Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Pf1N1B4_2243 N-acetylglutamate synthase (EC 2.3.1.1)
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2243 Length = 432 Score = 114 bits (285), Expect = 4e-30 Identities = 89/293 (30%), Positives = 145/293 (49%), Gaps = 24/293 (8%) Query: 15 LSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQIGD 74 L A PYI T V+ G+ +E D+VL+ ++G+ V+VHG PQI Sbjct: 8 LRHASPYINAHRDCTFVVMLPGDGVEHPNF-GNIVHDLVLLHSLGVRLVLVHGSRPQIET 66 Query: 75 LLKRLSIESHFIDGMRVTDAATMDVVEMVLG-------GQVNKDIVNLINRHGGSAIGLT 127 L + H+ GMR+TDAAT++ V +G +++ D+ + + GS + + Sbjct: 67 RLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMAS--SPMQGSRLRVA 124 Query: 128 GKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGV 187 L+ A+ + V E +D H GEV V+ +N L+ I +++P+G Sbjct: 125 S--GNLVTARPIGVL---------EGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGY 173 Query: 188 GSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQV-NELIADG 246 GE +N+ + VA + A L A+KL+L GL+D+ G+++ L +QV L G Sbjct: 174 SPTGEIFNLACEDVATRAAIDLGADKLLLFGADLGLIDENGRLVRELRPQQVPAHLQRLG 233 Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRK 299 + Y L + A EA +GGV +HI+ A+L E+FT G GTL++ + Sbjct: 234 SNYQAEL--LDAAAEACRGGVARSHIVSYAEDGALLTELFTRDGGGTLVAQEQ 284 Lambda K H 0.318 0.138 0.381 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: 280 Number of extensions: 13 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: 301 Length of database: 432 Length adjustment: 29 Effective length of query: 272 Effective length of database: 403 Effective search space: 109616 Effective search space used: 109616 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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