Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF2604 Psest_2654 fatty oxidation complex, alpha subunit FadB
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__psRCH2:GFF2604 Length = 715 Score = 136 bits (343), Expect = 1e-36 Identities = 80/180 (44%), Positives = 106/180 (58%), Gaps = 3/180 (1%) Query: 23 KALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKDLTAVEGRKF- 81 +++N N TL ++ A++ I D +V VI+T F+ GADI E D + + Sbjct: 27 ESVNKFNRLTLNDLRQAVDAIKADASVKGVIVTSGKDVFIVGADITEFVDNFKMADEELV 86 Query: 82 --SVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQPEVGLGIT 139 ++ NKIF E+L P +AAING ALGGG E+ ++ D R+ S+ AK G PEV LGI Sbjct: 87 AGNLEANKIFSDFEDLGVPTVAAINGIALGGGFEMCMAADYRVMSTTAKVGLPEVKLGIY 146 Query: 140 PGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEEAKALVDAII 199 PGFGGT RL R IGV A E I +GK AE+AL++ V+ VV PDKL A LV I Sbjct: 147 PGFGGTVRLPRLIGVDNAVEWIASGKENRAEDALKVHAVDAVVAPDKLQAAALDLVKRAI 206 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: 399 Number of extensions: 22 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: 715 Length adjustment: 32 Effective length of query: 227 Effective length of database: 683 Effective search space: 155041 Effective search space used: 155041 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