Align BadI (characterized)
to candidate WP_110804536.1 C8J30_RS04555 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_003217355.1:WP_110804536.1 Length = 258 Score = 120 bits (300), Expect = 4e-32 Identities = 89/265 (33%), Positives = 131/265 (49%), Gaps = 20/265 (7%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M ++ LI EI +GVA I +NRP+ +NA EL +AL D V VL G+ D+ Sbjct: 1 MSYQTLIVEIEDGVALIRLNRPEALNALNSQLLGELAEALKTLDADPAVRCFVLTGS-DK 59 Query: 61 AFCTGGD-QSTHDGNY------DGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNV 113 AF G D + D ++ D GT G AI KP+IA V GYA+GGG Sbjct: 60 AFAAGADIKEMADKSFTDMFLQDFFGTEG-------DAILRTRKPIIAAVAGYALGGGCE 112 Query: 114 LATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAE 173 LA +CD +C+E A FGQ +G V GT L R VG+ K+ E+ + EAE Sbjct: 113 LAMMCDFILCAENAKFGQPEINLGVVAGIGGTQRLTRFVGKSKSMEMHLTGRFMDAAEAE 172 Query: 174 AMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKL 233 GL + +P +L E ++ +S A +AK N A++ + +Y ++ Sbjct: 173 RSGLVSRVLPLADLVPEALTTARKIAAKSAIATMVAKDCVN--RAYETTLREGVLYERRV 230 Query: 234 Y---YDTDESREGVKALQEKRKPEF 255 + + T++ +EG+ A EKR +F Sbjct: 231 FHALFATEDQKEGMAAFTEKRPAKF 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: 155 Number of extensions: 10 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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