Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_084703913.1 BS73_RS08935 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::P9WPZ3 (404 letters) >NCBI__GCF_000744815.1:WP_084703913.1 Length = 404 Score = 407 bits (1047), Expect = e-118 Identities = 227/390 (58%), Positives = 263/390 (67%), Gaps = 8/390 (2%) Query: 15 GVTAPAGFRAAGVAAGIKASGALDLALVFNEGPDYAAAGVFTRNQVKAAPVLWTQQVLTT 74 GVTA GFRAAGVAAG+K SGA DLALV N+GP +AAAGVFT N+V+AAPV W+QQVL T Sbjct: 23 GVTAARGFRAAGVAAGLKESGAPDLALVVNDGPLHAAAGVFTSNRVQAAPVKWSQQVLKT 82 Query: 75 GRLRAVILNSGGANACTGPAGFADTHATAEAVAAALSDWGTETGAIEVAVCSTGLIGDRL 134 G L AV+LNSGGANACTG GF DTHATAE A AL GA EVAVCSTGLIG RL Sbjct: 83 GELAAVVLNSGGANACTGAPGFQDTHATAEKTAEALG-----VGAAEVAVCSTGLIGVRL 137 Query: 135 PMDKLLAGVAHVVHEMHGGLVGGDEAAHAIMTTDNVPKQVALHHHDNWTVGGMAKGAGML 194 PMD+L GV V E+ GGD AA AI TTD V K A+ + WTVGGMAKGAGML Sbjct: 138 PMDRLQPGVDAAVAELSED--GGDAAAIAIKTTDTVQK-TAVVRGEGWTVGGMAKGAGML 194 Query: 195 APSLATMLCVLTTDAAAEPAALERALRRAAAATFDRLDIDGSCSTNDTVLLLSSGASEIP 254 AP LATML VLTTDA E L+ LR A TFDR+D DG STNDTVLL++SGAS + Sbjct: 195 APGLATMLVVLTTDACVEGPELDGFLRAATRTTFDRVDSDGCMSTNDTVLLMASGASGVV 254 Query: 255 PAQADLDEAVLRVCDDLCAQLQADAEGVTKRVTVTVTGAATEDDALVAARQIARDSLVKT 314 P +AV VC DL QL DAEG +K + + + AATED+A+ AR IAR++L+K Sbjct: 255 PDTGSFADAVTAVCADLARQLIGDAEGASKDIRIDIVNAATEDEAVTVARSIARNNLLKC 314 Query: 315 ALFGSDPNWGRVLAAVGMAPITLDPDRISVSFNGAAVCVHGVGAPGAREVDLSDADIDIT 374 A+ G DPNWGRVL+A+G DPD + V+ NG VC G VD+S ++ IT Sbjct: 315 AIHGEDPNWGRVLSAIGTTDAAFDPDALDVAINGVWVCKGGSVGEDRELVDMSGREVVIT 374 Query: 375 VDLGVGDGQARIRTTDLSHAYVEENSAYSS 404 DL G A + T DL+ YV ENSAYSS Sbjct: 375 ADLHAGTAGATVWTNDLTADYVHENSAYSS 404 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: 521 Number of extensions: 22 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: 404 Length of database: 404 Length adjustment: 31 Effective length of query: 373 Effective length of database: 373 Effective search space: 139129 Effective search space used: 139129 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 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