Align BadH (characterized)
to candidate 6937839 Sama_1980 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__SB2B:6937839 Length = 248 Score = 145 bits (366), Expect = 8e-40 Identities = 89/251 (35%), Positives = 132/251 (52%), Gaps = 11/251 (4%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRD-AGGTAEAVRC 62 L K A++TG GIG A A+ GA + + +EK A AI D G + Sbjct: 7 LTGKVALVTGASRGIGKAIALTLAEAGATV----VGTATSEKGAAAISDYLGDKGFGLVL 62 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 ++ SV G VDILVNNAG + + EWE +I NLT + Sbjct: 63 NVTSSESVAEMYTAIKEKAGDVDILVNNAGITRDNLLMRMKDEEWEEIIDTNLTSLYRLS 122 Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182 V+ M+++RHGRI++I S +G++G+ Y+A K GL+ F+K+LARE A ITVN Sbjct: 123 KPVMRSMMKKRHGRIISIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVASRQITVNA 182 Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITG 242 + PG T + ++T PE+ + +P+ RLG+ ++A A+ F SD A +ITG Sbjct: 183 IAPGFIQTDMTDELT-----PEQQ-QGIMSQVPMERLGQAQEIANAVLFLASDAAAYITG 236 Query: 243 QVLSVSGGLTM 253 + L V+GG+ M Sbjct: 237 ETLHVNGGMYM 247 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: 162 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 255 Length of database: 248 Length adjustment: 24 Effective length of query: 231 Effective length of database: 224 Effective search space: 51744 Effective search space used: 51744 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