Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate RR42_RS25125 RR42_RS25125 3-oxoacyl-ACP reductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >FitnessBrowser__Cup4G11:RR42_RS25125 Length = 249 Score = 164 bits (415), Expect = 2e-45 Identities = 91/250 (36%), Positives = 144/250 (57%), Gaps = 7/250 (2%) Query: 18 RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQA 77 ++KD+V ++TG+A+G+G A A + AR+V++D+ ++ E A R G H + A Sbjct: 4 QIKDRVAIVTGSARGLGAATARRLAEEGARVVVTDVLRERAEETVAALRADGLQAHCVIA 63 Query: 78 DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 D++K +D+ + V G + +LVN AG + ++M+EEDW A+ L GA+ Sbjct: 64 DITKAEDVSRLVEETVAQFGGVHILVNNAGFPRDKYLVKMSEEDWDLVIAVMLKGAFLAT 123 Query: 138 KAVLPQMIEQGVGSIINIASVHSSHI-IPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 +AV+P IEQG G +INI+S +H+ P Y AK GL+G+ +AL IE GV VN Sbjct: 124 RAVMPHFIEQGWGRVINISS--RAHLGNPTQANYSAAKAGLIGVAKALAIEEGRYGVTVN 181 Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFIN 256 +APG+IET++ ++RA+ + P +RVG+P ++A FLAS+ A FI Sbjct: 182 CVAPGFIETEM----VQALPSYETIKERAVQMQPIKRVGRPGDIADAVAFLASERAGFIT 237 Query: 257 ASCITIDGGR 266 + + GGR Sbjct: 238 GEVLHVSGGR 247 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: 151 Number of extensions: 5 Number of successful extensions: 3 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: 249 Length adjustment: 24 Effective length of query: 248 Effective length of database: 225 Effective search space: 55800 Effective search space used: 55800 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