Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate RR42_RS13035 RR42_RS13035 amino acid acetyltransferase
Query= curated2:Q67KD3 (293 letters) >FitnessBrowser__Cup4G11:RR42_RS13035 Length = 478 Score = 146 bits (368), Expect = 1e-39 Identities = 93/280 (33%), Positives = 150/280 (53%), Gaps = 6/280 (2%) Query: 12 LAEALPYIREFSGKTVVIKYGGAAMAAADLKAAVMQDIALMKYVGMHPIVVHGGGPEVSE 71 L PYI F GKT VI +GG + A++ A++ D+AL+ +GM ++VHG P+V E Sbjct: 53 LRAVAPYIHAFRGKTFVIAFGGE-LVKANILDALVNDVALLHAMGMQIVLVHGSRPQVEE 111 Query: 72 LARRMGIEPQFVDGLRVTDAATMEIAQMVLVGKTNREIVTHLCAQGVKAVGLSGQDAGLI 131 +E QF DG+RVTD A +E A+ G+ +I +QG+ ++G +I Sbjct: 112 QLALRHVESQFADGVRVTDNAALECAKEA-AGELRLDIEAAF-SQGLPNTPMAGAQLSVI 169 Query: 132 RAARHLHRSRETGEMVDLGFVGDVAAVDTEVLTTLTTAGYVPVIAPIGVGPGGQPYNINA 191 R + VD G V +D E + + G + +++P+G P GQ +N++ Sbjct: 170 SGNFVTARPLGIVDGVDYQHTGLVRKIDGESVRMSLSHGKIVLLSPLGFSPTGQAFNLSM 229 Query: 192 DTVAGAIAAAMKAEKLVLLTDVEGVRADKDDPSSLLSRVTAQEVKSWIARGRLQGGMIPK 251 + VA A A A+KA+KLV +T+V GV +D L+ ++ + + L + Sbjct: 230 EDVASATAIALKADKLVFITEVPGV---QDPVGKLMPEMSLRTAIERLQNNHLPPDVSYY 286 Query: 252 LQCCLTALEGGVNRVHIIDGRVPHSLLLEIFTDEGVGTMV 291 L+ + AL+GGV R H+I ++ S+LLE+F +GVGTM+ Sbjct: 287 LEHLVKALKGGVPRAHLIPFQLDGSVLLELFLHDGVGTMI 326 Lambda K H 0.319 0.136 0.386 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: 269 Number of extensions: 13 Number of successful extensions: 4 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: 293 Length of database: 478 Length adjustment: 30 Effective length of query: 263 Effective length of database: 448 Effective search space: 117824 Effective search space used: 117824 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 (21.8 bits) S2: 50 (23.9 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