Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate BWI76_RS23220 BWI76_RS23220 amino-acid N-acetyltransferase
Query= BRENDA::Q9X2A4 (282 letters) >FitnessBrowser__Koxy:BWI76_RS23220 Length = 443 Score = 139 bits (350), Expect = 1e-37 Identities = 92/286 (32%), Positives = 150/286 (52%), Gaps = 11/286 (3%) Query: 2 RIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHG 61 R + V ++PYI GKTFVI GG A++ +N + + DI LL GI+ ++V+G Sbjct: 6 RTELVEGFRHSVPYINAHRGKTFVIMLGGEAIEHDNFS-SIVNDIGLLHSLGIRLVVVYG 64 Query: 62 GGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEM---VLVGKINKEIVMNLNLHGGRAV 118 P I + + EPV+ RVTD KT+E+V+ +L +I + M+LN + Sbjct: 65 ARPQIDANLAEHRHEPVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTPLQGA 124 Query: 119 GICGKDSKLIVAEKETKHGDIGYV--GKVKKVNPEILHALIENDYIPVIAPVGIGEDGHS 176 I I+A+ + Y G++++++ E +H ++N I ++ PV + G S Sbjct: 125 HINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEEAIHRQLDNGAIVLMGPVAVSVTGES 184 Query: 177 YNINADTAAAEIAKSLMAEKLILLTDVDGVL-KDGKLISTLTPDEA----EELIRDGTVT 231 +N+ ++ A ++A L AEK+I GV +DG+++ L P+EA EE+ D + Sbjct: 185 FNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQDGEIVPELFPNEAQARVEEIEADEDYS 244 Query: 232 GGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMI 277 G + + AV A R GV H+I+ +L E+FSR GIGT I Sbjct: 245 SGTVRFLRGAVKACRSGVRRCHLISYQENGTLLQELFSRDGIGTQI 290 Lambda K H 0.318 0.140 0.393 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: 284 Number of extensions: 21 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: 282 Length of database: 443 Length adjustment: 29 Effective length of query: 253 Effective length of database: 414 Effective search space: 104742 Effective search space used: 104742 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: 49 (23.5 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