Align Glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_013259665.1 DEBA_RS14330 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= reanno::DvH:206250 (393 letters) >NCBI__GCF_000143965.1:WP_013259665.1 Length = 416 Score = 286 bits (733), Expect = 6e-82 Identities = 173/394 (43%), Positives = 233/394 (59%), Gaps = 8/394 (2%) Query: 7 GFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSARPVARAV 66 GF+ A V+ G RK+ R DLALIV+D AAG+FTTNR AAPV VA+ ++ A AR + Sbjct: 24 GFKGAAVACGLRKDGREDLALIVADHAVDAAGLFTTNRLFAAPVAVAKNHIQAGR-ARVI 82 Query: 67 VINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKWREAAPR 126 + NSG ANA TG G+ C + P EVLP STGVIG L K R P Sbjct: 83 LANSGGANAATGQAGLEACLRACQEAARVADCPLTEVLPCSTGVIGQVLDDQKIRAKLPE 142 Query: 127 LAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNMATMLSV 186 L A+ A AIMTTDAF K+A E I G V ++G+AKGAGMI P+MAT+L Sbjct: 143 LFASADDQGLARAAGAIMTTDAFRKMARAEAIIDGKKVSVLGLAKGAGMIRPDMATLLCF 202 Query: 187 VLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANG-ASGVTVEGE--DLA 243 VL DAA +P+A AV+++FNR+TVDGD STNDT+ LA+G A+ +EG+ L+ Sbjct: 203 VLTDAAASPQALGLALGRAVEQSFNRITVDGDMSTNDTILLLASGRAANTRLEGDGPGLS 262 Query: 244 KLGEALTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLVKTAMYG 303 L EALT V LA M+V DGEGA ++ + ++GA D + A + +G+S LVKTA+ Sbjct: 263 ALTEALTAVCQDLAQMMVCDGEGAGRMALLHITGAADQSSARKLCFAIGNSPLVKTALAS 322 Query: 304 RDANWGRIVAAVG----RSGASFKAEDVVVTLCGVELFRNGQPTDLDFDTLLREPLKGRD 359 D WGR+++A G R F+ E V + G+ + +G L+ + ++ Sbjct: 323 PDPYWGRMLSAAGAEAARENLPFQPEKTRVWIEGILVGDHGARASLEAEEAAGRAMQKPR 382 Query: 360 VTVDIELGAGTGHYELLASDLTHDYVNCNADYRS 393 V+V I+LG G G Y ++ASDL H+Y+ N YRS Sbjct: 383 VSVRIDLGLGQGQYWVMASDLDHNYITLNVSYRS 416 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: 455 Number of extensions: 21 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: 393 Length of database: 416 Length adjustment: 31 Effective length of query: 362 Effective length of database: 385 Effective search space: 139370 Effective search space used: 139370 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