Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_012331635.1 M446_RS08185 3-oxoacyl-ACP reductase FabG
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_000019365.1:WP_012331635.1 Length = 275 Score = 162 bits (411), Expect = 6e-45 Identities = 101/248 (40%), Positives = 133/248 (53%), Gaps = 5/248 (2%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77 RL +KV L+TG A+GIG A+ AFA + A LVI+D+ E AA E G A+ Sbjct: 4 RLADKVALVTGGARGIGLAVARAFAREGAALVIADVNRAGAEAAAAGLAEAGGRAMAVAV 63 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 DV++ + AM + RHGR+D+LVN AGV LE EDW R I+L GA+ Sbjct: 64 DVADPASIAAMVEAILARHGRLDILVNNAGVGGNTPFLETRLEDWNRIIGINLTGAFLVA 123 Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197 +A +M+ G G I+NIAS G Y AK GL LT+ + +E + G+ VN Sbjct: 124 QACAREMVRGGGGKIVNIASLSGQRGGDGRAAYGAAKAGLELLTKVMAVELSEHGINVNN 183 Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 IAPG IET++ FA A R L P R G P E+A AVFL SDEA ++ Sbjct: 184 IAPGAIETEM-----ARFAHDAATRAAYGYLIPMTRYGTPEEIADAAVFLCSDEARYVQG 238 Query: 258 SCITIDGG 265 + +DGG Sbjct: 239 HTLNVDGG 246 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: 189 Number of extensions: 11 Number of successful extensions: 2 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: 275 Length adjustment: 25 Effective length of query: 247 Effective length of database: 250 Effective search space: 61750 Effective search space used: 61750 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