Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_002117405.1:WP_085770280.1 Length = 246 Score = 133 bits (335), Expect = 3e-36 Identities = 87/251 (34%), Positives = 131/251 (52%), Gaps = 9/251 (3%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKAD 78 L K L+TGA+ G+G AI A + +S + E +ET+A +ER H L + Sbjct: 4 LTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERA---HILPCN 60 Query: 79 VSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138 +S++ + + A G +D+LVN AG+ + M +EDW A++L A+ + Sbjct: 61 LSDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLSR 120 Query: 139 AVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198 AVL M+ + G IINI S + PG Y AK GL G+T++L E A +GV VN + Sbjct: 121 AVLRGMMRKRHGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCV 180 Query: 199 APGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINAS 258 APG IE+ + A+R+R L L P R G E+ ++LASDEA FI Sbjct: 181 APGVIESPMTQ------VLNEAQRERLLKLIPMERFGSADEIGAAVLYLASDEAAFITGQ 234 Query: 259 CITIDGGRSVM 269 + I+GG +++ Sbjct: 235 TLHINGGMAMI 245 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: 141 Number of extensions: 8 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: 246 Length adjustment: 24 Effective length of query: 248 Effective length of database: 222 Effective search space: 55056 Effective search space used: 55056 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 (21.8 bits) S2: 47 (22.7 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