Align Glutamate N-acetyltransferase; Ornithine acetyltransferase; OATase; Ornithine transacetylase; EC 2.3.1.35 (characterized)
to candidate WP_007474675.1 CMTB2_RS05580 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q57645 (402 letters) >NCBI__GCF_000170735.1:WP_007474675.1 Length = 391 Score = 276 bits (705), Expect = 1e-78 Identities = 181/391 (46%), Positives = 241/391 (61%), Gaps = 21/391 (5%) Query: 13 GFKANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKNRDKFRAIVANSG 72 G KA G+K+ + V I S+ A FTTNK A P+ + +KN + I+ANS Sbjct: 21 GVKA-GFKKDDYDVGFIRSDTSLDIAYLFTTNKFQAAPIKYVK--LKNINNTNFILANSK 77 Query: 73 NANCFTKDGMEDAKEMQRLVAELFN-INEDEVLVASTGVIGRKMDMNIIKDRINKVYNLI 131 NAN T G+E K+++ ++ L I+ +++STGVIG +++ + IK I K Sbjct: 78 NANALT--GIEGIKDIEDILEFLSTKIDVINPIMSSTGVIGVRLNKDKIKSAIEKFD--F 133 Query: 132 KEGNSSINAAKAIMTTDTKPKEIAVEFEVNGKTVRVGGIAKGAGMIAPNMLHATMLCFIT 191 E NS+ A+AIMTTD+ KEIA E E ++GG+AKGAGMI P M ATMLCFIT Sbjct: 134 NERNSN-KFARAIMTTDSFEKEIAFEVEGEFGKFKIGGVAKGAGMINPAM--ATMLCFIT 190 Query: 192 TDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGVNYEECGEEFENAL 251 TD I + + +IL+++ + TFN ISVDGDTSTND+VF++ N E F+ AL Sbjct: 191 TDANIPQNEMQDILREINEITFNAISVDGDTSTNDSVFLMTTREGDYNKEA----FKEAL 246 Query: 252 LYVCRELAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSLLVKTAVFGGDPNWG 311 V ++LA IV+DGEGATK + VV GAK + +A A+KA+ NSLLVKTA+FG DPNWG Sbjct: 247 KKVMQKLALDIVRDGEGATKAVAFVVSGAKNKNEAKIAAKALTNSLLVKTALFGEDPNWG 306 Query: 312 RIVAAVGYSGADFNPEVVDVILSNYKDEVYLVKDGIPLADEGTEELKKAEEIMKSDEIKI 371 RI + +G SG + + E + + N V L G L DE E KKA EIMK E KI Sbjct: 307 RIASTIGASGVECDEEKLKISFEN----VILYNRGKILFDEEIE--KKAHEIMKRREFKI 360 Query: 372 VVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402 VDL +G+ + YGCDLSY+YV+INAEY T Sbjct: 361 YVDLGIGDGKFTAYGCDLSYDYVKINAEYRT 391 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: 465 Number of extensions: 28 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: 391 Length adjustment: 31 Effective length of query: 371 Effective length of database: 360 Effective search space: 133560 Effective search space used: 133560 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