Align BadK (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS19405 Length = 258 Score = 300 bits (768), Expect = 2e-86 Identities = 150/257 (58%), Positives = 194/257 (75%) Query: 1 MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60 MS I ET +VG+I L+RP LNAL+D LM LG ALLAFDA + IG I+I G+ +A Sbjct: 1 MSYENIQVETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIITGSEKA 60 Query: 61 FAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 FAAGADI++MA + Y DV+ FITRNWET+R+IRKPV+AAVAG A GGGCELA+ CD + Sbjct: 61 FAAGADISAMAGYDYMDVFKGEFITRNWETLRRIRKPVIAAVAGYALGGGCELAMMCDFI 120 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 IA +AKF PEIKLG++PGAGGTQRLPRA+ KAKAMD+ L+ R ++AEEA+R GLVSR+ Sbjct: 121 IAADNAKFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGLVSRI 180 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240 V D+L +E +A A IA M +K+S+NRA+E+TL+EG+ +ER ++ FA+ D Sbjct: 181 VAADKLLEEAMAAAIIIAEMPRQVAMMVKDSVNRAYETTLSEGMKYERALFYSCFATEDQ 240 Query: 241 REGIQAFLEKRAPCFSH 257 +EG++AFLEKR P F H Sbjct: 241 KEGMKAFLEKRQPVFKH 257 Lambda K H 0.321 0.135 0.389 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: 169 Number of extensions: 2 Number of successful extensions: 1 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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 (21.9 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