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 207334 DVU1868 dihydrodipicolinate synthase (TIGR)
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__DvH:207334 Length = 292 Score = 149 bits (376), Expect = 8e-41 Identities = 91/290 (31%), Positives = 158/290 (54%), Gaps = 6/290 (2%) Query: 7 FTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKAIAR 66 FTG + T F +G++D+ LI+ I+ G++GL G+ GE + L +E + + R Sbjct: 3 FTGAFTAIVTPFR-NGRVDEERFRELIEWQIEQGINGLVPCGTTGESATLSHDEHRDVIR 61 Query: 67 FAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRYFEQ 126 ++ V R+PVL G G N RE I+L++ A++AGADG ++I PYY K ++ L +F+ Sbjct: 62 ICVEQVKGRIPVLAGAGSNNTREAIDLTRFAKEAGADGALLITPYYNKPTQEGLYLHFKA 121 Query: 127 VADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTVKGA 186 +A V++P ++YN P+ TG ++ P + L ++G+K ++ +L + ++ Sbjct: 122 IASEVSMPFIVYNVPSRTGTNICPETLARLNRDIPEVVGVK---EATGNLIQVSEILEYC 178 Query: 187 HPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLL 246 F VL G D + L +GG G IS + N P ++ +A++ GD+A A H L Sbjct: 179 GTDFQVLSGDDFTVLPLLSVGGCGVISVTSNVVPAKMSDMCRAFKAGDLATARRLHFELS 238 Query: 247 QIPQMYQLDTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLL 296 I + L+T + V K A+ L GR + + P PL + +++L+ +L Sbjct: 239 PINRAMFLETNPIPV-KTALALMGR-IDLEMRLPLCPLQQVNQSRLRDIL 286 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: 204 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: 302 Length of database: 292 Length adjustment: 26 Effective length of query: 276 Effective length of database: 266 Effective search space: 73416 Effective search space used: 73416 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 Apr 09 2024. 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