Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_015943020.1 DHAF_RS03880 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000021925.1:WP_015943020.1 Length = 408 Score = 354 bits (908), Expect = e-102 Identities = 207/405 (51%), Positives = 270/405 (66%), Gaps = 21/405 (5%) Query: 4 PRGFSYAGVHCRIKRKRK-DLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGI 62 PRGF GV IK K D+ +++SEVP AAGVFT N VKA P+I + L +GI Sbjct: 14 PRGFRATGVKAEIKYPDKYDVALVYSEVPAQAAGVFTRNKVKAHPLILTKKHL---ENGI 70 Query: 63 -RAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVES 121 RA+ NSG ANAC G+ G A MA KTA+ L I E VLV+STGVIGV+LP+E V Sbjct: 71 ARAMVANSGNANACVGKPGDEAAWAMAVKTAEVLGIAPEDVLVASTGVIGVELPVESVTR 130 Query: 122 GIEEAVKNLSKDPVP---------FAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSG 172 GIE+A +++ P A AIMTTDT +K + +++ E I + +AKGSG Sbjct: 131 GIEKASLEIAEKISPEEMTQNSHQAALAIMTTDTAVKEAACELSTENGVIRLGAMAKGSG 190 Query: 173 MIHPNMATMLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAG 232 MIHPNM TML FITTDA + L++LL+ +V+DS+NM+ VDGDTSTNDMV++LANG +G Sbjct: 191 MIHPNMGTMLGFITTDAAIPASELQELLREAVEDSFNMVTVDGDTSTNDMVLVLANGKSG 250 Query: 233 NAPIQEETDGFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAI 292 EE F +++ A V Q LA+ I DGEGATK +EV+V A AR IA++I Sbjct: 251 ITLNPEEWAEFRRMFWA---VCQKLAQDIARDGEGATKFLEVQVLGAAAVEDARKIAKSI 307 Query: 293 VSSNLVKTAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDE 352 S+LVK A+YGEDANWGR++AAAGYSGA+F+P++++++ G + VA+ GQGV F E Sbjct: 308 CGSSLVKIALYGEDANWGRILAAAGYSGAEFNPNQVEIYL----GHVLVAKEGQGVHFSE 363 Query: 353 DTAKKILSEKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 + AKK+LS K V I L +++G+ A AWGCDLT YV ING YRT Sbjct: 364 EEAKKVLSRKDVLIKLLLQEGQAQATAWGCDLTHDYVTINGDYRT 408 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: 452 Number of extensions: 16 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: 408 Length adjustment: 31 Effective length of query: 366 Effective length of database: 377 Effective search space: 137982 Effective search space used: 137982 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