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 7026208 Shewana3_3350 fructose-1,6-bisphosphate aldolase (RefSeq)
Query= SwissProt::P0C8J6 (284 letters) >FitnessBrowser__ANA3:7026208 Length = 355 Score = 171 bits (433), Expect = 2e-47 Identities = 111/329 (33%), Positives = 175/329 (53%), Gaps = 45/329 (13%) Query: 1 MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTHAGTE 60 M ++S +Q+L++A GY VPAFN++NLE M+ +++ A +PVI+ + G +A + Sbjct: 1 MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60 Query: 61 NLLALVSAMAKQYHH-PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLP-------FAQ 112 L L++A +QY P+ IH DH T D + ++ G+ SVM+D S + + Sbjct: 61 FLKYLMTAALEQYPDIPVCIHQDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASYEY 120 Query: 113 NISRVKEVVDFCHRFDVSVEAELGQLG-------GQEDDVQ---VNEADALYTNPAQARE 162 N+ + V F H VSVE E+G LG G+ED V V D L T+P +A Sbjct: 121 NVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGVGAEGVLSHDQLLTSPEEAAR 180 Query: 163 FAEATGIDSLAVAIGTAHGMY--ASAPALDFSRLENIRQW----VNLPLVLHGAS----- 211 F T +D+LA+AIGT+HG Y + P D R++ I++ N LV+HG+S Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQE 240 Query: 212 ----------------GLSTKDIQQTIKLGICKINVATELKNAFSQALKNYLTEHPEATD 255 G+ ++I + IK G+ K+N+ T+L+ A + A++ YL EHP D Sbjct: 241 WLQIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSEFD 300 Query: 256 PRDYLQSAKSAMRDVVSKVIADCGCEGRA 284 PR +L+++ AM D+ + GC G+A Sbjct: 301 PRKFLKASMEAMADICTVRYEAFGCAGQA 329 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: 248 Number of extensions: 13 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: 284 Length of database: 355 Length adjustment: 27 Effective length of query: 257 Effective length of database: 328 Effective search space: 84296 Effective search space used: 84296 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