Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate BWI76_RS00850 BWI76_RS00850 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__Koxy:BWI76_RS00850 Length = 257 Score = 91.7 bits (226), Expect = 1e-23 Identities = 74/238 (31%), Positives = 124/238 (52%), Gaps = 36/238 (15%) Query: 2 IVVKAGGRTLLNNMDEIVKSISRL--------EKAVFVHGGGDLVDEWERKMGMEPQFKV 53 +++K GG LL++ + + + + L + VHGGG +VDE +++ + K Sbjct: 4 LIIKLGG-VLLDSEEALERLFTALVNYRESHQRPLIIVHGGGCVVDELMKQLNLPVNKK- 61 Query: 54 SASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKV 113 +G+ R T ++++ L G NK ++A +G AVGL DG SV K Sbjct: 62 --NGL--RVTPADQIDIITGALAGTANKTLLAWAKKHGLAAVGLFLGDGDSV-----KVT 112 Query: 114 IVQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGD 173 + E++G + G + LI L+ G +PVV+ I ++ EGEL+NVN D Sbjct: 113 QLDEELG-----------HVGFAQPGSPALINTLLAGGYMPVVSSIGVTDEGELMNVNAD 161 Query: 174 QMAAELAKALSAEYLVLLTDVPGVLMDGK--VVPEIKSSEAEEVAKK--VGPGMNIKI 227 Q A LA L A+ L+LL+DV G+L DGK + E+ + +AE++ ++ + GM +K+ Sbjct: 162 QAATALAATLGAD-LILLSDVSGIL-DGKGQRIAEMTAEKAEQLIEQGIITDGMIVKV 217 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: 192 Number of extensions: 17 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: 257 Length adjustment: 25 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 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 Aug 03 2021. The underlying query database was built on Aug 03 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