Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_011938690.1 GURA_RS09105 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000016745.1:WP_011938690.1 Length = 393 Score = 323 bits (827), Expect = 7e-93 Identities = 184/397 (46%), Positives = 257/397 (64%), Gaps = 11/397 (2%) Query: 5 RGFSYAGVHCRIKRK-RKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGI- 62 +GF ++ V +K+ R DLG+IFSEVP AGVFTTN VKAAPV+ ME + +G+ Sbjct: 4 KGFKFSAVEAAVKKPGRLDLGLIFSEVPAAVAGVFTTNKVKAAPVLLGME---RMKNGLC 60 Query: 63 RAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESG 122 +A+ VNSG ANACTG QG+ +AR A A+ L IP E+V VSSTGVIG LPME++ Sbjct: 61 QAVVVNSGNANACTGPQGIEDARETARLVAEGLGIPDEAVQVSSTGVIGQPLPMERLRRA 120 Query: 123 IEEAVKNLSKDPVP-FAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATM 181 I ++ L A AIMTTDT KI ++ G ++ GIAKG+GMI PNMATM Sbjct: 121 IPALIEGLGTGTFDDVARAIMTTDTFPKIEARNGVAGGIPYSIAGIAKGAGMIMPNMATM 180 Query: 182 LSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETD 241 L+FI TDA V LKK+ K + D S+N+I VDGDTSTND +I+ANG+AGN I+ T Sbjct: 181 LAFIVTDAAVEPAWLKKVFKEANDASFNVISVDGDTSTNDTALIMANGMAGNPQIKAGTP 240 Query: 242 GFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTA 301 + +V LA++IV+DGEGATK++E+ ++ A A+ A A+ +S LVKTA Sbjct: 241 DADSFVLHLRDVLLALAKQIVKDGEGATKLVEITIKGARSGADAKRAAMAVANSLLVKTA 300 Query: 302 IYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFD-EDTAKKILS 360 +G+DANWGR++AA GYSGA+ DPD+ +LFF+ +++ +NG D E ++L Sbjct: 301 FFGQDANWGRILAAVGYSGAEVDPDKAELFFDD----VQMVKNGIFAGGDAEARGTEVLR 356 Query: 361 EKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 +K+ + +++K G+ ++ + DL+ YV+IN YRT Sbjct: 357 KKEFAVTVNLKLGEGISTVYTSDLSYDYVKINADYRT 393 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: 431 Number of extensions: 19 Number of successful extensions: 5 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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