Align Arginine biosynthesis bifunctional protein ArgJ, chloroplastic; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_011319855.1 AVA_RS15765 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q3C251 (460 letters) >NCBI__GCF_000204075.1:WP_011319855.1 Length = 413 Score = 454 bits (1167), Expect = e-132 Identities = 240/416 (57%), Positives = 312/416 (75%), Gaps = 10/416 (2%) Query: 49 WKQIDGGVTAAKGFKAAGLYGGLRAKGEKPDLALVTCDVDAISAGAFTKNVVAAAPVLYC 108 W++I GG+TA KG++AAG+ GL+ G PDLAL+ DV+AI+AG FT + V AA V YC Sbjct: 4 WQEITGGITAPKGYRAAGITAGLKPSG-LPDLALIVSDVEAIAAGVFTTSQVKAACVDYC 62 Query: 109 KKALDISETARAVLINAGQANAATGDAGYQDVIECVNNLSKILQIRPEEILVESTGVIGH 168 ++ L ++ARA+L NAGQANAATG G +D E + L+K L I PE IL+ STGVIG Sbjct: 63 RQRLQAKQSARAILCNAGQANAATGSQGIKDAEESADLLAKELNISPESILLASTGVIGQ 122 Query: 169 RIKKDALLNSLPQLVRSLSSSVGGAASAAVAITTTDLVSKSVAIESQVGGSTIRIGGMAK 228 RIK DAL N +P+LV SL+ + G+ +AA AI TTDLV+KS+A+E+ +G +RIGG+AK Sbjct: 123 RIKMDALRNGIPKLVASLTDA--GSDAAAGAIITTDLVTKSIALETTIGDRPVRIGGIAK 180 Query: 229 GSGMIHPNMATMLGVVTTDAVVACDVWRKMVQISVDRSFNQITVDGDTSTNDTVIALSSG 288 GSGMIHPNMATML VT DA V+ +W++M+ + DRSFN ITVDGDTSTND++IAL++G Sbjct: 181 GSGMIHPNMATMLAFVTCDAAVSPHLWQQMLTRAADRSFNSITVDGDTSTNDSLIALANG 240 Query: 289 LSGFNSNIISSLKSREAGQLQECLDVVMQGLAKSIAWDGEGATCLIEITVSGASTEAEAA 348 S + I+ + + E+ +L+ L V Q LAK+I DGEGATCLIE+ V+GA E A Sbjct: 241 QS--RTPAITEVGA-ESEKLEAMLTAVCQHLAKAITRDGEGATCLIEVQVTGAHDEQAAR 297 Query: 349 KVARSVAGSSLVKSAIYGRDPNWGRIAAAAGYAGVPFDQMKLKVSLGNILLMDGGEPQSF 408 ++A+++AGSSLVKSAI+GRDPNWGRIAAAAG AGVPF+Q L++ LG+ LL+D G+P F Sbjct: 298 QIAKTIAGSSLVKSAIFGRDPNWGRIAAAAGRAGVPFEQENLQIQLGDFLLLDNGQPLPF 357 Query: 409 DRAAASNYLRRAGE----THDTVRIFISIGDGQGEGRAWGCDLSYDYVKINAEYTT 460 DRAAAS YL++A DTV I +++G+G G G+AWGCDLSYDYVKINAEYTT Sbjct: 358 DRAAASAYLKQAATGAYLQQDTVLISVNVGNGHGTGKAWGCDLSYDYVKINAEYTT 413 Lambda K H 0.316 0.131 0.375 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: 493 Number of extensions: 17 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: 460 Length of database: 413 Length adjustment: 32 Effective length of query: 428 Effective length of database: 381 Effective search space: 163068 Effective search space used: 163068 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: 51 (24.3 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