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 RR42_RS06250 RR42_RS06250 dihydrodipicolinate synthase
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__Cup4G11:RR42_RS06250 Length = 294 Score = 143 bits (360), Expect = 5e-39 Identities = 92/277 (33%), Positives = 140/277 (50%), Gaps = 7/277 (2%) Query: 9 GIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIARFA 68 G I + T DG LD P AL+D + G DG+ +G+ GE + +E + R A Sbjct: 6 GSIVAIVTPMQEDGSLDFPALRALVDWHVAEGTDGIVIVGTTGESPTVNVDEHCELIRVA 65 Query: 69 IDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQVA 128 ++ D+R+P++ GTGG + +E IEL+ A+Q GAD + + PYY K ++ + R+F +A Sbjct: 66 VEQADKRIPIIAGTGGNSTKEAIELTAFAKQVGADASLQVVPYYNKPTQEGMYRHFRTIA 125 Query: 129 DSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHP 188 ++V LPV+LYN P T D+ + LA IIG+K+ ++ +I K A Sbjct: 126 EAVELPVVLYNVPGRTVADMQHDTILRLAQV-PGIIGVKEATGNIDRAAQLI---KDAPQ 181 Query: 189 HFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQI 248 F++ G D +LLGG G IS + N AP+ L A GD A H L+ + Sbjct: 182 GFSIYSGDDPTAIALMLLGGHGNISVTANVAPRKMHELCVAALKGDAITARRIHMELVAL 241 Query: 249 PQMYQLDTPFVNVIKEAIVLCGRPVSTHVLP--PASP 283 + ++ + V K A+ GR LP P SP Sbjct: 242 NKAMFVEANPIPV-KWALQQMGRMQGGIRLPLTPLSP 277 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: 230 Number of extensions: 12 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: 302 Length of database: 294 Length adjustment: 26 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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