Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate Synpcc7942_1496 Synpcc7942_1496 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__SynE:Synpcc7942_1496 Length = 301 Score = 124 bits (311), Expect = 2e-33 Identities = 89/263 (33%), Positives = 136/263 (51%), Gaps = 33/263 (12%) Query: 2 IVVKAGGRTLLNN------MDEIVKSISRLEKAVFVHGGGDLVDEWERKMGMEPQFKVSA 55 +VVK GG + M +IV + V VHGGG ++ W ++G+EPQF Sbjct: 32 VVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGGPEINAWLGRVGIEPQFH--- 88 Query: 56 SGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVIV 115 +G+ R TD +EV VL G +NK IV+ + G AVG G DG V+A Sbjct: 89 NGL--RVTDADTMEVVEMVLVGRVNKDIVSRINTTGGRAVGFCGTDGRLVLARPHD---- 142 Query: 116 QEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQM 175 QE +G + G++ V +++I+ L+ERG +PV++ +A G+ N+N D + Sbjct: 143 QEGIG-----------FVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQSFNINADTV 191 Query: 176 AAELAKALSAEYLVLLTDVPGVLMDGK----VVPEIKSSEAEEVAKK--VGPGMNIKIIM 229 A E+A AL+AE L+LLTD G+L D K ++P + ++ E+ + VG GM K+ Sbjct: 192 AGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGGGMIPKVDC 251 Query: 230 AGRVASGGTKVV-ICDGTVPDPL 251 R + G + I DG +P L Sbjct: 252 CIRSLAQGVRAAHIIDGRIPHAL 274 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: 217 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: 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