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 SM_b20199 SM_b20199 fructose-1,6-bisphosphate aldolase
Query= SwissProt::Q8VS16 (284 letters) >FitnessBrowser__Smeli:SM_b20199 Length = 359 Score = 152 bits (384), Expect = 1e-41 Identities = 106/325 (32%), Positives = 161/325 (49%), Gaps = 47/325 (14%) Query: 4 ISSKNMLLKAQRLGYAVPAFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAGTGNVV 63 I+ + +L A Y VPAFNI+N+E ++E A +P+IL + G SYA + Sbjct: 4 ITLRQLLDHAAERSYGVPAFNINNMEQGLAIMEAARASDAPVILQVSRGARSYANDVMLA 63 Query: 64 AIARDLAKIW-DLPLAVHLDHHEDLADITRKVQAGIRSVMIDGS-------HSPFEENVA 115 + L +++ D+PL +H DH ++A +Q G SVM+DGS + ++ NV+ Sbjct: 64 KMMEALEEMYPDIPLCIHQDHGNNVATCLTAIQHGFTSVMMDGSLKEDAKTPADYDYNVS 123 Query: 116 LVKSVVELSHRYDASVEAELGRLGGVEDDLGVDAKDA-----------LYTNPEQGREFV 164 + V L+H ASVE ELG LG +E G +A+D L T+P++ FV Sbjct: 124 ITAEVSRLAHMVGASVEGELGCLGSLETGHG-EAEDGHGFEGALDRSQLLTDPDEAARFV 182 Query: 165 ARTGIDSLAVVIGTAHGLYAAEPK-----LGFAALPPISERV-DVPLVLHGASKLPD--- 215 A TG+D+LAV IGT+HG Y K L + I ER+ D +V+HG+S +P Sbjct: 183 AETGVDALAVAIGTSHGAYKFTRKPTGEVLAMDVIEKIHERLPDTHIVMHGSSSVPQEWQ 242 Query: 216 ------------------SDIRRAISLGVCKVNVATELKIAFSDALKHYFEENPDANEPR 257 +I R I GV KVN+ T+L++A + A + + + +PR Sbjct: 243 DVFNAHGGQMRETYGVPVEEIVRGIRFGVRKVNIDTDLRLAAAAAFRRVADTSRSEFDPR 302 Query: 258 HYMKPAKAAMKDVVRKVIHVCGCEG 282 ++KPA AM V + G G Sbjct: 303 KFLKPAMDAMSAVCKARFEAFGTAG 327 Lambda K H 0.319 0.135 0.389 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: 252 Number of extensions: 12 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: 359 Length adjustment: 28 Effective length of query: 256 Effective length of database: 331 Effective search space: 84736 Effective search space used: 84736 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 (21.7 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