Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate 3606894 Dshi_0324 acetylglutamate kinase (RefSeq)
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__Dino:3606894 Length = 287 Score = 110 bits (275), Expect = 3e-29 Identities = 86/266 (32%), Positives = 123/266 (46%), Gaps = 33/266 (12%) Query: 1 MIVVKAGGRTL--LNNMDEIVKSISRLEKA----VFVHGGGDLVDEWERKMGMEPQFKVS 54 ++V+K GG + M + I + + V VHGGG +++ K+ + F Sbjct: 31 IVVIKFGGHAMGDAEAMASFARDIVLMRQVGVNPVIVHGGGPMINAMLAKLDINSDFVNG 90 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 R TD +EV VL GL+NK+IV + G A+GL+G D ++ + + Sbjct: 91 K-----RVTDAATIEVVEMVLSGLVNKRIVQAINREGGRAIGLSGKDANLIVCDPADPAL 145 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 G+ G+ EV D + LV ++PV+API EGE N+NGD Sbjct: 146 ----------------GFVGEPVEVTPDTLLQLVRSEIIPVIAPIGTGREGETFNINGDT 189 Query: 175 MAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEV--AKKVGPGMNIKIIMAG 231 A +A AL A+ L+LLTDV GV GKVV E+ EE+ A + GM K Sbjct: 190 AAGAIAAALKADRLLLLTDVSGVKDAQGKVVTELTVENIEEMTAAGVIAGGMIPKTETCV 249 Query: 232 RVASGGTK-VVICDGTVPDPLKCLEE 256 GG + VI DG P+ CL E Sbjct: 250 TAIRGGVRAAVILDGRAPN--ACLLE 273 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: 221 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: 287 Length adjustment: 25 Effective length of query: 239 Effective length of database: 262 Effective search space: 62618 Effective search space used: 62618 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