Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_013459237.1 SULKU_RS01910 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000183725.1:WP_013459237.1 Length = 395 Score = 275 bits (702), Expect = 2e-78 Identities = 183/409 (44%), Positives = 245/409 (59%), Gaps = 24/409 (5%) Query: 1 MRVIDGGVTAPKGFKANGY-----KEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSR 55 + I+GGV A KGF A+G KEG +A I SEK A FTTNK+ A P+ R Sbjct: 4 LNTIEGGVCAAKGFFADGIHIGLKKEGAKDLAFIYSEKPCAIASVFTTNKMTAAPIRHFR 63 Query: 56 ELIKNRDKFRAIVANSGNANCFT-KDGMEDAKEMQRLVAELFNINEDEVLVASTGVIGRK 114 L + F ++ NS NAN T + G++D E+ + F ++ V+ +STGVIG + Sbjct: 64 SLGEFEGNF--VLINSKNANAMTGRAGIDDITEVLGELKSKFPQIQNPVM-SSTGVIGVR 120 Query: 115 MDMNIIKDRINKVYNLIKEGNSSINAAKAIMTTDTKPKEIAVEFEV-NGKTVRVGGIAKG 173 + I + K +EG INA++AIMTTDT K +A E + NG++ R+G +AKG Sbjct: 121 LPKAKIIEGAMKFDLTRREG---INASEAIMTTDTFSKRLAYEVTLENGQSFRIGAMAKG 177 Query: 174 AGMIAPNMLHATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLAN 233 AGMI P M ATMLCFITTD +DK ++ +IL + V TFN SVDGDTSTNDTV V+AN Sbjct: 178 AGMINPAM--ATMLCFITTDAAVDKTTMQDILDECVHTTFNAASVDGDTSTNDTVVVMAN 235 Query: 234 GLSGVNYEECGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAI 293 GLSG + F+ AL + LAK +V+DGEGATK + V GA ++A A+KA+ Sbjct: 236 GLSGAFHAGA---FKEALESIMLFLAKEMVRDGEGATKLVTYKVTGAINHKEAEIAAKAL 292 Query: 294 VNSLLVKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEG 353 NSLLVKTA+FG DPNWGRI + VG SG + + LS + D++ + K G L DE Sbjct: 293 SNSLLVKTALFGQDPNWGRIASTVGASGIMCD----EAFLSIWFDDICVYKKGELLFDEK 348 Query: 354 TEELKKAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 E L A +M+ I D+ + + E YGCDL +EYV+INA+Y T Sbjct: 349 LEPL--AAAVMQKSSFTIHCDIGLQDGEFTAYGCDLGHEYVKINADYRT 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: 409 Number of extensions: 21 Number of successful extensions: 7 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