Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Miya:8502394 Length = 247 Score = 124 bits (311), Expect = 2e-33 Identities = 78/242 (32%), Positives = 124/242 (51%), Gaps = 7/242 (2%) Query: 25 LLTGAAQGIGEAIVAAFASQQARLVISDI-QAEKVETVAAHWRERGADVHALKADVSNQQ 83 L+TG ++GIG+A+ A + ++ ++ + + E+ E VAA G A + DVS+ Sbjct: 9 LVTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSDAA 68 Query: 84 DLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLPQ 143 + A + + +DVLVN AG+ L M ++D+ R ++L GA+ + Sbjct: 69 AVAAFFQEEIREKVTLDVLVNNAGITKDGLILRMKDDDFDRVLDVNLSGAFTCLREAAKL 128 Query: 144 MIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYI 203 M Q G I+NI S G Y AK GL+G+T++ E A + V VNA+APG+I Sbjct: 129 MTRQRKGRIVNITSVVGQMGNAGQVNYSAAKAGLIGMTKSAAKELAGRNVTVNAVAPGFI 188 Query: 204 ETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCITID 263 ET + + Y ++ P RR+GQP ++A FLASD+A +I I ++ Sbjct: 189 ETDMTAKLTDEVRAAY------IEAIPLRRLGQPQDIADAVAFLASDKAGYITGQVIAVN 242 Query: 264 GG 265 GG Sbjct: 243 GG 244 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: 141 Number of extensions: 6 Number of successful extensions: 3 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: 247 Length adjustment: 24 Effective length of query: 248 Effective length of database: 223 Effective search space: 55304 Effective search space used: 55304 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