKEAEQYGTLAGGQIPSAATMFEDVYKEMPEHLKRQRQQLGI 411


Lambda     K      H
   0.319    0.134    0.404 

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: 754
Number of extensions: 17
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