Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate YP_428422.1 Rru_A3341 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000013085.1:YP_428422.1 Length = 310 Score = 93.6 bits (231), Expect = 5e-24 Identities = 78/259 (30%), Positives = 126/259 (48%), Gaps = 22/259 (8%) Query: 2 IVVKAGGRTLLNNMDEIVKSISR----LEKA----VFVHGGGDLVDEWERKMGMEPQFKV 53 IV+K GG + + E+ K+ +R L++ V VHGGG + + ++ F Sbjct: 41 IVIKYGGHAMGD--PELAKTFARDVVLLKQVGMNPVVVHGGGPQIGRMLDTLRIQSTF-- 96 Query: 54 SASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKV 113 G+ R TD ++V VL G +NK IV G AVGL+G DG + A +K+ Sbjct: 97 -IDGL--RVTDAATVDVVEMVLAGSINKAIVTEINQAGGCAVGLSGKDGRLIQA---RKM 150 Query: 114 IVQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGD 173 + + E ++R + G+ G+ + ++ + ++PV+API + GE N+N D Sbjct: 151 VRKRHDPESNIERVLDLGFVGEPVVIDPHVLIQFRDSDIIPVIAPIGIGEAGETFNINAD 210 Query: 174 QMAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAKK--VGPGMNIKI-IM 229 A LA + A L++LTDV GVL D +++ E+ A + ++ + GM K+ Sbjct: 211 TAAGALAAQMKAARLLMLTDVKGVLDKDKQLIQELSVDRARLLKQEGTISGGMIPKVETC 270 Query: 230 AGRVASGGTKVVICDGTVP 248 V G VI DG VP Sbjct: 271 IDAVERGVEAAVIVDGRVP 289 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: 209 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: 264 Length of database: 310 Length adjustment: 26 Effective length of query: 238 Effective length of database: 284 Effective search space: 67592 Effective search space used: 67592 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 10 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