Align BadH (characterized)
to candidate AZOBR_RS08390 AZOBR_RS08390 3-oxoacyl-ACP synthase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__azobra:AZOBR_RS08390 Length = 245 Score = 162 bits (410), Expect = 6e-45 Identities = 94/253 (37%), Positives = 139/253 (54%), Gaps = 9/253 (3%) Query: 1 MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60 M L K A++TG GGIG R +GA +A+ + E +A + G A V Sbjct: 1 MFDLTGKKALVTGASGGIGAQIARALHAQGATVALSGTRVAPLEALAAEL---GERALVV 57 Query: 61 RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120 ++AD + LG +DILVNNAG + + + +W+ ++ +NLT A Sbjct: 58 PGNLADAAGTEQLAKDAEAALGQIDILVNNAGLTRDQLAMRMKDDDWQSVLDVNLTAAFR 117 Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180 + AVL GM++RR GRI+ I S G+ G+A YAA K G++ SK+LA E A GITV Sbjct: 118 LSRAVLRGMMKRRWGRIIGITSIVGVTGNPGQANYAASKAGMIGMSKSLAAEVASRGITV 177 Query: 181 NVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFI 240 N V PG TA+ + A N E+ + T AIP GR+G+P ++A + + SD+A ++ Sbjct: 178 NCVAPGFITTAM-----TDALNSEQKDKLLT-AIPSGRMGEPGEIAAGVVYLASDEAAYV 231 Query: 241 TGQVLSVSGGLTM 253 TGQ L ++GG+ M Sbjct: 232 TGQTLHINGGMAM 244 Lambda K H 0.318 0.135 0.398 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: 174 Number of extensions: 5 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: 255 Length of database: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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