Align Glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_012470536.1 GLOV_RS12330 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= reanno::DvH:206250 (393 letters) >NCBI__GCF_000020385.1:WP_012470536.1 Length = 393 Score = 341 bits (875), Expect = 2e-98 Identities = 192/396 (48%), Positives = 253/396 (63%), Gaps = 10/396 (2%) Query: 4 SPKGFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSARPVA 63 S KG+ F+ V A +K R DLALI S+TPATAA VFTTN +AAPV+++ ++ A Sbjct: 2 SLKGYTFSVVEAAIKKPGRKDLALIFSETPATAAAVFTTNAVKAAPVLLSAGRIAGGK-A 60 Query: 64 RAVVINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKWREA 123 +A+V+NSG ANACTG +GM + R T L+ GI V +STGVIG L M++ R A Sbjct: 61 QALVVNSGNANACTGAQGMLDARETSRLLAAGLGIAEELVQVSSTGVIGVPLPMERLRNA 120 Query: 124 APRLAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNMATM 183 P L A G T D A AIMTTD FPK +R AG + + G+AKGAGMI PNMATM Sbjct: 121 LPGLVAGCGSATIDDLAAAIMTTDTFPKAVQRTGCAAGVSYTVAGVAKGAGMIMPNMATM 180 Query: 184 LSVVLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANGASGVTV------ 237 LS V+ DAA+ PE LF AVDR+FN +T+DGDTSTNDT +ANGA+G V Sbjct: 181 LSFVMTDAALAPELIDTLFRGAVDRSFNAITIDGDTSTNDTCLLMANGAAGTAVITAGSP 240 Query: 238 EGEDLAKLGEALTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLV 297 E E+ A+L L +VL LA ++V+DGEGATK + +++SGA DA+A+ A V +S LV Sbjct: 241 EAEEFARL---LDEVLLELAKLIVRDGEGATKFVEIRISGAASDADAKQAAMAVANSSLV 297 Query: 298 KTAMYGRDANWGRIVAAVGRSGASFKAEDVVVTLCGVELFRNGQPTDLDFDTLLREPLKG 357 KTA +G+DANWGRI AAVG SGA + + + V + R G + D + E L+ Sbjct: 298 KTAFFGQDANWGRIFAAVGYSGAKVDPDLLALWFDDVCMARAGVFSGGDAEAQGTEVLRK 357 Query: 358 RDVTVDIELGAGTGHYELLASDLTHDYVNCNADYRS 393 ++ V ++LG G G + SDL+H+YV+ NADYR+ Sbjct: 358 KEFRVQVDLGLGQGSATVYTSDLSHEYVSINADYRT 393 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: 417 Number of extensions: 17 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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