Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_013644558.1 METBO_RS04845 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000191585.1:WP_013644558.1 Length = 398 Score = 406 bits (1043), Expect = e-118 Identities = 225/405 (55%), Positives = 282/405 (69%), Gaps = 10/405 (2%) Query: 1 MRVIDGGVTAPKGFKANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKN 60 M+++DGGV A G A G + +GVA+I+ KD+ FT+NK+VA PV+L++ ++N Sbjct: 1 MKIVDGGVCAVNGVLAAGACDDDYGVAVIVC-KDSDSTAVFTSNKIVAAPVILTKNAVEN 59 Query: 61 RDKFRAIVANSGNANCFTKD-GMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMDMNI 119 K A+VANSGNANCFT D G+ED K M +VAE + ++V VASTGVIGR M M+I Sbjct: 60 -GKLSAVVANSGNANCFTGDQGIEDGKAMASVVAEELDFKFEDVAVASTGVIGRLMPMDI 118 Query: 120 IKDRINK-VYNLIKEGNSSINAAKAIMTTDTKPKEIAVEFEV-NGKTVRVGGIAKGAGMI 177 I I K V L +S NAA+AIMTTDT KE AVE + NGK++R+GGI KG+GMI Sbjct: 119 IGSLIKKAVLRLENSAEASKNAAEAIMTTDTYSKEFAVETTLKNGKSIRIGGITKGSGMI 178 Query: 178 APNMLHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSG 237 APNM TMLCFITTD++ L L+K VD +FN + VDGD STNDTV ++ANG SG Sbjct: 179 APNM--GTMLCFITTDVKASSSELNTALKKAVDASFNMVVVDGDESTNDTVILMANGESG 236 Query: 238 VNYEECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSL 297 E E FE AL YVC +LA M+ KDGEGATKFMEV V GA E+A A+KA+V+S Sbjct: 237 ---ESIDENFEEALEYVCCQLASMMAKDGEGATKFMEVEVNGAVNTEEARLAAKAVVSSS 293 Query: 298 LVKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTEEL 357 LVKTA+FG DPNWGRIVAAVGYSGAD +P+VV V L + V +V GI A EGT +L Sbjct: 294 LVKTALFGADPNWGRIVAAVGYSGADIDPKVVSVSLQSLNKRVDIVDHGIIAAFEGTSQL 353 Query: 358 KKAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 ++AE+IM+ I+I++DL +G YGCDLSY+YV INAEYTT Sbjct: 354 EEAEDIMEEKNIRIIIDLGLGNGNATAYGCDLSYDYVSINAEYTT 398 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: 504 Number of extensions: 19 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: 398 Length adjustment: 31 Effective length of query: 371 Effective length of database: 367 Effective search space: 136157 Effective search space used: 136157 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