Align tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate 15891 b1773 predicted aldolase (NCBI)
Query= CharProtDB::CH_024465 (286 letters) >FitnessBrowser__Keio:15891 Length = 278 Score = 171 bits (432), Expect = 2e-47 Identities = 103/275 (37%), Positives = 151/275 (54%), Gaps = 8/275 (2%) Query: 7 KYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALEEIYALC 66 +Y DA YA+ FN+ NAE + +++ E +SPVI++ G + + E+ + Sbjct: 6 RYWENDATNKHYAIAHFNVWNAEMLMGVIDAAEEAKSPVIISFGTGFVGNTSFEDFSHMM 65 Query: 67 SAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHS 126 + + +P+ H DH S++ I G+ S M D S F F EN++L K VDF H Sbjct: 66 VSMAQKATVPVITHWDHGRSMEIIHNAWTHGMNSLMRDASAFDFEENIRLTKEAVDFFHP 125 Query: 127 QDCSVEAELGRLGGVEDDMSVDAESAF-LTDPQEAKRFVELTGVDSLAVAIGTAHGLYSK 185 VEAELG +G + + +A + + TDP +A FVE TG DSLAVAIG HG+Y+ Sbjct: 126 LGIPVEAELGHVGN--ETVYEEALAGYHYTDPDQAAEFVERTGCDSLAVAIGNQHGVYTS 183 Query: 186 TPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELKIAFAGAVKA 245 P+++F+ + +R+ V VPLVLHGAS + D ++ I LG+ K+N+ TEL A AVK Sbjct: 184 EPQLNFEVVKRVRDAVSVPLVLHGASGISDADIKTAISLGIAKINIHTELCQAAMVAVK- 242 Query: 246 WFAENPQGNDPRYYMRVGMDAMKEVVRNKINVCGS 280 EN Q + R A+KE KI + GS Sbjct: 243 ---EN-QDQPFLHLEREVRKAVKERALEKIKLFGS 273 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: 206 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: 286 Length of database: 278 Length adjustment: 26 Effective length of query: 260 Effective length of database: 252 Effective search space: 65520 Effective search space used: 65520 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: 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