Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_011868469.1 MMARC5_RS03560 ornithine acetyltransferase
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000016125.1:WP_011868469.1 Length = 408 Score = 508 bits (1309), Expect = e-149 Identities = 261/402 (64%), Positives = 310/402 (77%), Gaps = 2/402 (0%) Query: 3 VIDGGVTAPKGFKANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKNRD 62 V+DGGV APKGFK+NG+K+ K+G A+I SE DAV AG FTTNKV AHPV LS++++ N + Sbjct: 7 VVDGGVVAPKGFKSNGHKDRKYGAALIYSETDAVAAGVFTTNKVFAHPVALSKDVLVNNN 66 Query: 63 KFRAIVANSGNANCFTKDGMEDAKEMQRLVAELFNINEDEVLVASTGVIGRKMDMNIIKD 122 FRAIVANSGNANCFTK GMEDA+ + + AEL I E++VL ASTGVIGRKM M+II Sbjct: 67 VFRAIVANSGNANCFTKGGMEDAELLVKKAAELLKIPENQVLSASTGVIGRKMPMDIITL 126 Query: 123 RINKVYNLIKEGNSSINAAKAIMTTDTKPKEIAVEFEVNGKTVRVGGIAKGAGMIAPNML 182 + + + + NS+ NA+KAIMTTD PK +AVEFEV K +R+GGIAKGAGMIAPNML Sbjct: 127 EVERAFENMDLENSNENASKAIMTTDAFPKTVAVEFEVKDKKIRIGGIAKGAGMIAPNML 186 Query: 183 HATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGVNYEE 242 HATML FITTDIEI KE LTN LQK D++FNN VDGD STNDTV+VLAN SGV Y + Sbjct: 187 HATMLGFITTDIEISKEDLTNSLQKATDESFNNAVVDGDMSTNDTVYVLANAQSGVKYTD 246 Query: 243 CGEEFENALLYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSLLVKTA 302 C +EF+ AL YV +ELAKMIV DGEGA K +E V GA+T+EDA KAS +IV SLL+KTA Sbjct: 247 CKDEFDEALTYVSKELAKMIVSDGEGAKKLIEATVYGAETKEDAKKASMSIVRSLLLKTA 306 Query: 303 VFGGDPNWGRIVAAVGYSGADFNPEVVDVILSNYKDE--VYLVKDGIPLADEGTEELKKA 360 FG DPNWGRI AAVGYSGA+ + D+I+ + E LVK G +AD GT ELK A Sbjct: 307 FFGADPNWGRIAAAVGYSGAEMDMANFDIIIGDISSEKQAILVKAGEQIADCGTPELKLA 366 Query: 361 EEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 EEIMK D+IKI+VDLKMG FEN +GCDL YEYV+IN+EYTT Sbjct: 367 EEIMKEDKIKIIVDLKMGSFENTAFGCDLGYEYVKINSEYTT 408 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: 546 Number of extensions: 12 Number of successful extensions: 2 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: 408 Length adjustment: 31 Effective length of query: 371 Effective length of database: 377 Effective search space: 139867 Effective search space used: 139867 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