Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_092348811.1 BLU87_RS12045 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q07908 (410 letters) >NCBI__GCF_900107645.1:WP_092348811.1 Length = 396 Score = 322 bits (826), Expect = 9e-93 Identities = 180/392 (45%), Positives = 254/392 (64%), Gaps = 4/392 (1%) Query: 21 PEGFQAAGVNAGLRYS-KNDLGVILCDVPASAAAVYTQSHFQAAPLKVTQASLAVEQKLQ 79 P GF+ +G+ +G++ + K DLG+I+ D PA+ A V+TQ+ AAPL +T+ +A + K Q Sbjct: 7 PAGFRFSGMASGIKKTGKLDLGLIVSDSPANCAGVFTQNKVVAAPLILTKPRIA-KGKCQ 65 Query: 80 AVIVNRPCANACTGAQGLKDAYEMRELCAKQFGLALHHVAVASTGVIGEYLPMEKIRAGI 139 A++VN ANACTGA+GL+ A EL A + ++ V++ASTGVIGE LP+ GI Sbjct: 66 AILVNSGNANACTGAEGLRVAEATMELLAGELQISTDLVSLASTGVIGELLPLSPFVDGI 125 Query: 140 KQLVPGVTMADAEAFQTAILTTDTVMKRACYQTTIDGKTVTVGGAAKGSGMIHPNMATML 199 +LV G++ A+ AI+TTD K A T + V G AKG+GMIHPNMATML Sbjct: 126 SELVAGLSADHAQVVAEAIMTTDAFSKVAS-ATEYGEQGYKVLGMAKGAGMIHPNMATML 184 Query: 200 AFITTDANVSSPVLHAALRSITDVSFNQITVDGDTSTNDMVVVMASGLAGNDELTPDHPD 259 F+ TDA VS +L++AL+ SFN ITVDGDTSTNDMV+++A+G + + D P+ Sbjct: 185 GFVLTDAQVSLDLLNSALQQAVKKSFNSITVDGDTSTNDMVLLLANGSSDGKRIEADTPE 244 Query: 260 WENFYEALRKTCEDLAKQIAKDGEGATKLIEVRVRGAKTDEEAKKIAKQIVGSNLVKTAV 319 E F + L + DLAK I +DGEGATKL++++V G E A+K+A+ + S+LVKTA Sbjct: 245 AEIFCQHLDEVLLDLAKMIVRDGEGATKLVKIKVVGGSNVESARKVARSVATSSLVKTAF 304 Query: 320 YGADANWGRIIGAIGYSDAEVNPDNVDVAIGPM-VMLKGSEPQPFSEEEAAAYLQQETVV 378 +G DANWGRII A+GYS +VNPD +D++ + V + G SE EA LQ + V Sbjct: 305 FGEDANWGRIIAAVGYSGVDVNPDRIDISFNQVPVAVNGLACGGESEAEATKVLQLDEFV 364 Query: 379 IEVDLHIGDGVGVAWGCDLTYDYVKINASYRT 410 + +DLH G+ + DL+Y+YVKIN+ YR+ Sbjct: 365 VTIDLHQGEAEASYYTSDLSYEYVKINSDYRS 396 Lambda K H 0.316 0.130 0.373 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: 429 Number of extensions: 15 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: 410 Length of database: 396 Length adjustment: 31 Effective length of query: 379 Effective length of database: 365 Effective search space: 138335 Effective search space used: 138335 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 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