Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >FitnessBrowser__Phaeo:GFF1301 Length = 257 Score = 138 bits (347), Expect = 1e-37 Identities = 91/260 (35%), Positives = 139/260 (53%), Gaps = 17/260 (6%) Query: 17 ERLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQ 76 +RL K L+TGAA+GIG A A+A++ AR+VI+DI + EA AA + GA A++ Sbjct: 2 KRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAA---QIGAAAIAVE 58 Query: 77 ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 DV+ Q + R VE G +D+L+N A V +E+T E ++R F I++ G + Sbjct: 59 LDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFM 118 Query: 137 CKAVLPQMIEQGV-GSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195 +A QMI QG G IIN+AS P Y K ++ LT++ G+ G+ V Sbjct: 119 MQAAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINV 178 Query: 196 NAIAPGYIETQLNVDYWNG----FAD-----PHAERQRALDLHPPRRVGQPIEVAMTAVF 246 NAIAPG ++ ++W+G FA P ++ P R+G ++ AVF Sbjct: 179 NAIAPGVVDG----EHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVF 234 Query: 247 LASDEAPFINASCITIDGGR 266 LAS++A ++ A +DGG+ Sbjct: 235 LASEDADYVVAQTYNVDGGQ 254 Lambda K H 0.321 0.137 0.419 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: 168 Number of extensions: 7 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: 272 Length of database: 257 Length adjustment: 25 Effective length of query: 247 Effective length of database: 232 Effective search space: 57304 Effective search space used: 57304 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