Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate CCNA_00285 CCNA_00285 acetylglutamate kinase
Query= curated2:A0RWW1 (266 letters) >FitnessBrowser__Caulo:CCNA_00285 Length = 304 Score = 112 bits (280), Expect = 9e-30 Identities = 84/276 (30%), Positives = 137/276 (49%), Gaps = 30/276 (10%) Query: 2 ITIKIGGSIVDSLHPSAIPDIKKAAAGGVVL----------VHGGGKEVTKVCEQLGKEP 51 + IK GG H D+ K A VL VHGGG +++++ ++ G + Sbjct: 31 VVIKYGG------HAMGQEDVAKVFAADAVLLKLLGVHPVVVHGGGPQISRMLDKAGVKS 84 Query: 52 RFVTSPGNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNA----VGLSGIDGGLI 107 FV R TD+ T E+ MV+SG INK I + G A VGLSG D LI Sbjct: 85 TFVDG-----LRVTDEATMEVAEMVLSGAINKEIANWITLAGAEADVRGVGLSGKDARLI 139 Query: 108 RAERKSRLVIVNERGRKQAIEGGYTGRITSVNSELLETLLGK--GIVPVVSPIAMGNEYE 165 AE+ +R + +QA++ G+ G T V+ +L+E LL +PVV+PI + + + Sbjct: 140 TAEKVTRTKKDPDSNIEQAVDLGFVGEPTKVDPQLIEALLTSEHDYIPVVAPIGVSPDGD 199 Query: 166 LLNVDGDRAAANIAGATKSERILFVTDVDGLM-MDEKLVSRLSAAEAEEI--RPKIGPGM 222 N++ D A +AGA K++R+L +TD+ G++ + +L+ ++ +A + GM Sbjct: 200 TFNINADTVAGALAGALKAKRMLMLTDIKGVLDGNGELIREMTIEQARALIDTGVATGGM 259 Query: 223 EKKVLAATEALKMGVREAIIARGSRENPVSAAIAHE 258 K+ A A++ GV +I G R + + + E Sbjct: 260 IPKLENAIHAIESGVEAVVILDGRRPHAMLVELFSE 295 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: 180 Number of extensions: 5 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: 266 Length of database: 304 Length adjustment: 26 Effective length of query: 240 Effective length of database: 278 Effective search space: 66720 Effective search space used: 66720 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