Align BadK (characterized)
to candidate GFF1164 HP15_1141 enoyl-CoA hydratase/isomerase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Marino:GFF1164 Length = 257 Score = 135 bits (341), Expect = 6e-37 Identities = 85/251 (33%), Positives = 128/251 (50%), Gaps = 1/251 (0%) Query: 6 ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGA 65 +LTE + R+ I+ LNRP+ NAL A+ A+G AL D I ++ G++ F AG Sbjct: 5 VLTEIKARILIVRLNRPERKNALTHAMYTAMGDALEQARDDANIRCVLFTGSSECFTAGN 64 Query: 66 DIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRS 125 D+ AA D + + R + KPV+A+V G A G G + L CD+V AG + Sbjct: 65 DLGEFAAGLPGD-FEQTPVGRFLLLLASATKPVVASVNGAAVGIGTTMLLHCDLVFAGNN 123 Query: 126 AKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDR 185 F +P LGL P G + LP IG+ ++ ++ + +AEEA R GL++RV + ++ Sbjct: 124 TAFQMPFASLGLCPEGGSSLLLPSWIGRVRSAELLMLGGAFSAEEALRLGLINRVCEPEQ 183 Query: 186 LRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQ 245 + + A+ A K LN+ L E +L E + R S +A E + Sbjct: 184 TDANAFEACQRLTEKAPAAIRATKALLNKPTIEALRETMLEEGQLFAERLKSPEAAEAFR 243 Query: 246 AFLEKRAPCFS 256 AF+EKRAP FS Sbjct: 244 AFMEKRAPDFS 254 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: 122 Number of extensions: 2 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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