Align crotonase (EC 4.2.1.150) (characterized)
to candidate 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__PV4:5209977 Length = 706 Score = 131 bits (330), Expect = 3e-35 Identities = 79/186 (42%), Positives = 117/186 (62%), Gaps = 5/186 (2%) Query: 11 DGNVASITLNRP-KALNALNAATLKEIDAAINDIAEDDNVYAV-IITGSGKAFVAGADIA 68 D +A +T++ P + +N L A EI + +I D + V II+G +FVAGADI+ Sbjct: 11 DNGIAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGKKDSFVAGADIS 70 Query: 69 EMKDL-TAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIA--SS 125 + TA + R+ S G+++F LE+L PV+AAING LGGG EL+L+C R+ S+ Sbjct: 71 MLDACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELALACHQRVCTDSN 130 Query: 126 KAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPD 185 K G PEV LG+ PG GGTQRL R +G+ + +++ TGK + A++AL++GLV+ VV Sbjct: 131 KTMLGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALKMGLVDDVVPES 190 Query: 186 KLLEEA 191 LL+ A Sbjct: 191 ILLQTA 196 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: 410 Number of extensions: 17 Number of successful extensions: 3 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: 706 Length adjustment: 32 Effective length of query: 227 Effective length of database: 674 Effective search space: 152998 Effective search space used: 152998 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: 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