Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate BPHYT_RS29250 BPHYT_RS29250 dihydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS29250 Length = 307 Score = 102 bits (253), Expect = 1e-26 Identities = 77/241 (31%), Positives = 119/241 (49%), Gaps = 16/241 (6%) Query: 5 ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAI 64 ++F+GI P+ T F ADG +D AL+ AG+ GL LG+ GE + L A E+ A+ Sbjct: 2 SIFSGIWVPLITPF-ADGAVDHAALRALVRRYTGAGIAGLVALGTTGEPAALDAAEQDAV 60 Query: 65 ARFAID------HVDRRVPVLIGTGGTNARETIELSQHAQQAGA---DGIVVINPYYWKV 115 +D H+ R L G + T + Q A G+++ PYY + Sbjct: 61 LATILDEAQSAAHLARDGQALPVVAGVSGNHTASMRVRIGQLNALPLAGVLMAAPYYIRP 120 Query: 116 SEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAH 175 S+A ++ +F +AD+ PV+LY+ P TG L + LA + I +KD S+ Sbjct: 121 SQAGIVAHFMALADASEKPVVLYDIPYRTGVRLELDTLLALA-THPRIQAVKDCAGSLDT 179 Query: 176 LRSMIHTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDV 235 ++I + VL G D ++FNTL LGG GAI+AS + P+ V + +A G + Sbjct: 180 TLALIRDAR-----LQVLAGEDINIFNTLCLGGSGAIAASAHVRPERFVEMYRALAAGRL 234 Query: 236 A 236 A Sbjct: 235 A 235 Lambda K H 0.320 0.138 0.407 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: 216 Number of extensions: 10 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: 302 Length of database: 307 Length adjustment: 27 Effective length of query: 275 Effective length of database: 280 Effective search space: 77000 Effective search space used: 77000 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: 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