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_b21192 SM_b21192 fructose-1,6-bisphosphate aldolase
Query= SwissProt::Q8VS16 (284 letters) >FitnessBrowser__Smeli:SM_b21192 Length = 347 Score = 169 bits (428), Expect = 8e-47 Identities = 112/318 (35%), Positives = 177/318 (55%), Gaps = 45/318 (14%) Query: 1 MFIISSKNMLLKAQRLGYAVPAFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAGTG 60 M +I+ + +L A YA+PAFN++NLE +Q V+ A SP+IL + G +YAG Sbjct: 1 MALITLRQLLDDAAENDYALPAFNVNNLEYIQAVMRAADATDSPVILQASRGARAYAGDA 60 Query: 61 NVVAIARDLAKIWD-LPLAVHLDHHEDLADITRKVQAGIRSVMIDGSH-------SPFEE 112 + + A+ + +P+ +HLDH + + + G SVM+DGS + +E Sbjct: 61 FLRHLILGAAEEYPHIPVCLHLDHGDQPSTCISAITNGFTSVMMDGSLEKDGKTVASYEY 120 Query: 113 NVALVKSVVELSHRYDASVEAELGRLGGVE-------DDLGVDAK---DALYTNPEQGRE 162 NVA+ VV+++H SVE ELG LG +E D G + K + L T+PEQ + Sbjct: 121 NVAVTAEVVKIAHAAGVSVEGELGCLGNLETGAGDKEDGHGFEGKLSREELLTDPEQALD 180 Query: 163 FVARTGIDSLAVVIGTAHGLY--AAEPK---LGFAALPPISERV-DVPLVLHGASKLPD- 215 FV++TG+D+LAV IGT+HG Y EP L + I++R+ + LV+HG+S +P Sbjct: 181 FVSKTGVDALAVAIGTSHGAYKFTREPDGEILSIETIAKINKRLPNTHLVMHGSSSVPAD 240 Query: 216 --------------------SDIRRAISLGVCKVNVATELKIAFSDALKHYFEENPDANE 255 S+I++AI LGV KVN+ T+L++AF+ ++ + E+PD + Sbjct: 241 LQELFNAYGGKMKKTWGVPVSEIQKAIPLGVRKVNIDTDLRLAFTGEIRKHHIEHPDNFD 300 Query: 256 PRHYMKPAKAAMKDVVRK 273 PR+Y+KPA A M +V ++ Sbjct: 301 PRNYLKPAIAHMTEVCKE 318 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: 255 Number of extensions: 14 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: 347 Length adjustment: 27 Effective length of query: 257 Effective length of database: 320 Effective search space: 82240 Effective search space used: 82240 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