Align BadI (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 110 bits (275), Expect = 3e-29 Identities = 79/250 (31%), Positives = 121/250 (48%), Gaps = 18/250 (7%) Query: 19 INRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQSTHDG-NYDG 77 +NRP+K NA + D L AL A + D+G V+ GAGD AFC+GGD + +G Sbjct: 17 LNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGD-AFCSGGDLGRRAAESAEG 75 Query: 78 RGTVGLPME----------ELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKA 127 T P+E ++ AI + KP+IA V G A+G G L+ CD+ SE A Sbjct: 76 DPT---PLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQCDMRFASESA 132 Query: 128 IFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDEL 187 F + ++G + G L R+VG KA E+ + S +EA A+G+ N DEL Sbjct: 133 RFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIVNRVFSDDEL 192 Query: 188 DAEVQKWGEELCERSPTALAIAKRSF--NMDTAHQAGIAGMGMYALKLYYDTDESREGVK 245 + + L + P K+ ++ T + + + + + TD+ +E +K Sbjct: 193 MQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAA-QMAVVQSTDDYKEAIK 251 Query: 246 ALQEKRKPEF 255 A +EKRKP F Sbjct: 252 AYKEKRKPRF 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: 147 Number of extensions: 8 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 Apr 09 2024. 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