Align D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate Ac3H11_658 Fructose-bisphosphate aldolase class II (EC 4.1.2.13)
Query= SwissProt::P0C8J6 (284 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_658 Length = 349 Score = 166 bits (420), Expect = 7e-46 Identities = 107/323 (33%), Positives = 175/323 (54%), Gaps = 47/323 (14%) Query: 7 KQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTHAGTENLLALV 66 +++L++A Y +PAFN++NLE +Q V+ A + APVI+ + G +AG + L+ Sbjct: 2 RELLDHAAANSYGIPAFNVNNLEQVQAVMAAADEVGAPVILQASAGARKYAGEPFIKHLI 61 Query: 67 SAMAKQYHH-PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLP-------FAQNISRVK 118 A + + H PL +H DH T A + G SVM+D S + F N+ + Sbjct: 62 QAAVEAFPHIPLVMHQDHGTSPKVCAGAIDLGFGSVMMDGSLMEDGKTPSSFEYNVEVTR 121 Query: 119 EVVDFCHRFDVSVEAELGQLG-------GQED----DVQVNEADALYTNPAQAREFAEAT 167 +VVD H+ V+VE ELG LG G+ED DV+++ + L T+P +A F +AT Sbjct: 122 KVVDMAHKVGVTVEGELGCLGNLETGEAGEEDGIGADVKLDHSQML-TDPEEAAVFVKAT 180 Query: 168 GIDSLAVAIGTAHGMYA-----SAPALDFSRLENIRQWV-NLPLVLHGAS---------- 211 +D+LA+AIGT+HG Y + L SR++ I + + N LV+HG+S Sbjct: 181 QLDALAIAIGTSHGAYKFSRKPTGDILAISRVKEIHKRIPNTHLVMHGSSSVPAELLAII 240 Query: 212 -----------GLSTKDIQQTIKLGICKINVATELKNAFSQALKNYLTEHPEATDPRDYL 260 G+ ++IQ+ IK G+ KIN+ T+++ A + A++ +L E+P+ D R++L Sbjct: 241 NQYGGKMKETYGVPVEEIQEAIKHGVRKINIDTDIRLAMTGAVRKFLAENPDKFDAREWL 300 Query: 261 QSAKSAMRDVVSKVIADCGCEGR 283 + A+ A + V + GCEG+ Sbjct: 301 KPAREAAKQVCKARYLEFGCEGQ 323 Lambda K H 0.318 0.131 0.376 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: 226 Number of extensions: 14 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: 284 Length of database: 349 Length adjustment: 27 Effective length of query: 257 Effective length of database: 322 Effective search space: 82754 Effective search space used: 82754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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