Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_077276827.1 BW732_RS11280 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_001998885.1:WP_077276827.1 Length = 244 Score = 127 bits (320), Expect = 2e-34 Identities = 83/250 (33%), Positives = 132/250 (52%), Gaps = 15/250 (6%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISD---IQAEKVETVAAHWRERGADVHAL 75 LKNK V++TG+++GIG+ + +FA Q A +V++ I E +E + + G H + Sbjct: 2 LKNKTVVITGSSRGIGQELARSFAKQGANIVLNGRKPISKELIEEIESF----GVKTHCV 57 Query: 76 KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWY 135 D+ + A E G +D+L+N AG+ + MTE+D+ ++L G + Sbjct: 58 IGDIQYFAQAEQLILEAKEVFGSVDILINNAGITRDTLLMRMTEDDFNSVLQVNLTGTFN 117 Query: 136 GCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195 K M++Q G IIN+AS G Y +K G++GLT+++ E A +G+ Sbjct: 118 TIKHASKIMLKQRSGIIINMASVVGLTGNAGQANYAASKAGVVGLTKSVARELASRGITC 177 Query: 196 NAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255 NAIAPGYI T + D N +++ + P RRIG +VA TA+FLA+ +P+I Sbjct: 178 NAIAPGYISTDM-TDVLN-----EKVKEQVVQQIPLRRIGSVTDVAQTAIFLAT--SPYI 229 Query: 256 NASCITIDGG 265 I +DGG Sbjct: 230 TGQVINVDGG 239 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: 133 Number of extensions: 10 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: 244 Length adjustment: 24 Effective length of query: 248 Effective length of database: 220 Effective search space: 54560 Effective search space used: 54560 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 Sep 24 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