Align D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate WP_009140764.1 HMPREF9452_RS03670 class II fructose-bisphosphate aldolase
Query= SwissProt::Q9KIP8 (286 letters) >NCBI__GCF_000225705.1:WP_009140764.1 Length = 282 Score = 244 bits (622), Expect = 2e-69 Identities = 127/281 (45%), Positives = 174/281 (61%), Gaps = 1/281 (0%) Query: 3 IISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALEEI 62 +++TK +L DAQ N YAV AFN+ N E + A+L E +SPVI+ T GT K L+ Sbjct: 2 LVTTKEMLLDAQKNHYAVGAFNVENLEFVMAVLAAAEETKSPVIMQTTSGTIKKTGLDYF 61 Query: 63 YALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVD 122 Y + A + ++P+ALHLDH + D + + G S MIDGSH F +N+ L K V D Sbjct: 62 YGMVKAAAERASVPVALHLDHGDGYDRCMKALRTGYTSVMIDGSHETFEDNIALTKLVAD 121 Query: 123 FCHSQDCSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAIGTAHGL 182 + VEAELG++GG EDD+ V+ ES + TDP EAK FVE TG SLA+ +GTAHG+ Sbjct: 122 AGAAMGIPVEAELGKVGGKEDDVEVEGESPY-TDPVEAKEFVERTGCTSLAIGVGTAHGV 180 Query: 183 YSKTPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELKIAFAGA 242 Y++ P ID + IR VDVPLVLHG S VPDE V ++ G+ KVN ATEL+ A+ Sbjct: 181 YTEEPHIDQDVVKAIRAAVDVPLVLHGTSGVPDEQVAEAVKNGICKVNYATELRQAYTKG 240 Query: 243 VKAWFAENPQGNDPRNYMRVGMDAMKEVVRNKINVCGSANR 283 A+ AENP DP+N + G + + ++V+ ++ GS R Sbjct: 241 YMAYMAENPNNFDPKNPGKAGAEEITKIVKIRMENLGSVGR 281 Lambda K H 0.319 0.133 0.384 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: 217 Number of extensions: 11 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: 282 Length adjustment: 26 Effective length of query: 260 Effective length of database: 256 Effective search space: 66560 Effective search space used: 66560 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 24 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