Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_028585527.1 G494_RS0117365 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000429965.1:WP_028585527.1 Length = 394 Score = 317 bits (812), Expect = 4e-91 Identities = 176/397 (44%), Positives = 250/397 (62%), Gaps = 10/397 (2%) Query: 5 RGFSYAGVHCRIK-RKRKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGIR 63 +GF+ + V I+ R DLG+I S+VP AGVFTTN VKAAPV+ DM+ L ++ Sbjct: 4 KGFNASAVQAGIRYADRLDLGLITSDVPAVTAGVFTTNTVKAAPVLIDMDRLRNGQ--VQ 61 Query: 64 AITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESGI 123 A+ +NSG ANACTGE+GM A + A++L I E V ++STGVIG QLP+ + + Sbjct: 62 AVLINSGNANACTGEEGMETALATSSLVARQLEIQEELVQLASTGVIGEQLPLAPFQEHV 121 Query: 124 EEAVKNLSKDPVP-FAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATML 182 E V L+ + P A+A+MTTDT K V ++G +++LG+AKGSGMI P+MATML Sbjct: 122 AELVAGLAPENFPKLAQAMMTTDTMAKTAFTSVDLDGTTVSLLGVAKGSGMIMPDMATML 181 Query: 183 SFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETDG 242 F+ TDA + L +L+ VD S+N I VDGDTSTNDMV+++ANG AGN I E+ Sbjct: 182 CFVVTDAQIVFPVLNSMLRSGVDRSFNRITVDGDTSTNDMVLVMANGAAGNTWIDEDNPE 241 Query: 243 FWKLY-EAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTA 301 +++ A+ ++ LA IVEDGEGATK + + V A + A A+ I +S LVKTA Sbjct: 242 GTRIFAAALEKILLELALMIVEDGEGATKTVTIRVNGARESEEAMSAAQTIANSALVKTA 301 Query: 302 IYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDT-AKKILS 360 +GEDANWGR+IAA G S FDP+++ + F+ + + ENG + +++ A K+L+ Sbjct: 302 FFGEDANWGRIIAALGRSECLFDPNKVSIAFDD----VVLVENGLALGAEQEALASKVLA 357 Query: 361 EKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 KK + +D+ G E A + CD + YV+IN YR+ Sbjct: 358 NKKFSVTVDLHDGMESAEVYTCDFSYDYVKINADYRS 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: 416 Number of extensions: 20 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: 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