Align crotonase (EC 4.2.1.150) (characterized)
to candidate 5207485 Shew_0019 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__PV4:5207485 Length = 716 Score = 140 bits (352), Expect = 1e-37 Identities = 83/193 (43%), Positives = 113/193 (58%), Gaps = 6/193 (3%) Query: 11 DGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEM 70 + N+A + N ++N + TL ++ A++ +A+ V +++T AF+ GADI E Sbjct: 14 EDNIARLCFNAEGSVNKFDRETLNSLNDALDALAQTQGVKGLMLTSGKDAFIVGADITEF 73 Query: 71 KDLTAVEGRKFSVL---GNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKA 127 L A + NK+F KLE+L P I+AI GFALGGGCE L+ D+RIA + A Sbjct: 74 LGLFAQDDNVLQGWLEDANKVFNKLEDLPFPTISAIKGFALGGGCETILATDLRIADTSA 133 Query: 128 KFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKL 187 + G PE LGI PGFGGT RL R IG A E I TGK E AL++G ++ VV P+ L Sbjct: 134 RIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEAALKVGAIDAVVAPE-L 192 Query: 188 LEEA--KALVDAI 198 LE A + L DAI Sbjct: 193 LETAACQMLQDAI 205 Lambda K H 0.318 0.136 0.376 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: 422 Number of extensions: 17 Number of successful extensions: 2 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: 259 Length of database: 716 Length adjustment: 32 Effective length of query: 227 Effective length of database: 684 Effective search space: 155268 Effective search space used: 155268 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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