Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_041576504.1 XAUT_RS06800 3-oxoacyl-ACP reductase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119 (272 letters) >NCBI__GCF_000017645.1:WP_041576504.1 Length = 249 Score = 146 bits (369), Expect = 4e-40 Identities = 90/252 (35%), Positives = 136/252 (53%), Gaps = 5/252 (1%) Query: 18 RLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAIKA 77 RL K L+TGAA G G I FA + A++ I D+ GE KVA + G +A+ A Sbjct: 2 RLSGKTALVTGAASGFGAEIARVFAREGAKVAIVDLNGEGARKVA---EEIGPAAIAVTA 58 Query: 78 DVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWYG 136 DV+ + D+ A I G++D++VN AG PL E+TEE++ R +AI++ +Y Sbjct: 59 DVTSRADIEAAVAATIAHGGKLDIVVNNAGWTHRNKPLMEVTEEEFDRVYAINVKSIYYM 118 Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 ++P M QG G ++N+ S PG Y +K + TR+L +E AP+ +RVN Sbjct: 119 THTIVPIMSGQGGGVVVNVGSVAGIRPRPGLTWYNSSKGAVNLATRSLAVELAPQKIRVN 178 Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256 +AP T L +D + G D R R P R+ +P ++A ++LASDEA FI Sbjct: 179 CVAPVMGATGL-LDSFMGVPDTPENRARFIATIPLGRLSEPKDIANACLYLASDEAEFIT 237 Query: 257 ASCITIDGGRSV 268 + +DGGR++ Sbjct: 238 GVVLEVDGGRTI 249 Lambda K H 0.322 0.138 0.426 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: 143 Number of extensions: 5 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: 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 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