Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_012674118.1 SULAZ_RS02205 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000021545.1:WP_012674118.1 Length = 386 Score = 268 bits (685), Expect = 2e-76 Identities = 166/402 (41%), Positives = 238/402 (59%), Gaps = 21/402 (5%) Query: 1 MFVPRGFSYAGVHCRIKRKRKDLGIIFSEVPCTA-AGVFTTNVVKAAPVIYDMEILGKNP 59 M + G + AG+ + D I+ + P + + VFT N + AAPV+YD ++ + Sbjct: 1 MNIKMGVAKAGI-----KPSGDYDILVVKFPLSVYSAVFTQNSLAAAPVLYD-RLVCEIQ 54 Query: 60 SGIRAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKV 119 I A+ +NSG ANA TG++G NA +M E TA+ L + V+V STGVIGVQLPM+KV Sbjct: 55 DRILALVINSGNANAATGQKGFENAEKMVEITAECLGLDKSEVMVFSTGVIGVQLPMDKV 114 Query: 120 ESGIEEAVKNLSK-DPVPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNM 178 E+GI++A +NL D A AI TTDT K + I+G+ TV GIAKG+GMIHPNM Sbjct: 115 ENGIKQACQNLQDLDLELAARAISTTDTFYKYYETTGMIDGEVFTVKGIAKGAGMIHPNM 174 Query: 179 ATMLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQE 238 ATML++I TD + +D L K K+ VD ++N I VDG STND +++A G I + Sbjct: 175 ATMLAYIFTDVKIDKDLLDKATKLVVDRTFNSISVDGCESTNDSFVVVATG-ESKVEIND 233 Query: 239 ETDGFW--KLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSN 296 ++ KLYE E LA+ IV+DGEGATK+IE+ V A + A+ + AI +SN Sbjct: 234 SNRVYFTKKLYEVALE----LAKMIVKDGEGATKLIEINVFQASSKEEAKKVGEAIATSN 289 Query: 297 LVKTAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAK 356 L KTA++G D NWGR+++A G D ++ L+ + NG+ ++FD A Sbjct: 290 LFKTAMFGNDPNWGRILSAVGQLHLDIDFSKVKLYLGDF-----LLYNGEPIEFDRSAAI 344 Query: 357 KIL-SEKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 + L + K++ I L + +G++ + CDL KYVEIN Y T Sbjct: 345 EYLKNNKEIVINLYLSRGEQEWTFYTCDLGYKYVEINAEYTT 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: 393 Number of extensions: 26 Number of successful extensions: 6 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 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