Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate BPHYT_RS12985 BPHYT_RS12985 amino acid acetyltransferase
Query= curated2:Q188A2 (286 letters) >FitnessBrowser__BFirm:BPHYT_RS12985 Length = 462 Score = 142 bits (358), Expect = 1e-38 Identities = 88/279 (31%), Positives = 146/279 (52%), Gaps = 11/279 (3%) Query: 15 PYIEKHQGKTIVVKYGGSAMKKDGLKESVMEDLVLMSYVGINIVLVHGGGAEINKMLAKV 74 PYI + KT VV +GG + + GL +++ D+ L+ +GI IVLVHG ++ + ++ Sbjct: 39 PYIHAFRNKTFVVGFGGEVVHQ-GLLNALVSDIALLQAMGIQIVLVHGSRPQVEEQMSLH 97 Query: 75 DIESKFVNGLRYTDEETMEIVKMVLAGKVNKDLVNKI-----HTKGGKAVGLCGIDNNMI 129 +ES+F +G+R TD +E K AG+V D+ I +T A + + N + Sbjct: 98 GVESEFSHGMRITDARALESAKEA-AGEVRLDIEAAISQGLPNTPMAHA-HISVVSGNFV 155 Query: 130 LCDPY---KNYELGFVGEIKKVNVELIESCLKSGYISVIATIGVGDDGETYNINGDTAAS 186 P + G ++K++ + I L S + +++ +G GE +N+ + AS Sbjct: 156 TARPVGILDGVDFAHTGVVRKIDADSIRHSLASRKLVLLSPLGFSPTGEAFNLAMEDVAS 215 Query: 187 AIAKELNADKLILLTDVPGLLREPDEEKSLITEVILEDVDKLFEEGIITGGMIPKIEGCV 246 A A L ADK++ LT+ PGL+ +E L+ E+ L+D KL E G +TG ++ + Sbjct: 216 AAAIALRADKIVFLTETPGLMEAGEEGPVLVRELSLDDAYKLHESGEVTGDAGFYLKHSI 275 Query: 247 DALNNGVNRVHILDGRVPHSIITELFTDSGIGTLIRKEN 285 A GV R HI+ + S++ ELF G+GT+I EN Sbjct: 276 RACRGGVARAHIIPYALDGSLLLELFLHDGVGTMISYEN 314 Lambda K H 0.316 0.139 0.384 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: 294 Number of extensions: 11 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: 286 Length of database: 462 Length adjustment: 29 Effective length of query: 257 Effective length of database: 433 Effective search space: 111281 Effective search space used: 111281 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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