Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate WP_092345871.1 BLU87_RS06340 fuculose phosphate aldolase
Query= BRENDA::P0AB87 (215 letters) >NCBI__GCF_900107645.1:WP_092345871.1 Length = 215 Score = 160 bits (406), Expect = 1e-44 Identities = 83/206 (40%), Positives = 137/206 (66%), Gaps = 5/206 (2%) Query: 8 RQIIDTCLEMTRLGLNQGTAGNVSV--RYQDGMLITPTGIPYEKLTESHIVFIDGNGKHE 65 +QI+D +++ R GL G+ GN+S+ R D + I+P+GI Y +T + +V +D +G+ Sbjct: 8 QQIVDYGMQLIRSGLTTGSGGNLSILSREDDLIAISPSGINYHDMTIADVVIVDRSGQRV 67 Query: 66 EGKL-PSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGGNSIP 124 EG+L PSSE FH+A Y +R D N++VH H+V+ T ++ L+ IPA+HY++A +G + +P Sbjct: 68 EGELKPSSELGFHLALYSAREDINSIVHTHSVYATTIACLHWEIPAVHYLVAFSG-DKVP 126 Query: 125 CAPYATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQLYLTT 184 APYATFG+ L++++ ++ A LL +HGL+A + KA A E+E++A++Y Sbjct: 127 LAPYATFGSAALADNIIASIGAYNAVLLANHGLVAVGDGMSKAFNTAEEIELVARIYYQA 186 Query: 185 LAITDPVPVLSDEEIAVVLEKFKTYG 210 +I +PV ++ EE+ VV EKF +YG Sbjct: 187 KSIGEPV-LVDAEEMKVVSEKFCSYG 211 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: 125 Number of extensions: 9 Number of successful extensions: 5 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: 215 Length adjustment: 22 Effective length of query: 193 Effective length of database: 193 Effective search space: 37249 Effective search space used: 37249 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