Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate H281DRAFT_00643 H281DRAFT_00643 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Burk376:H281DRAFT_00643 Length = 246 Score = 151 bits (381), Expect = 1e-41 Identities = 92/248 (37%), Positives = 133/248 (53%), Gaps = 6/248 (2%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77 +L KV ++TGA QGIG A FAS+ A ++ D+ + V TVA RE G A Sbjct: 2 KLNGKVAIITGAGQGIGAATALKFASEGAVVIACDMNLDAVATVAHLCREAGGKADAFAV 61 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 DV+N+ + M +GRIDV+VN AG+ +MT + + ++L G ++ Sbjct: 62 DVTNRTQVDEMVAKVRGTYGRIDVVVNNAGITRDARLQKMTLQQFDDVIDVNLRGVFHTA 121 Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197 +AV+ MIEQG G I+N +S + G Y AK G++G T+ E PKG+RVNA Sbjct: 122 QAVVDTMIEQGSGVILNASSVVGVYGNYGQTNYAAAKFGVIGFTKTWSRELGPKGIRVNA 181 Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 +APG+I+T + P + D P RR+G+P E+A FLASDEA ++N Sbjct: 182 VAPGFIDTPILKTI------PEDVLTKMRDQVPLRRLGKPEEIASIYAFLASDEASYVNG 235 Query: 258 SCITIDGG 265 + I GG Sbjct: 236 AVIEATGG 243 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: 123 Number of extensions: 3 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: 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 Sep 17 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