Align BadK (characterized)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834 Length = 256 Score = 175 bits (444), Expect = 7e-49 Identities = 98/254 (38%), Positives = 145/254 (57%), Gaps = 1/254 (0%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62 S P++ E G V I+ LNR + NAL+ ++ A+ A+ + D G+ IVI G FA Sbjct: 2 SAPVVVERNGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGDSVFA 61 Query: 63 AGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIA 122 AGAD+ + V + + + W + + +KP++AAV+G A G GCELA+ CDI++A Sbjct: 62 AGADLNLLVDKGAQQVAELD-LGQYWAPVAKSQKPLIAAVSGFALGAGCELAMMCDILVA 120 Query: 123 GRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVD 182 SA+F PE ++G++PGAGGTQRL RA+GK A M L+ L+AE A + GLVS +V Sbjct: 121 DNSARFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQLGLVSELVT 180 Query: 183 DDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADARE 242 + + LA A AL A+K L + +L + E RE F + D E Sbjct: 181 EGSALARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLLFDTQDKTE 240 Query: 243 GIQAFLEKRAPCFS 256 G++AFL+KR P ++ Sbjct: 241 GMRAFLDKRPPRYT 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: 117 Number of extensions: 7 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: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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