Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_012991869.1 THAL_RS04200 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000025605.1:WP_012991869.1 Length = 378 Score = 236 bits (602), Expect = 8e-67 Identities = 151/380 (39%), Positives = 226/380 (59%), Gaps = 20/380 (5%) Query: 20 RKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGIRAITVNSGVANACTGEQ 79 + D+ ++ C A+ +FTTN ++ VIY ++ K + +RA+ +NSG AN G + Sbjct: 17 KPDILVVLLPQSCNASFLFTTNHFRSGSVIYSEKVFRKRGT-VRALVINSGNANCGVGPE 75 Query: 80 GMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESGIEEAVKNLSK-DPVPFA 138 +++A MAEK A L+I E VLV STGVIG LP+++V IE+A K L D + Sbjct: 76 AVLHAEMMAEKAAALLDIDPEEVLVFSTGVIGKPLPIDRVLQAIEDACKLLEPLDLKRAS 135 Query: 139 EAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATMLSFITTDANVSEDALKK 198 E I TTD K K +GK + V G AKG+GMIHP M TML+F+ T+A + ED L + Sbjct: 136 EVISTTDRYPKYDFVK---DGK-LEVYGFAKGAGMIHPQMGTMLAFLFTNALLEEDVLHE 191 Query: 199 LLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETDGFWKLYEAVHEVNQVLA 258 L + D ++N I VDG TSTND +++ G+ ++E+ K+ +AV EV+ LA Sbjct: 192 LHREVCDRTFNSITVDGCTSTNDSFGLISLGV-----VREDLQ---KVRKAVEEVSLSLA 243 Query: 259 EKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTAIYGEDANWGRVIAAAGY 318 KIVEDGEGATKVI+V V+NA AR++A + +S LVKTA++G D NWGR++AA G Sbjct: 244 TKIVEDGEGATKVIKVVVKNASIELKARMLAEKVATSLLVKTAVHGRDPNWGRIVAALGS 303 Query: 319 SGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKKILSEKKV-KIILDMKQGKELA 377 + D + + ++ + + +G+ + A+K + E V +II+D+++GK Sbjct: 304 TPFPIDQNSIRVYIGN-----HLLYDGKVHSKAVEAARKYMEENSVIEIIVDLREGKSSW 358 Query: 378 RAWGCDLTEKYVEINGRYRT 397 + CDL+ +YV IN Y T Sbjct: 359 TYYTCDLSCEYVRINSEYTT 378 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: 364 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: 378 Length adjustment: 30 Effective length of query: 367 Effective length of database: 348 Effective search space: 127716 Effective search space used: 127716 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