Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_011973538.1 MAEO_RS04145 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000017185.1:WP_011973538.1 Length = 412 Score = 533 bits (1374), Expect = e-156 Identities = 268/405 (66%), Positives = 326/405 (80%), Gaps = 4/405 (0%) Query: 2 RVIDGGVTAPKGFKANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKN- 60 ++ID GV APKGF ANG KEGK+GV II SEK+ + TFTTNKVVAHPV+LS+E+++N Sbjct: 8 KIIDNGVVAPKGFNANGLKEGKYGVGIIYSEKECETSATFTTNKVVAHPVILSKEILENN 67 Query: 61 RDKFRAIVANSGNANCFTKDGMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMDMNII 120 R K RAIV NSGNANCFTK+G D+KEM + A L NI E+ VLVASTGVIGRKM M+II Sbjct: 68 RSKIRAIVVNSGNANCFTKNGYYDSKEMIKETANLLNIPENSVLVASTGVIGRKMPMDII 127 Query: 121 KDRINKVYNLIKEGNSSINAAKAIMTTDTKPKEIAVEFEVNGKTVRVGGIAKGAGMIAPN 180 KDRI+K L+K+ N++ N AK+IMTTD PK +AVEFEVNG VR+G +AKGAGMIAP+ Sbjct: 128 KDRIHKTNELLKKENNNDNIAKSIMTTDAFPKTVAVEFEVNGTPVRIGAVAKGAGMIAPD 187 Query: 181 MLHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGVNY 240 MLHATMLCFITTDI I + LT LQ V+++FNN VDGDTSTNDTVFV+ANG SGVNY Sbjct: 188 MLHATMLCFITTDINISNKDLTKSLQNAVNESFNNAVVDGDTSTNDTVFVMANGESGVNY 247 Query: 241 ---EECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSL 297 EC E F+ AL +VC E+AK++VKDGEGATK MEV+VKGA ++EDAVKASK++V SL Sbjct: 248 SNNNECKELFDEALQFVCVEMAKLMVKDGEGATKLMEVMVKGAPSKEDAVKASKSVVRSL 307 Query: 298 LVKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTEEL 357 LVKTA++G DPNWGRI A+VGYSG D + + +D+I+ + +EV LV G P+ADEGTEEL Sbjct: 308 LVKTALYGEDPNWGRIAASVGYSGIDIDMDKIDIIIGDSNNEVMLVNSGAPIADEGTEEL 367 Query: 358 KKAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 AE IMKS EIKI+VDLKMG++EN +GCDL +EYV+IN+EYTT Sbjct: 368 MVAENIMKSKEIKIIVDLKMGDYENTAFGCDLGHEYVKINSEYTT 412 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: 575 Number of extensions: 17 Number of successful extensions: 3 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: 412 Length adjustment: 31 Effective length of query: 371 Effective length of database: 381 Effective search space: 141351 Effective search space used: 141351 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