Align BadI (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS19405 Length = 258 Score = 113 bits (283), Expect = 3e-30 Identities = 84/260 (32%), Positives = 127/260 (48%), Gaps = 8/260 (3%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M +E++ E V I ++RP +NA EL +AL +++G I++ G+ ++ Sbjct: 1 MSYENIQVETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIITGS-EK 59 Query: 61 AFCTGGDQSTHDGNYDGRGTV-GLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICD 119 AF G D S G YD G + +R + KPVIA V GYA+GGG LA +CD Sbjct: 60 AFAAGADISAMAG-YDYMDVFKGEFITRNWETLRRIRKPVIAAVAGYALGGGCELAMMCD 118 Query: 120 LTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLAN 179 I ++ A FGQ K+G V GT L R V + KA ++ + +EAE GL + Sbjct: 119 FIIAADNAKFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGLVS 178 Query: 180 LCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYD--- 236 V D+L E + E + K S N A++ ++ Y L+Y Sbjct: 179 RIVAADKLLEEAMAAAIIIAEMPRQVAMMVKDSVN--RAYETTLSEGMKYERALFYSCFA 236 Query: 237 TDESREGVKALQEKRKPEFR 256 T++ +EG+KA EKR+P F+ Sbjct: 237 TEDQKEGMKAFLEKRQPVFK 256 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: 166 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 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