Align L-fuculose phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate 3608148 Dshi_1553 class II aldolase/adducin family protein (RefSeq)
Query= reanno::Koxy:BWI76_RS22915 (215 letters) >FitnessBrowser__Dino:3608148 Length = 216 Score = 83.6 bits (205), Expect = 3e-21 Identities = 64/208 (30%), Positives = 96/208 (46%), Gaps = 18/208 (8%) Query: 6 LARQIIDTCLEMTRLGLNQGTAGNVSVRYQ-GGMLITPTGIPYEKLTEAHIVYIDAEGQH 64 LAR I D GL G+ GN+S R + GG+L++PTG + +L + DA G Sbjct: 14 LARSIFDR-------GLTGGSTGNISARTEDGGLLVSPTGTSFGRLDPGRLSRFDAAGHL 66 Query: 65 EQGKLPSSEWRFHLAAYQTRPDAHAVVHNHAVHCTAVSIL------NRPIPAIHYMIAAA 118 G P+ E H A Y+TR A AVVH H+ H A+S++ + P Y I Sbjct: 67 VSGDKPTKEMPLHSAFYETRSTAGAVVHLHSCHSVALSMMPDVDPEDFLPPLTPYGIMKL 126 Query: 119 GGNSIPCAPYATFGTRELSEHVAVALKNRKATLLQHHGLIACEENLEKALWLAHEVEVLA 178 G + P G + + V R A +L +HG + +++E A E+E A Sbjct: 127 G--RVKLLPVFLPGDPAMGDAVRGLAGRRSAVMLANHGPVVAGKDVEAACNAVEELEETA 184 Query: 179 QLYLSTLAIIDPVPVLDDEAIAVVLEKF 206 +L + T + +L E + V+EKF Sbjct: 185 RLAMLTRGL--QPRMLSPEQVRAVVEKF 210 Lambda K H 0.320 0.135 0.402 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: 81 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: 216 Length adjustment: 22 Effective length of query: 193 Effective length of database: 194 Effective search space: 37442 Effective search space used: 37442 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 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