Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_013683457.1 ARCVE_RS03780 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000194625.1:WP_013683457.1 Length = 388 Score = 306 bits (784), Expect = 7e-88 Identities = 182/402 (45%), Positives = 253/402 (62%), Gaps = 22/402 (5%) Query: 4 IDGGVTAPKGFKANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKNRDK 63 ID G+T G G KEGK+G+ I+ + AG FT NK+ A PV+++ E IK + Sbjct: 6 IDAGITDVDGVYCCGIKEGKYGLGIVKCKGKV--AGVFTLNKLKAAPVIVTMEHIKGGE- 62 Query: 64 FRAIVANSGNANCFT-KDGMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMDMNIIKD 122 I+ NSGNAN FT + G+++AK M ++AE ++ ++ VASTGVIG ++DM I+ Sbjct: 63 IEGIIVNSGNANAFTGEQGIKNAKRMAEMLAERLGVDASKIAVASTGVIGVQLDMGWIET 122 Query: 123 RINKVYNLIKEGNSSINA-AKAIMTTDTKPKEIAVEFEVNGKTVRVGGIAKGAGMIAPNM 181 ++ + + ++ AKAI+TTD KE AV+ V + G+AKGAGMIAPNM Sbjct: 123 TFESIFPSLNSSRDAAHSFAKAIVTTDAFTKEYAVK----AGDVIIAGVAKGAGMIAPNM 178 Query: 182 LHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGVNYE 241 ATML FI TD + + L +L+ VD +FN VDGDTSTND V ++A G V+ + Sbjct: 179 --ATMLAFIFTDADFESHELQEMLKNAVDVSFNVTVVDGDTSTNDMVLLVATGKKKVDRD 236 Query: 242 ECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSLLVKT 301 F+ L VC LAKMI DGEGA+K +EV V+GAK++EDA KA++++V+S LVKT Sbjct: 237 V----FQQGLNEVCINLAKMIAMDGEGASKLIEVYVRGAKSKEDAFKAARSVVSSTLVKT 292 Query: 302 AVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTEELKKAE 361 AVFG DPNWGRI+AA+GYSGAD + + + ++L V L+ G E +KA+ Sbjct: 293 AVFGNDPNWGRIIAALGYSGADVD-DCITLVLEGEAGSVKLLDRG-----EIMNTRQKAK 346 Query: 362 EIMK-SDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 EIM+ S EIK V+DL G E GCDL+++YV +NA+YTT Sbjct: 347 EIMRNSKEIKFVIDLHKGSEEGYAIGCDLTHDYVNLNAKYTT 388 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: 405 Number of extensions: 21 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: 388 Length adjustment: 31 Effective length of query: 371 Effective length of database: 357 Effective search space: 132447 Effective search space used: 132447 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