Align Glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_027720416.1 H589_RS0101700 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= reanno::DvH:206250 (393 letters) >NCBI__GCF_000425265.1:WP_027720416.1 Length = 394 Score = 395 bits (1014), Expect = e-114 Identities = 198/394 (50%), Positives = 267/394 (67%), Gaps = 1/394 (0%) Query: 1 MSASPKGFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSAR 60 M +PKG++FA++ AGF+ R DLALI+SD PA AA VFT N+FQAAPV V ++ L+ Sbjct: 1 MLKTPKGYKFASIDAGFKYSGRNDLALILSDVPAVAAAVFTKNKFQAAPVTVGKDILADS 60 Query: 61 PVARAVVINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKW 120 + R +IN+G ANACTG+EG+ +C+ +L+L K G+ ++LP+STGVIG + M+KW Sbjct: 61 KIVRGAIINAGLANACTGEEGIADCKESLELAAKHLGLTPRDLLPSSTGVIGPRFDMEKW 120 Query: 121 REAAPRLAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNM 180 + APRLA +G++ + A+AIMTTD FPK+A E+ G + ++GM KGAGMI PNM Sbjct: 121 KAVAPRLAEQVGKDDAVNTAKAIMTTDKFPKLAWGEITCEGKQITMLGMCKGAGMISPNM 180 Query: 181 ATMLSVVLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANGASGVTVEGE 240 ATML ++CDA V WQ ++++FN VTVDGDTSTNDTV ANGASG+ + + Sbjct: 181 ATMLGFIICDADVDENWWQETLNKCINKSFNCVTVDGDTSTNDTVQAFANGASGIKADTD 240 Query: 241 DLAKLGEA-LTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLVKT 299 EA L D+ +L+YM+VQD EG TKVM + VSGA D +AE + R VG+S LVKT Sbjct: 241 VKRSALEALLLDICQQLSYMIVQDAEGGTKVMTIDVSGAATDQDAELMVRAVGNSPLVKT 300 Query: 300 AMYGRDANWGRIVAAVGRSGASFKAEDVVVTLCGVELFRNGQPTDLDFDTLLREPLKGRD 359 A++G D NWGRIVAA GRSGA F + ++ + +F G+P D D LL ++ +D Sbjct: 301 ALFGEDPNWGRIVAAAGRSGAEFDPNKLTLSFGKIVVFEKGKPVQGDLDALLAPLMRKQD 360 Query: 360 VTVDIELGAGTGHYELLASDLTHDYVNCNADYRS 393 + + I LG G GH L ASDLT +Y+N NADYRS Sbjct: 361 IDIFITLGDGEGHSILKASDLTREYININADYRS 394 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: 438 Number of extensions: 20 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: 393 Length of database: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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 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