Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate Echvi_3850 Echvi_3850 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__Cola:Echvi_3850 Length = 266 Score = 110 bits (274), Expect = 4e-29 Identities = 75/225 (33%), Positives = 123/225 (54%), Gaps = 28/225 (12%) Query: 3 VVKAGGRTLLN--NMDEIVKSISRLE-KAVFVHGGGDLVDEWERKMGMEPQFKVSASGIK 59 +VK GG + + + E + +RLE K + VHGGG + ++ +++G+EP+ Sbjct: 5 IVKIGGNVIDDPAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDGR---- 60 Query: 60 FRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVIVQEKV 119 R TDE L+V V G++NKKIVA + A+G TGADG ++I K+ V Sbjct: 61 -RITDEATLDVVTMVYAGMINKKIVAKLQQLEQNAMGFTGADG-NLIRSAKRPV------ 112 Query: 120 GERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQMAAEL 179 + I G+ G +KEV T+L++ L+E+ +VPV + I +G LLN N D +A+E+ Sbjct: 113 ------KDIDYGFVGDVKEVDTELMEVLLEKDVVPVFSAITHDRKGNLLNTNADTIASEI 166 Query: 180 AKALSAEYLVLL---TDVPGVLM----DGKVVPEIKSSEAEEVAK 217 A A++ ++ V L + GVL+ D +VP+I +E+ + Sbjct: 167 ATAMAVKHTVRLYFCFNKAGVLIDEHNDDSLVPKINEDIYDELKR 211 Lambda K H 0.316 0.136 0.379 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: 180 Number of extensions: 9 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: 264 Length of database: 266 Length adjustment: 25 Effective length of query: 239 Effective length of database: 241 Effective search space: 57599 Effective search space used: 57599 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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