Align BadI (characterized)
to candidate WP_011423740.1 RHE_RS01800 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_000092045.1:WP_011423740.1 Length = 257 Score = 117 bits (294), Expect = 2e-31 Identities = 89/270 (32%), Positives = 132/270 (48%), Gaps = 29/270 (10%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGY-DKDVGAIVLAGAGD 59 M +E LI E R V + +NRP +NA T EL KA Y A + D+ +GAIV+ G+ + Sbjct: 1 MAYETLIVETRGNVGLVTLNRPQALNALNSTVLKEL-KAAYAAFHADEAIGAIVITGS-E 58 Query: 60 RAFCTGGDQSTHDGNYDGRGTVGLPMEELHTA--------IRDVPKPVIARVQGYAIGGG 111 RAF G D L +++ + I KPVIA V G+A+GGG Sbjct: 59 RAFAAGADIKEMQS---------LQFADIYKSDFISGWDDIAKARKPVIAAVSGFALGGG 109 Query: 112 NVLATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKE 171 LA +CD I SE A FGQ +G + G+ L R VG+ KA ++ + E Sbjct: 110 CELAMMCDFIIASETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLVLTGRMMDAAE 169 Query: 172 AEAMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFN--MDTAHQAGIAGMGMY 229 AE GL + V + L E E++ S ++ +AK + N +T + G+ + Sbjct: 170 AERSGLVSRVVAPERLLDEALAAAEKIASLSQPSVMMAKEAVNRAFETTLEEGL----RF 225 Query: 230 ALKLYYD---TDESREGVKALQEKRKPEFR 256 +L++ TD+ +EG+ A EKRKP F+ Sbjct: 226 ERRLFHSLFATDDQKEGMAAFVEKRKPAFK 255 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: 152 Number of extensions: 12 Number of successful extensions: 4 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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