Align L-fuculose phosphate aldolase; EC 4.1.2.17; L-fuculose-1-phosphate aldolase (uncharacterized)
to candidate WP_004299660.1 C665_RS02965 fuculose phosphate aldolase
Query= curated2:Q8FEF0 (215 letters) >NCBI__GCF_000310185.1:WP_004299660.1 Length = 229 Score = 162 bits (411), Expect = 4e-45 Identities = 88/202 (43%), Positives = 124/202 (61%), Gaps = 2/202 (0%) Query: 10 IIDTCLEMTRLGLNQGTAGNVSVRYQDG-MLITPTGIPYEKLTESHIVFIDGNGKHEEGK 68 ++ T M LN GT+GN S R + G MLI+P+GIP E+ +V ++ +G++ + Sbjct: 25 LLHTLRAMGAARLNVGTSGNASQRLEGGRMLISPSGIPAERCRTEDMVVVEADGRYAGAR 84 Query: 69 LPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGGNSIPCAPY 128 PSSEW H Y + P A AV+H HA TA++ IP HYMIA GG ++ CA Y Sbjct: 85 APSSEWPLHHDVYTAFPAAGAVLHAHAPFATALACQRLDIPPFHYMIARFGGTTVRCARY 144 Query: 129 ATFGTRELSEHVALALKNRKATLLQHHGLIACEANLEKALWLAHEVEVLAQLYLTTLAIT 188 ATFGT+ LS+ AL+ R A LL +HG++ +LE AL +A E E L + Y TL + Sbjct: 145 ATFGTQALSDATVAALQERSACLLANHGMVVLGRDLEHALAMAIEFETLCEQYWRTLQLG 204 Query: 189 DPVPVLSDEEIAVVLEKFKTYG 210 +PV +LS+EE+A V+E+FK YG Sbjct: 205 EPV-LLSEEEMAEVIERFKWYG 225 Lambda K H 0.319 0.134 0.397 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: 129 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: 215 Length of database: 229 Length adjustment: 22 Effective length of query: 193 Effective length of database: 207 Effective search space: 39951 Effective search space used: 39951 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: 45 (21.9 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