Align BadI (characterized)
to candidate WP_058860024.1 AS188_RS15810 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_001482365.1:WP_058860024.1 Length = 264 Score = 119 bits (298), Expect = 6e-32 Identities = 82/249 (32%), Positives = 122/249 (48%), Gaps = 4/249 (1%) Query: 10 IRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQS 69 +R+ +A + +NRP+ NA D + AL +DV A+V GAG++AF G D S Sbjct: 15 VRDRIAVVTVNRPEVRNALNFGVLDGIEAALDAFERREDVDAVVFTGAGEKAFVAGADIS 74 Query: 70 THDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKAIF 129 G Y + + M+ L+ I+D+ P IA V G+A+GGGN LA CD+ I + A F Sbjct: 75 QLIG-YTLQDGLRARMQRLYDRIQDLELPTIAAVNGFALGGGNELAMSCDIRIAAANARF 133 Query: 130 GQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDELDA 189 G +G + GT L+R+VG +A+E+ + +EA +GL VP +EL Sbjct: 134 GLPETNLGILPGAGGTQRLSRLVGLGRAQEMILTGRIIDAEEALRIGLVTSVVPAEELMD 193 Query: 190 EVQKWGEELCERSPTALAIAKRSF--NMDTAHQAGIAGMGMYALKLYYDTDESREGVKAL 247 + + P A+ +AK +T + G+ + A L Y DE EG A Sbjct: 194 TAHATARTILAKGPLAVRLAKLVVRNGAETDQRTGLL-LERLAQSLLYAADEKAEGASAF 252 Query: 248 QEKRKPEFR 256 EKR FR Sbjct: 253 LEKRPARFR 261 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: 157 Number of extensions: 11 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: 260 Length of database: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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 24 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