Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_012675741.1 PERMA_RS08130 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000021565.1:WP_012675741.1 Length = 386 Score = 280 bits (715), Expect = 7e-80 Identities = 171/400 (42%), Positives = 240/400 (60%), Gaps = 17/400 (4%) Query: 1 MFVPRGFSYAGVHCRIKRKRKDLGIIFSEVPCTAAGVFTT-NVVKAAPVIYDMEILGKNP 59 M + G S AG+ + D I+ P + VF T N + AAPV YD ++ + Sbjct: 1 MDIKAGISKAGI-----KPSGDYDILVMSFPSSVYSVFLTQNSLSAAPVQYD-RMVREIQ 54 Query: 60 SGIRAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKV 119 I AI VNSG ANA TGE+G+ NA RMAE A L+I E VLV STGVIGVQLPM+KV Sbjct: 55 DEISAIVVNSGNANAATGEEGLRNAERMAEIVADLLDIDKEEVLVFSTGVIGVQLPMDKV 114 Query: 120 ESGIEEAVKNLSK-DPVPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNM 178 E GI+EAVKNL + D A AIMTTD+ K + I+GK + GIAKG+GMIHPNM Sbjct: 115 EKGIKEAVKNLERWDLERSARAIMTTDSFPKFYQTSGMIDGKTFHIKGIAKGAGMIHPNM 174 Query: 179 ATMLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQE 238 ATML++I TD + + L+K K+ V+ ++N IDVDG STND +++A G + ++ Sbjct: 175 ATMLAYIFTDVKIDKSLLEKASKLVVERTFNSIDVDGCESTNDSFLVVA---TGESDLEI 231 Query: 239 ETDGFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLV 298 + + ++EV LA+ IV+DGEGATK+I++ V NA + A+ + +AI SNL Sbjct: 232 NDKNKIEFAKKLYEVALQLAKMIVKDGEGATKLIQINVHNAESKEEAKEVGQAIARSNLF 291 Query: 299 KTAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKKI 358 KTA++G D NWGR+++A G D + L+ + +G+ VD+D + A + Sbjct: 292 KTAMFGNDPNWGRILSAVGQLHRDIDFSNVKLYIGD-----YLIYSGEPVDYDREGAVRY 346 Query: 359 LSE-KKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 L E ++ I L +++G+ + CDLT +YVEIN Y T Sbjct: 347 LKENSEITIDLYLERGESEWTYYTCDLTYRYVEINAEYTT 386 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: 382 Number of extensions: 21 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: 397 Length of database: 386 Length adjustment: 31 Effective length of query: 366 Effective length of database: 355 Effective search space: 129930 Effective search space used: 129930 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