Align BadI (characterized)
to candidate Pf1N1B4_5593 4-hydroxycinnamoyl CoA hydratase/lyase (Enoyl-CoA hydratase/lyase) (EC 4.2.1.17)
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5593 Length = 276 Score = 99.0 bits (245), Expect = 9e-26 Identities = 68/213 (31%), Positives = 97/213 (45%), Gaps = 11/213 (5%) Query: 9 EIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQ 68 EI G+AW+I+NRP+K NA T E+I L D D G +VL GAG+ A+ G D Sbjct: 14 EIEEGIAWVILNRPEKRNAMSPTLNREMIDVLETLEQDPDAGVLVLTGAGE-AWTAGMDL 72 Query: 69 STHDGNYDGRGTVGLPMEELH--------TAIRDVPKPVIARVQGYAIGGGNVLATICDL 120 + D + E++ +R KP IA V G+ GGG CDL Sbjct: 73 KEYFREVDAGPEI--LQEKIRREASQWQWKLLRMYAKPTIAMVNGWCFGGGFSPLVACDL 130 Query: 121 TICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANL 180 IC+++A FG G + +A VG +++ K + G++A MGL N Sbjct: 131 AICADEATFGLSEINWGIPPGNLVSKAMADTVGHRQSLYYIMTGKTFGGQKAAEMGLVNE 190 Query: 181 CVPHDELDAEVQKWGEELCERSPTALAIAKRSF 213 VP +L + L E++P L AK F Sbjct: 191 SVPLAQLREVTIELARNLLEKNPVVLRAAKHGF 223 Lambda K H 0.319 0.138 0.418 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: 182 Number of extensions: 10 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: 260 Length of database: 276 Length adjustment: 25 Effective length of query: 235 Effective length of database: 251 Effective search space: 58985 Effective search space used: 58985 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: 47 (22.7 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