Align Glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate 8502162 DvMF_2872 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein (RefSeq)
Query= reanno::DvH:206250 (393 letters) >FitnessBrowser__Miya:8502162 Length = 412 Score = 567 bits (1462), Expect = e-166 Identities = 286/391 (73%), Positives = 318/391 (81%) Query: 3 ASPKGFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSARPV 62 A+PKGFRFAT AGFRK R DLAL+VSDTPA AA VFT N FQAAPV+VAR+ L+ P Sbjct: 22 AAPKGFRFATAGAGFRKAGRDDLALVVSDTPAVAAAVFTKNLFQAAPVLVARDTLAHAPK 81 Query: 63 ARAVVINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKWRE 122 ARAV+INSGQANACTGDEG+ NCR TL+LV A G+ ++LPASTGVIGAQL MDKW Sbjct: 82 ARAVLINSGQANACTGDEGLANCRATLELVAAATGLAPQDILPASTGVIGAQLAMDKWAA 141 Query: 123 AAPRLAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNMAT 182 A P LAA LG DFA+AIMTTDAFPK A R + ++G TV LVGMAKGAGMICPNMAT Sbjct: 142 AVPALAADLGNKGPEDFAKAIMTTDAFPKFASRTVELSGGTVTLVGMAKGAGMICPNMAT 201 Query: 183 MLSVVLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANGASGVTVEGEDL 242 ML+ VLCDA V P AWQ LF DAVD TFNRVTVDGDTSTNDTVFGLANGASGV G DL Sbjct: 202 MLATVLCDADVEPAAWQALFRDAVDATFNRVTVDGDTSTNDTVFGLANGASGVAARGADL 261 Query: 243 AKLGEALTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLVKTAMY 302 LG ALT VL +AYMLV+DGEGATKV+ + V+GA DDA+AE ARTVGHSQLVKTAMY Sbjct: 262 TVLGAALTGVLGDVAYMLVKDGEGATKVIHINVAGARDDADAELAARTVGHSQLVKTAMY 321 Query: 303 GRDANWGRIVAAVGRSGASFKAEDVVVTLCGVELFRNGQPTDLDFDTLLREPLKGRDVTV 362 GRDANWGRIVAA+GRSGA+F V+V+LCGVELFR GQPT+LDFD LL+EPL GRD+ V Sbjct: 322 GRDANWGRIVAALGRSGATFNPAAVIVSLCGVELFRGGQPTNLDFDALLKEPLAGRDIVV 381 Query: 363 DIELGAGTGHYELLASDLTHDYVNCNADYRS 393 +I LG G G Y LLASDLTHDY++CNADYRS Sbjct: 382 NIMLGNGPGSYRLLASDLTHDYISCNADYRS 412 Lambda K H 0.318 0.132 0.382 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: 577 Number of extensions: 11 Number of successful extensions: 1 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: 393 Length of database: 412 Length adjustment: 31 Effective length of query: 362 Effective length of database: 381 Effective search space: 137922 Effective search space used: 137922 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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