Align L-fuculose phosphate aldolase; EC 4.1.2.17; L-fuculose-1-phosphate aldolase (uncharacterized)
to candidate WP_076580931.1 BB347_RS09575 class II aldolase/adducin family protein
Query= curated2:Q8FEF0 (215 letters) >NCBI__GCF_001971705.1:WP_076580931.1 Length = 213 Score = 133 bits (334), Expect = 3e-36 Identities = 77/209 (36%), Positives = 122/209 (58%), Gaps = 10/209 (4%) Query: 8 RQIIDTCLEMTRLGLNQGTAGNVSVRYQ---DGMLITPTGIPYEKLTESHIVFIDGNGKH 64 RQ+++ E+ L GN+SVR D ITPTG+PY+ + + +G+ Sbjct: 8 RQVVEHAAELAEL--TPARTGNLSVRESTDGDAFAITPTGVPYDSFDVAETPVVGVDGEQ 65 Query: 65 EEGKL-PSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGGNSI 123 +G++ PSSE H A Y+ R D A+VH H+ TA++ ++P+P IHYMI A G + Sbjct: 66 RDGEMAPSSEVPMHSAIYR-REDVGAIVHTHSPWSTAMATAHQPLPPIHYMIVAV-GKRV 123 Query: 124 PCAPYATFGTRELSEHV--ALALKNRKATLLQHHGLIACEANLEKALWLAHEVEVLAQLY 181 P A YA +GT +L+E++ A++ + A +++HGL+ +LE AL H VE LA+LY Sbjct: 124 PVASYAPYGTDKLAENIVEAMSAADSTAAFIENHGLVVTAPDLETALENTHHVESLARLY 183 Query: 182 LTTLAITDPVPVLSDEEIAVVLEKFKTYG 210 L + + L+DE++ VLE+F++YG Sbjct: 184 LEIRSASLEPRPLTDEQLETVLEQFESYG 212 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: 114 Number of extensions: 5 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: 215 Length of database: 213 Length adjustment: 22 Effective length of query: 193 Effective length of database: 191 Effective search space: 36863 Effective search space used: 36863 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