Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_052667394.1 NITAL_RS16985 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::P9WPZ3 (404 letters) >NCBI__GCF_000969705.1:WP_052667394.1 Length = 407 Score = 277 bits (708), Expect = 5e-79 Identities = 169/398 (42%), Positives = 231/398 (58%), Gaps = 19/398 (4%) Query: 15 GVTAPAGFRAAGVAAGIKASGALDLALVFNEGPDYAAAGVFTRNQVKAAPVLWTQQVLTT 74 GVTA GFRA G+A G+K SG DLAL+ + A V T NQVKA T+Q Sbjct: 21 GVTAAPGFRAGGLATGVKPSGKPDLALLVADEVASVAV-VTTTNQVKAPSCTLTEQHAAD 79 Query: 75 GRLRAVILNSGGANACTGPAGFADTHATAEAVAAALSDWGTETGAIEVAVCSTGLIGDRL 134 GR + V++NSG AN CT P G AE AAA T T + +V V STG+IG L Sbjct: 80 GRAQVVVVNSGNANVCT-PDGDEHNRRIAEGAAAA-----TGTASTDVLVMSTGVIGVPL 133 Query: 135 PMDKLLAGVAHVVHEMHGGLV--GGDEAAHAIMTTDNVPKQVALHHHD---NWTVGGMAK 189 P++++ A + ++ G+ GG AA A++TTD KQVA D + T+GGMAK Sbjct: 134 PIERIEAALP----DLAAGVTVDGGATAAEAMLTTDTRTKQVAYRVSDEQGSCTIGGMAK 189 Query: 190 GAGMLAPSLATMLCVLTTDAAAEPAALERALRRAAAATFDRLDIDGSCSTNDTVLLLSSG 249 G GM+ P++AT+L VLTTDA + L L R +F+R+ +DG ST+DT +L+SG Sbjct: 190 GVGMIEPAMATLLVVLTTDAPVQHRILGNLLTRGVDTSFNRVSVDGDRSTSDTAAILASG 249 Query: 250 ASEIPPAQADLDEAVLRVCDDLCAQLQADAEGVTKRVTVTVTGAATEDDALVAARQIARD 309 + PP+ A L AV VC DL Q+ AD EG T+ VTV GAA+E+ A AR +A Sbjct: 250 LARTPPSAATLGRAVQAVCADLAEQVVADGEGATRVAAVTVHGAASEEAAERMARAVATS 309 Query: 310 SLVKTALFGSDPNWGRVLAAVGMAPITLDPDRISVSFNGAAVCVHGVGA---PGAREVDL 366 LV+ A+ G+DPNWGR++ A+G A + LDP R+S++ G VC GV G + Sbjct: 310 LLVRAAIHGADPNWGRIIMALGNAGVDLDPRRVSITCAGITVCRFGVATVFDRGQAAAAM 369 Query: 367 SDADIDITVDLGVGDGQARIRTTDLSHAYVEENSAYSS 404 S +++I +D+G G A + T DL+ YV NS Y++ Sbjct: 370 SRPEVEIGIDVGAGRSSATVLTCDLTPEYVRFNSQYTT 407 Lambda K H 0.317 0.131 0.380 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: 457 Number of extensions: 23 Number of successful extensions: 6 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: 404 Length of database: 407 Length adjustment: 31 Effective length of query: 373 Effective length of database: 376 Effective search space: 140248 Effective search space used: 140248 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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