Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_013553115.1 NITSA_RS00770 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000186245.1:WP_013553115.1 Length = 397 Score = 249 bits (636), Expect = 1e-70 Identities = 167/407 (41%), Positives = 235/407 (57%), Gaps = 24/407 (5%) Query: 4 IDGGVTAPKGFKANGYKEG------KFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSREL 57 + G+ +GF +G G + +A I S++ A T+TTN+ A P+ + Sbjct: 7 LKNGLANVQGFYCDGINCGLRPDPSQGDLAFIRSDRLCDIAATYTTNRFQAAPIRHALRH 66 Query: 58 IKNRDKFRAIVANSGNANCFTKD-GMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMD 116 R + I+AN+ NAN T + G+ D + + L A +++STGVIG ++ Sbjct: 67 YGKRFQGNFILANAKNANAMTGEAGIADIETI--LAALPAEAEAQNPVMSSTGVIGYRLP 124 Query: 117 MNIIKDRINKVYNLIKEGNSSINAAKAIMTTDTKPKEIAVEFEV-NGKTVRVGGIAKGAG 175 ++ I ++K+ K +++ A+AIMTTD+ KE+ E E+ N ++ R+ IAKGAG Sbjct: 125 VDKIVKGLDKLDWHAKNSDAT---ARAIMTTDSFKKELCFEVELENDQSFRIAAIAKGAG 181 Query: 176 MIAPNMLHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGL 235 MI P M ATMLCFI TD + + + +L++ V +FN ISVDGDTSTNDTV+++ANG Sbjct: 182 MINPAM--ATMLCFIATDAAVPADEMEELLEEAVSLSFNRISVDGDTSTNDTVYLMANGA 239 Query: 236 SGVNYEECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVN 295 SG Y+ E F AL + ELA +I+KDGEGA K + V GA +E+A A+ + N Sbjct: 240 SGA-YDR--EAFAEALRKITFELAMLILKDGEGANKVVAFEVTGAANDEEAAIAATNLSN 296 Query: 296 SLLVKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTE 355 SLLVKTA+FG DPNWGRI + +G SG + E + + Y D + KD L E E Sbjct: 297 SLLVKTALFGEDPNWGRIASTIGASGIACDEEKLSIY---YDDLLIYNKDNRELDPEREE 353 Query: 356 ELKKAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 KA +IMK D +I DL MG YGCDLSYEYV+INAEY T Sbjct: 354 ---KAYKIMKKDSFRIRCDLGMGTGSFTSYGCDLSYEYVKINAEYRT 397 Lambda K H 0.315 0.134 0.371 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: 421 Number of extensions: 20 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: 402 Length of database: 397 Length adjustment: 31 Effective length of query: 371 Effective length of database: 366 Effective search space: 135786 Effective search space used: 135786 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: 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