Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate GFF3738 Psest_3807 acetylglutamate kinase
Query= curated2:A0RWW1 (266 letters) >FitnessBrowser__psRCH2:GFF3738 Length = 300 Score = 143 bits (361), Expect = 4e-39 Identities = 89/257 (34%), Positives = 145/257 (56%), Gaps = 12/257 (4%) Query: 2 ITIKIGGSIVDS--LHPSAIPDIKKAAAGGV--VLVHGGGKEVTKVCEQLGKEPRFVTSP 57 + IK GG+ ++S L DI A G+ V+VHGGG ++ + ++L E F+ Sbjct: 30 LVIKYGGNAMESEELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLNIESHFIDG- 88 Query: 58 GNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNAVGLSGIDGGLIRAERKSRLVI 117 R TD +T ++ MV+ G++NK IV ++ QHG +A+GL+G D GLIRA++ Sbjct: 89 ----MRVTDSQTMDVVEMVLGGQVNKSIVSLINQHGGSAIGLTGKDAGLIRAKKLKATRQ 144 Query: 118 VNERGRKQAIEGGYTGRITSVNSELLETLLGKGIVPVVSPIAMGNEYELLNVDGDRAAAN 177 E + + I+ G+ G +T VN+ELLE L+ +PV++PI +G E N++ D A Sbjct: 145 TPEMTKPEIIDIGHVGEVTGVNAELLEMLVKGNFIPVIAPIGVGENGESYNINADLVAGK 204 Query: 178 IAGATKSERILFVTDVDGLMMDE-KLVSRLSAAEAEEI--RPKIGPGMEKKVLAATEALK 234 +A A K+E+++ +T++ GLM + +++ LS A+ + + I GM K+ A EA++ Sbjct: 205 VAEALKAEKLMLLTNIAGLMDKQGSVLTGLSTAQVDALIADGTIYGGMLPKIRCALEAVQ 264 Query: 235 MGVREAIIARGSRENPV 251 GV A I G N V Sbjct: 265 GGVNSAHIIDGRVPNAV 281 Lambda K H 0.316 0.135 0.370 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: 212 Number of extensions: 7 Number of successful extensions: 1 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: 266 Length of database: 300 Length adjustment: 26 Effective length of query: 240 Effective length of database: 274 Effective search space: 65760 Effective search space used: 65760 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: 41 (21.6 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