GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20350 AO353_20350
           isovaleryl-CoA dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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