Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_011306983.1 MBAR_RS10640 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000195895.1:WP_011306983.1 Length = 395 Score = 350 bits (897), Expect = e-101 Identities = 198/405 (48%), Positives = 266/405 (65%), Gaps = 13/405 (3%) Query: 1 MRVIDGGVTAPKGFKANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKN 60 M+ I+GG+ A KG ANG K GK G+ +I+++ A AG FT NKV A PV LS+ +I+ Sbjct: 1 MKEIEGGICAVKGVSANGIKAGKLGLTVILAKGPA--AGVFTKNKVTAAPVTLSKGVIET 58 Query: 61 RDKFRAIVANSGNANCFT-KDGMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMDMNI 119 + ++ NSGNAN FT DG DA EM ++A+ ++ D V VASTGVIGR++D+++ Sbjct: 59 HHRLSGLIVNSGNANAFTGDDGFLDAMEMASVLAQKLDLEADTVAVASTGVIGRRLDVSL 118 Query: 120 IKDRINKVYN-LIKEGNSSINAAKAIMTTDTKPKEIAVEFEVNGKTVRVGGIAKGAGMIA 178 I + + +V N L S AAKA+MTTD KE+A+E + +R+G IAKG+GMI Sbjct: 119 ITEHLPEVLNGLGSSPECSREAAKAMMTTDRVVKEVAIEMDCG---IRIGAIAKGSGMIE 175 Query: 179 PNMLHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGV 238 PNM TMLCF TD ++ + L L+ VDKTFN + VDGDTSTND V + + SGV Sbjct: 176 PNM--GTMLCFAYTDAKVPADVLDAALRIAVDKTFNMVVVDGDTSTNDMVLLTSTCKSGV 233 Query: 239 N-YEECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSL 297 +C ++FE L+YV ELAK + KDGEGATK +E V GAKT EDA A+KAIV S Sbjct: 234 KPCMDCLDDFEEGLIYVFTELAKKMAKDGEGATKLIEARVVGAKTHEDAKLAAKAIVRSP 293 Query: 298 LVKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTEEL 357 LVK+A+FG DPNWGR+VAA GYSG++ E + + S +EV LV G + E L Sbjct: 294 LVKSAIFGKDPNWGRVVAAAGYSGSELEQERLALSFSGGGEEVELVNSGEISSSSDLELL 353 Query: 358 KKAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 KK IM ++EI I +DL +G+ + + +GCDL+Y+YVRIN+EYTT Sbjct: 354 KK---IMANEEIVITLDLNLGKEQAIAWGCDLTYDYVRINSEYTT 395 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: 433 Number of extensions: 26 Number of successful extensions: 8 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: 395 Length adjustment: 31 Effective length of query: 371 Effective length of database: 364 Effective search space: 135044 Effective search space used: 135044 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