Align BadH (characterized)
to candidate WP_009544893.1 CCE_RS11410 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000017845.1:WP_009544893.1 Length = 251 Score = 159 bits (402), Expect = 5e-44 Identities = 94/252 (37%), Positives = 141/252 (55%), Gaps = 11/252 (4%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAEAVRC 62 L + AV+TG GIG A G K+ V + + AAE+V I ++ G A AV+ Sbjct: 8 LNEQVAVVTGASRGIGRAIALALGSLGVKVVVNYASSSSAAEEVVKLITESSGEAIAVQG 67 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 D++ VD I TT G +DILVNNAG + +P +W+ +I +NLTG Sbjct: 68 DVSQNEQVDNLIKTTLDKFGRIDILVNNAGITRDTLLMRMKPEDWQAVIDLNLTGVFLCT 127 Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182 AV M++++ GRI+NI+S +G+ G+A Y+A K G++ +K +A+E A G+TVN Sbjct: 128 KAVTKPMLKQKSGRIINISSVVGEMGNPGQANYSAAKAGVIGLTKAVAKEVASRGVTVNA 187 Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDD-AGFIT 241 V PG ++ D+T + L + IPLGRLG +++AG + F +D A +IT Sbjct: 188 VAPG----FIVTDMTEKVKTDDLL-----QYIPLGRLGMAEEVAGMVRFLATDPAAAYIT 238 Query: 242 GQVLSVSGGLTM 253 GQV +V GG+ M Sbjct: 239 GQVFNVDGGMVM 250 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: 171 Number of extensions: 9 Number of successful extensions: 4 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: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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 Apr 09 2024. 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