Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_027178551.1 G496_RS0106395 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000429985.1:WP_027178551.1 Length = 394 Score = 275 bits (703), Expect = 2e-78 Identities = 168/399 (42%), Positives = 237/399 (59%), Gaps = 12/399 (3%) Query: 3 VPRGFSYAGVHCRIKRK-RKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSG 61 VP+G+ ++ K K R DL +I S+VP TAAGVFTTN +AAP+ L K+ Sbjct: 4 VPKGYKFSAAAAGFKYKDRNDLALICSDVPATAAGVFTTNRFQAAPITVCKANLEKDRK- 62 Query: 62 IRAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVES 121 RA+ +N+G+ANACTG +G+ + RR E +K + I +L +STGVIG + + E+ Sbjct: 63 TRALMINAGLANACTGNEGIEDCRRTTEMVSKAIGIESCEILPASTGVIGNRFDLSVWEA 122 Query: 122 GIEEAVKNL-SKDPVPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMAT 180 + + + L S D V A+AIMTTDT K+ KKV I +LG+ KGSGMI P MAT Sbjct: 123 AVPKIAEALGSTDAVKTAKAIMTTDTFPKLSWKKVDTANGSIRLLGMCKGSGMICPKMAT 182 Query: 181 MLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEET 240 ML F+ DA+V D ++ L + S+N + VDGDTSTND V+ LANG +G ++ ++ Sbjct: 183 MLGFVICDADVDPDWWQETLARCIQKSFNCVTVDGDTSTNDCVLALANGASG---VKADS 239 Query: 241 DGFWK-LYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVK 299 D + L +A+ ++ Q L+ I++D EG TKV+ + V A A L+ARA+ +S LVK Sbjct: 240 DTVKEALEQALLDICQALSYMIIQDAEGGTKVMSISVTGAESDEDAELVARAVGNSPLVK 299 Query: 300 TAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKKIL 359 TAI+GED NWGR++AAAG S A FDPD L L F G I V E G ++ D D L Sbjct: 300 TAIFGEDPNWGRIVAAAGRSEADFDPDMLTLAF----GDIIVFEKGCPIEGDIDAVLAPL 355 Query: 360 SEKK-VKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 +K+ + + + + G + D T YV IN YR+ Sbjct: 356 MKKQDIAVNISLGNGTGKSSLLASDFTHDYVSINADYRS 394 Lambda K H 0.315 0.133 0.371 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: 443 Number of extensions: 20 Number of successful extensions: 6 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: 397 Length of database: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 (21.6 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