Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate 3607101 Dshi_0523 L-fuculose-phosphate aldolase (RefSeq)
Query= BRENDA::P0AB87 (215 letters) >FitnessBrowser__Dino:3607101 Length = 231 Score = 175 bits (443), Expect = 7e-49 Identities = 93/207 (44%), Positives = 127/207 (61%), Gaps = 2/207 (0%) Query: 10 IIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFIDGNGKHEE-GK 68 +ID CL M LNQGT+GN+S R G+LITP+G+PYE LT +V I +G + G Sbjct: 17 LIDACLWMNARHLNQGTSGNISARIASGILITPSGVPYEYLTPDALVTIPLDGLPDSNGA 76 Query: 69 LPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGGNSIPCAPY 128 PSSEW FH +Q+RPD V+H H +C+ +++ RSIPA HYMIAA GGN +P A Y Sbjct: 77 QPSSEWPFHQGMHQARPDMPVVLHAHPPYCSVLAVQRRSIPACHYMIAAFGGNDVPLADY 136 Query: 129 ATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQLYLTTLAIT 188 A FG+ EL ++A + +R L+ +HG ++KA W E+E LA+ YL + +I Sbjct: 137 ALFGSPELCANMARIMADRHGCLMANHGATVLGETVDKARWRLEELETLARTYLFS-SIG 195 Query: 189 DPVPVLSDEEIAVVLEKFKTYGLRIEE 215 +LSD EIA V+ F +YG R E Sbjct: 196 GAPHILSDAEIAEVMVAFSSYGPRHPE 222 Lambda K H 0.319 0.134 0.394 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: 157 Number of extensions: 5 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: 215 Length of database: 231 Length adjustment: 22 Effective length of query: 193 Effective length of database: 209 Effective search space: 40337 Effective search space used: 40337 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: 46 (22.3 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