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 3607858 Dshi_1266 ketose-bisphosphate aldolase (RefSeq)
Query= SwissProt::P0C8J6 (284 letters) >FitnessBrowser__Dino:3607858 Length = 280 Score = 137 bits (344), Expect = 3e-37 Identities = 83/269 (30%), Positives = 129/269 (47%), Gaps = 13/269 (4%) Query: 1 MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTHAGTE 60 M + + ++L A GGYAV E M+ A P+I+ P H Sbjct: 1 MTLATLSEVLQPALEGGYAVGGLVCLGWEEMRAYTRAAEAEGVPLILQAGPSCRAHTPLP 60 Query: 61 NLLALVSAMAKQYHHPLAIHLDHHTKFDDIAQKVRSGVRSVMIDASHLPFAQNISRVKEV 120 L A+ +A++ P+ HLDH F + + + SG S+M D S LP +NI++ + Sbjct: 61 VLGAMFRHLAERASVPVVAHLDHGYSFAECQEALDSGFTSLMFDGSRLPLEENIAQTARI 120 Query: 121 VDFCHRFDVSVEAELGQLGGQEDDVQVNEADALYTNPAQAREFAEATGIDSLAVAIGTAH 180 VD H+ +S E E+G +G E D T+P +A FA TG+D++A+++G H Sbjct: 121 VDLAHKAGISCEGEIGFVGYAEGDASQG------TDPEEAARFARETGVDAMAISVGNVH 174 Query: 181 GMYASAPALDFSRLENIRQWVNLPLVLHGASGLSTKDIQQTIKLG----ICKINVATELK 236 LD R+ I +PLV+HG SG+ + Q +L ICK N+ TEL+ Sbjct: 175 LQQNREGGLDEGRIAEIAARTEVPLVIHGGSGV---PLAQRTRLARGSTICKFNIGTELR 231 Query: 237 NAFSQALKNYLTEHPEATDPRDYLQSAKS 265 AF AL+ +T P+ D L+ ++ Sbjct: 232 MAFGAALREAVTSDPDRFDRVQILREVEA 260 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: 188 Number of extensions: 8 Number of successful extensions: 3 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: 280 Length adjustment: 26 Effective length of query: 258 Effective length of database: 254 Effective search space: 65532 Effective search space used: 65532 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: 47 (22.7 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