Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate SMc02450 SMc02450 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__Smeli:SMc02450 Length = 413 Score = 295 bits (755), Expect = 2e-84 Identities = 173/410 (42%), Positives = 245/410 (59%), Gaps = 12/410 (2%) Query: 5 LTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIA 64 L KT ++P + G+ + TA AG+K TD+ ++ ++V VFT ++ +APV Sbjct: 8 LAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVDHC 67 Query: 65 KSHLFDEDGV-RALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVIL 123 + +L G+ RA+V+N+GNANA TG +GR AAA+ +GC +V STGVI Sbjct: 68 RQNL--PGGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGVIG 125 Query: 124 EPLPADKIIAALPKMQPA----FWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAK 179 EPL A K L K+ + FW EAA+AIMTTDT PK A+R ++G V GIAK Sbjct: 126 EPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVK-VAINGIAK 184 Query: 180 GSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATG 239 G+GMI P+MATML F+ TDA ++ LQ + Q + TFN++TVD DTST+D+ ++ ATG Sbjct: 185 GAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFATG 244 Query: 240 K---NSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEA 296 + Q+++++ ADPR + L L +LA +VRDGEGA K + V VE A+ A Sbjct: 245 AAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAAA 304 Query: 297 RQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRA 356 ++ A + A SPLVKTA D N G+ + A+G + + D + ++ DI VA G R Sbjct: 305 KRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEM-AERDRLAIWFGDIRVAVEGERD 363 Query: 357 ASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 +Y+EA AVM + I +R+ + G ATVYTCDL+ YV IN DYRS Sbjct: 364 PAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 Lambda K H 0.317 0.130 0.367 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: 361 Number of extensions: 18 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: 406 Length of database: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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: 41 (21.7 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