Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_012759867.1 RLEG_RS22955 3-oxoacyl-ACP reductase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >NCBI__GCF_000023185.1:WP_012759867.1 Length = 254 Score = 142 bits (357), Expect = 9e-39 Identities = 84/254 (33%), Positives = 141/254 (55%), Gaps = 8/254 (3%) Query: 18 RLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKA 77 RL NKV ++TGA+ GIG A FA++ A++V+ + +++ + A + +G D +AI Sbjct: 3 RLNNKVAIVTGASSGIGRATAKLFAAEGAKVVVGARRQGELDSLVAEIKAEGGDAIAIAG 62 Query: 78 DVSRQQDLH-AMARLAIELHGRIDVLVNCAGVNVFRDP-LQMTEEDWHRCFAIDLDGAWY 135 DV R +D H A+ A+ +G++D+ N AG P ++E + AI+L ++ Sbjct: 63 DV-RSEDYHKALVAAAVTNYGKLDIAFNNAGTLGEAGPSTAVSEAGFSEAVAINLTASFL 121 Query: 136 GCKAVLPQMIEQGIGSIINIAS-THSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIR 194 K M+E G GS+I ++ + PG Y +K GL+GLT+AL E+ +G+R Sbjct: 122 AAKHQTGAMVENGGGSVIFTSTFVGYSFAFPGVAAYAASKSGLIGLTQALAAEFGQQGVR 181 Query: 195 VNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPF 254 VNAI PG ++T D + D ++ +LH +R+ P E+A + ++LASD+A F Sbjct: 182 VNAILPGAVDT----DMYRDMNDTPEKQAFVTNLHALKRVATPEELARSVLYLASDDASF 237 Query: 255 INASCITIDGGRSV 268 + + +DGG S+ Sbjct: 238 VTGTASLVDGGASI 251 Lambda K H 0.321 0.138 0.424 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: 9 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: 254 Length adjustment: 25 Effective length of query: 247 Effective length of database: 229 Effective search space: 56563 Effective search space used: 56563 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