Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8)
Query= curated2:Q8ZU99 (261 letters) >FitnessBrowser__Korea:Ga0059261_2530 Length = 299 Score = 107 bits (268), Expect = 2e-28 Identities = 79/246 (32%), Positives = 126/246 (51%), Gaps = 16/246 (6%) Query: 3 VVKIGGSVV-----CKDASKVIQNLPKYADRAVVIHGGGCLVNELLKRMGIEPKFLTHPG 57 VVK GG + +D ++ + L VV+HGGG + ++LKR+G+E +F+ G Sbjct: 33 VVKYGGHAMGDPELARDFAEDVVLLKAVGINPVVVHGGGPQIGQMLKRLGVESEFV---G 89 Query: 58 GLVSRYTDWETLKVFVMAM-GWINKYIVASLHGLGVQALGLTGADLGVVVAKRKERVLVI 116 GL R TD ET ++ M + G INK IV+ + G +A+G++G D G+V A++ R Sbjct: 90 GL--RVTDAETARIAEMVLAGSINKEIVSWISAAGGKAIGISGKDSGLVTARKVTRSEAD 147 Query: 117 DERGRQRVVDGGYVGKIAEIRVDKLTPPP----LKVLAPVAVSEKGELLNIDGDQLAFDV 172 +G +R VD G+VG+ + LT + V+AP+A+ G NI+ D +A + Sbjct: 148 PLQGIERHVDLGFVGEPVAVDASVLTTLSAQGFIPVIAPIALGADGHTYNINADTMAGAI 207 Query: 173 AREAKAERLILLSDVEGLILGGK-VVPRLTPEEAEKLVKSEEVRGGMKRKLLMASEAAKL 231 A A R LL+DV G++ K ++ L P L + GGM K+ A Sbjct: 208 AGALGASRFFLLTDVPGVLSKDKQLLSDLDPGRIAALKADGTISGGMIPKVETCVAAVDA 267 Query: 232 GIEVVI 237 G++ + Sbjct: 268 GVDAAV 273 Lambda K H 0.319 0.139 0.393 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: 15 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: 261 Length of database: 299 Length adjustment: 26 Effective length of query: 235 Effective length of database: 273 Effective search space: 64155 Effective search space used: 64155 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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