GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pseudomonas fluorescens FW300-N2E3

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate AO353_20350 AO353_20350 isovaleryl-CoA dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_20350
         (387 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20350
          Length = 387

 Score =  774 bits (1998), Expect = 0.0
 Identities = 387/387 (100%), Positives = 387/387 (100%)

Query: 1   MSYPTLNFALGETIDMLRDQVRAFVSKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITV 60
           MSYPTLNFALGETIDMLRDQVRAFVSKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITV
Sbjct: 1   MSYPTLNFALGETIDMLRDQVRAFVSKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITV 60

Query: 61  PEEYGGAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKAKYLPKLI 120
           PEEYGGAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKAKYLPKLI
Sbjct: 61  PEEYGGAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKAKYLPKLI 120

Query: 121 SGEHIGALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLE 180
           SGEHIGALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLE
Sbjct: 121 SGEHIGALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLE 180

Query: 181 KGPHGITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVL 240
           KGPHGITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVL
Sbjct: 181 KGPHGITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVL 240

Query: 241 MSGLDYERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNAS 300
           MSGLDYERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNAS
Sbjct: 241 MSGLDYERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNAS 300

Query: 301 RAYLYAVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRD 360
           RAYLYAVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRD
Sbjct: 301 RAYLYAVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRD 360

Query: 361 AKLYEIGAGTSEIRRMLIGRELFNETR 387
           AKLYEIGAGTSEIRRMLIGRELFNETR
Sbjct: 361 AKLYEIGAGTSEIRRMLIGRELFNETR 387


Lambda     K      H
   0.319    0.137    0.400 

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: 653
Number of extensions: 5
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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 (21.7 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