Align tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate Synpcc7942_1443 Synpcc7942_1443 fructose-1,6-bisphosphate aldolase
Query= CharProtDB::CH_024465 (286 letters) >FitnessBrowser__SynE:Synpcc7942_1443 Length = 357 Score = 165 bits (417), Expect = 2e-45 Identities = 115/333 (34%), Positives = 171/333 (51%), Gaps = 50/333 (15%) Query: 1 MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALE 60 M+++ + +L A N Y +PAFN++N E +Q+IL+ E SPVIL + G + Sbjct: 1 MALVPLRLMLDHAAENEYGIPAFNVNNLEQVQSILQAADETDSPVILQASRGARSYAGEN 60 Query: 61 EIYALCSAYSTTY-NMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAE------- 112 + L A TY ++P+A+H DH S + G S M+DGS A+ Sbjct: 61 FLRHLILAAVETYPHIPIAMHQDHGNSPATCYSAIKNGFTSVMMDGSLEADAKTPASYEY 120 Query: 113 NVKLVKSVVDFCHSQDCSVEAELGRLGGVEDDMSVDAE-----------SAFLTDPQEAK 161 NV++ + VVD HS SVE ELG LG +E +AE S LTDP +A Sbjct: 121 NVEVTRQVVDVAHSIGVSVEGELGCLGSLETGKG-EAEDGHGFEGTLDHSQLLTDPDQAV 179 Query: 162 RFVELTGVDSLAVAIGTAHGLYSKTPK-----IDFQRLAEI-REVVDVPLVLHGASDVPD 215 FVE T VD+LAVAIGT+HG Y T K + R+ EI R + + LV+HG+S VP Sbjct: 180 DFVEKTQVDALAVAIGTSHGAYKFTRKPTGEILAISRIEEIHRRLPNTHLVMHGSSSVPQ 239 Query: 216 EF---------------------VRRTIELGVTKVNVATELKIAFAGAVKAWFAENPQGN 254 E +++ I+LGV K+N+ T+ ++AF AV+ A++P Sbjct: 240 ELLELINEYGGQIPETYGVPVEEIQKAIKLGVRKINIDTDNRLAFTAAVREAAAKDPSNF 299 Query: 255 DPRYYMRVGMDAMKEVVRNK---INVCGSANRI 284 DPR++ + + MK+V ++ N G A++I Sbjct: 300 DPRHFNKPAIKYMKQVCVDRYVAFNTAGQASKI 332 Lambda K H 0.319 0.134 0.386 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: 260 Number of extensions: 15 Number of successful extensions: 6 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: 286 Length of database: 357 Length adjustment: 28 Effective length of query: 258 Effective length of database: 329 Effective search space: 84882 Effective search space used: 84882 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: 48 (23.1 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