Align Amino-acid acetyltransferase; EC 2.3.1.1; N-acetylglutamate synthase; AGS; NAGS (uncharacterized)
to candidate BPHYT_RS01610 BPHYT_RS01610 acetylglutamate kinase
Query= curated2:Q9JW21 (436 letters) >FitnessBrowser__BFirm:BPHYT_RS01610 Length = 299 Score = 108 bits (270), Expect = 2e-28 Identities = 86/289 (29%), Positives = 132/289 (45%), Gaps = 11/289 (3%) Query: 2 IVPDLFVAHFREAAPYIRQMRGKTLVAGIDDRLLEGDTLNK-FAADIGLLSQLGIRLVLI 60 I P L EA PYIRQ GKT+V + + L + FA D+ LL +GI V++ Sbjct: 10 IAPTLKAEILAEALPYIRQYHGKTVVIKYGGNAMTEERLKQGFARDVILLKLVGINPVIV 69 Query: 61 HGARHFLDRHAAAQGRTPHYCRGLRVTDETSLEQAQQFAGTVRSRFEAALCGSVSGFARA 120 HG +D+ G+ + +G+RVTDE ++E + G + L G A Sbjct: 70 HGGGPQIDQALKKIGKQGTFIQGMRVTDEETMEVVEWVLGGEVQQDIVTLINHFGG--HA 127 Query: 121 PSVPLVSGNFLTARPIGVIDG------TDMEYAGVIRKTDTAALRFQLDAGNIVWLPPLG 174 + G + AR + + D D+ G + + A ++ D I + P+G Sbjct: 128 VGLTGKDGGLIHARKMLMPDRDNPGQYVDIGQVGEVEAINPAVVKALQDDAFIPVISPIG 187 Query: 175 HSYSGKTFHLDMLQTAASVAVSLQAEKLVYLTLSDGISRPDGTLAVTLSAQEAQSLAEHA 234 G +++++ A +AV L AEKLV +T G+ +G L LSA+E L Sbjct: 188 FGEDGLSYNINADLVAGKLAVVLNAEKLVMMTNIPGVMDKEGNLLTDLSAREIDGLFADG 247 Query: 235 --GGETRRLISSAVAALEGGVHRVQILNGAADGSLLQELFTRNGIGTSI 281 G ISSA+ A + GV V I++G + S+L E+ T GT I Sbjct: 248 TISGGMLPKISSALDAAKSGVRSVHIIDGRIEHSVLLEILTEQPFGTMI 296 Lambda K H 0.321 0.136 0.394 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: 322 Number of extensions: 19 Number of successful extensions: 4 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: 436 Length of database: 299 Length adjustment: 29 Effective length of query: 407 Effective length of database: 270 Effective search space: 109890 Effective search space used: 109890 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 (21.9 bits) S2: 49 (23.5 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