Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_012966700.1 FERP_RS11200 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000025505.1:WP_012966700.1 Length = 290 Score = 144 bits (364), Expect = 2e-39 Identities = 97/280 (34%), Positives = 159/280 (56%), Gaps = 26/280 (9%) Query: 1 MIVVKAGGRTLLNN--MDEIVKSISRLE----KAVFVHGGGDLVDEWERKMGMEPQFKVS 54 ++V+K GG ++N ++ V+ + L K + VHGGG + E ++G++P+F Sbjct: 21 VMVIKIGGHAMVNEKILESAVRDVILLYFVGIKPIVVHGGGPEISEKMERLGIKPKF--- 77 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 G+ R TDE+ +EV VL G +N KIV+ F G AVG++G DG V+A++KK Sbjct: 78 VDGL--RVTDEETIEVVQMVLDGKINSKIVSLFIKNGGKAVGMSGKDGLLVVAKKKK--- 132 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 V++K+G+ V+ + GY G+ + V +++K L++ G +PVV+P+A+ G + N+N D Sbjct: 133 VKKKIGDSEVELDL--GYVGETEIVNPEILKILIDNGFIPVVSPVAVDLNGNIYNMNADT 190 Query: 175 MAAELAKALSAEYLVLLTDVPGVLMD----GKVVPEIKSSEAEEVAKK--VGPGMNIKII 228 +A ++A AL A+ L++LTDVPG+L D V+ +I E EE+ KK + GM K Sbjct: 191 VAGDIAAALKAKKLIILTDVPGILRDVNDPNSVISKISLKELEEMLKKGELSGGMIPKAE 250 Query: 229 MAGRVASGGT-KVVICDGTVPDPLKC---LEERSGTWVVP 264 + GG + I +G+V + +E GT V P Sbjct: 251 AIIKALKGGVERGHIINGSVEHAILLELFTKEGIGTMVYP 290 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: 241 Number of extensions: 9 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: 290 Length adjustment: 25 Effective length of query: 239 Effective length of database: 265 Effective search space: 63335 Effective search space used: 63335 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