Align Glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_027178551.1 G496_RS0106395 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= reanno::DvH:206250 (393 letters) >NCBI__GCF_000429985.1:WP_027178551.1 Length = 394 Score = 413 bits (1062), Expect = e-120 Identities = 208/390 (53%), Positives = 272/390 (69%), Gaps = 1/390 (0%) Query: 5 PKGFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSARPVAR 64 PKG++F+ +AGF+ + R DLALI SD PATAAGVFTTNRFQAAP+ V + NL R Sbjct: 5 PKGYKFSAAAAGFKYKDRNDLALICSDVPATAAGVFTTNRFQAAPITVCKANLEKDRKTR 64 Query: 65 AVVINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKWREAA 124 A++IN+G ANACTG+EG+ +CR T ++V KA GI + E+LPASTGVIG + + W A Sbjct: 65 ALMINAGLANACTGNEGIEDCRRTTEMVSKAIGIESCEILPASTGVIGNRFDLSVWEAAV 124 Query: 125 PRLAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNMATML 184 P++A ALG A+AIMTTD FPK++ +++ A ++RL+GM KG+GMICP MATML Sbjct: 125 PKIAEALGSTDAVKTAKAIMTTDTFPKLSWKKVDTANGSIRLLGMCKGSGMICPKMATML 184 Query: 185 SVVLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANGASGVTVEGEDLAK 244 V+CDA V P+ WQ + ++FN VTVDGDTSTND V LANGASGV + + + + Sbjct: 185 GFVICDADVDPDWWQETLARCIQKSFNCVTVDGDTSTNDCVLALANGASGVKADSDTVKE 244 Query: 245 -LGEALTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLVKTAMYG 303 L +AL D+ L+YM++QD EG TKVM + V+GA D +AE VAR VG+S LVKTA++G Sbjct: 245 ALEQALLDICQALSYMIIQDAEGGTKVMSISVTGAESDEDAELVARAVGNSPLVKTAIFG 304 Query: 304 RDANWGRIVAAVGRSGASFKAEDVVVTLCGVELFRNGQPTDLDFDTLLREPLKGRDVTVD 363 D NWGRIVAA GRS A F + + + + +F G P + D D +L +K +D+ V+ Sbjct: 305 EDPNWGRIVAAAGRSEADFDPDMLTLAFGDIIVFEKGCPIEGDIDAVLAPLMKKQDIAVN 364 Query: 364 IELGAGTGHYELLASDLTHDYVNCNADYRS 393 I LG GTG LLASD THDYV+ NADYRS Sbjct: 365 ISLGNGTGKSSLLASDFTHDYVSINADYRS 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: 459 Number of extensions: 18 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 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