Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate AO353_09240 AO353_09240 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__pseudo3_N2E3:AO353_09240 Length = 301 Score = 117 bits (293), Expect = 3e-31 Identities = 86/262 (32%), Positives = 136/262 (51%), Gaps = 22/262 (8%) Query: 2 IVVKAGGRTLLNNMDEIVKSISR---LEKAV-----FVHGGGDLVDEWERKMGMEPQFKV 53 +V+K GG + +E+ +R L KAV VHGGG + + +++ +E F Sbjct: 30 LVIKYGGNAM--ESEELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLSIESHF-- 85 Query: 54 SASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKV 113 G+ R TD + ++V VLGG +NK IV +G A+GLTG D + R KK+ Sbjct: 86 -IDGM--RVTDAQTMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDAELI---RAKKL 139 Query: 114 IVQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGD 173 V + E I G G++ + TDL+ LV+ +PV+API + GE N+N D Sbjct: 140 TVTRQTPEMTQPEIIDIGQVGEVVGINTDLLNLLVKGDFIPVIAPIGVGANGESYNINAD 199 Query: 174 QMAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKIIMA 230 +A ++A+AL AE L+LLT++ G++ G V+ + + + +E+ + GM KI A Sbjct: 200 LVAGKVAEALKAEKLMLLTNIAGLMDKSGTVLTGLSTQQVDELIADGTIYGGMLPKIRCA 259 Query: 231 GRVASGGT-KVVICDGTVPDPL 251 GG +I DG VP+ + Sbjct: 260 LEAVQGGVGSSLIIDGRVPNAI 281 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: 261 Number of extensions: 14 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: 301 Length adjustment: 26 Effective length of query: 238 Effective length of database: 275 Effective search space: 65450 Effective search space used: 65450 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