Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Pf1N1B4_3987 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Query= reanno::pseudo3_N2E3:AO353_20350 (387 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3987 Length = 387 Score = 755 bits (1950), Expect = 0.0 Identities = 378/387 (97%), Positives = 384/387 (99%) Query: 1 MSYPTLNFALGETIDMLRDQVRAFVSKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITV 60 MSYP+LNFALGETIDMLRDQV++FV+KEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITV Sbjct: 1 MSYPSLNFALGETIDMLRDQVQSFVAKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITV 60 Query: 61 PEEYGGAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKAKYLPKLI 120 PEEYGGAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQK+KYLPKLI Sbjct: 61 PEEYGGAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKSKYLPKLI 120 Query: 121 SGEHIGALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLE 180 SGEHIGALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLE Sbjct: 121 SGEHIGALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLE 180 Query: 181 KGPHGITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVL 240 KGPHGITAFIVERD KGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVL Sbjct: 181 KGPHGITAFIVERDSKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVL 240 Query: 241 MSGLDYERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNAS 300 MSGLDYERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNAS Sbjct: 241 MSGLDYERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNAS 300 Query: 301 RAYLYAVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRD 360 RAYLYAVAQACERGET RKDAAGVILYSAE AT+MALDAIQILGGNGYINEFPAGRLLRD Sbjct: 301 RAYLYAVAQACERGETARKDAAGVILYSAECATRMALDAIQILGGNGYINEFPAGRLLRD 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: 641 Number of extensions: 6 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.
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:
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