Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_013009801.1 DACET_RS02315 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000025725.1:WP_013009801.1 Length = 399 Score = 305 bits (782), Expect = 1e-87 Identities = 184/404 (45%), Positives = 248/404 (61%), Gaps = 20/404 (4%) Query: 7 GVTAPKGFKAN-------GYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIK 59 GV P G+ A+ G K+GK + ++ SE A FT N + A P+ + + ++ Sbjct: 8 GVCTPLGYLASSVAADIKGNKKGKKDLTLLYSEVPFTLAAVFTKNTIKAAPLKHAIKALE 67 Query: 60 NRDKFRAIVANSGNANCFT-KDGMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMDMN 118 +F AIV NSGNAN T K G+E + + + E VL+ STG IG KM + Sbjct: 68 TNREFSAIVVNSGNANASTGKQGLEAVDTIVKAFEDELGTGEGSVLMGSTGTIGVKMPVE 127 Query: 119 IIKDRINKVYNLIKEGNSSINAAKAIMTTDTKPKEIAVEFEVNGKTVRVGGIAKGAGMIA 178 + + ++ + + + NS AA AIMTTDT PKEI V E V G KGAGMIA Sbjct: 128 KVTSSVKELVDELDDANSHDFAA-AIMTTDTVPKEIGVLVETPNGAYVVAGTTKGAGMIA 186 Query: 179 PNMLHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGV 238 P+M ATMLC+ITTD I ++L N+L V ++FN+I++D D STNDTVF++ANG+SG+ Sbjct: 187 PHM--ATMLCYITTDALIGADNLQNVLNNAVGESFNSITIDNDMSTNDTVFLMANGMSGI 244 Query: 239 NYEECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSLL 298 + ++F+ A+ +V ELAKMIVKDGEGATKF+ + VK A++E DA K + AI NS L Sbjct: 245 IPDI--DQFQEAVNHVALELAKMIVKDGEGATKFVTIKVKNAQSEADAKKCAFAIANSPL 302 Query: 299 VKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTEELK 358 VKT +G DPNWGR++A VG SG E +D+ D++ VKDGI + DE EE Sbjct: 303 VKTMFYGEDPNWGRLIATVGASGVAAVEEKIDICF----DDLAYVKDGI-IIDEKLEE-- 355 Query: 359 KAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 KA +IMK+DEI+I +DL MG F Y CD S EYV INA+Y T Sbjct: 356 KAAKIMKNDEIEITIDLNMGTFGKTVYTCDFSKEYVSINADYRT 399 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: 474 Number of extensions: 27 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: 399 Length adjustment: 31 Effective length of query: 371 Effective length of database: 368 Effective search space: 136528 Effective search space used: 136528 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 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