Align BadK (characterized)
to candidate H281DRAFT_05725 H281DRAFT_05725 short chain enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Burk376:H281DRAFT_05725 Length = 258 Score = 336 bits (861), Expect = 3e-97 Identities = 164/253 (64%), Positives = 202/253 (79%) Query: 6 ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGA 65 IL ET+GRVG++TLNRP LNALNDALMD LG AL FDADD IGAIV+ G+ +AFAAGA Sbjct: 6 ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVLTGSEKAFAAGA 65 Query: 66 DIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRS 125 DI M+ +SY DVY ++ITRNWET+R IRKP++AAVAG A GGGCELA+ CD++ A + Sbjct: 66 DIGMMSTYSYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDMIFAADT 125 Query: 126 AKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDR 185 AKF PEIKLG++PGAGGTQRLPRA+ KAKAMD+CL+AR ++A EA+R GLVSRV+ Sbjct: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAAS 185 Query: 186 LRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQ 245 L DE +A A TIA F PA+M +KES+NRA+E+TLAEG+ FERR H+ FA+ D +EG+ Sbjct: 186 LIDEAIAAAATIAEFPLPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMA 245 Query: 246 AFLEKRAPCFSHR 258 AF+EKR P F HR Sbjct: 246 AFVEKRKPVFKHR 258 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: 170 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