Align Arginine biosynthesis bifunctional protein ArgJ, chloroplastic; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate 8502162 DvMF_2872 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein (RefSeq)
Query= SwissProt::Q3C251 (460 letters) >FitnessBrowser__Miya:8502162 Length = 412 Score = 273 bits (697), Expect = 1e-77 Identities = 169/408 (41%), Positives = 232/408 (56%), Gaps = 13/408 (3%) Query: 51 QIDGGVTAAKGFKAAGLYGGLRAKGEKPDLALVTCDVDAISAGAFTKNVVAAAPVLYCKK 110 +I A KGF+ A G R G + DLALV D A++A FTKN+ AAPVL + Sbjct: 16 EIPAPCAAPKGFRFATAGAGFRKAG-RDDLALVVSDTPAVAAAVFTKNLFQAAPVLVARD 74 Query: 111 ALDISETARAVLINAGQANAATGDAGYQDVIECVNNLSKILQIRPEEILVESTGVIGHRI 170 L + ARAVLIN+GQANA TGD G + + ++ + P++IL STGVIG ++ Sbjct: 75 TLAHAPKARAVLINSGQANACTGDEGLANCRATLELVAAATGLAPQDILPASTGVIGAQL 134 Query: 171 KKDALLNSLPQLVRSLSSSVGGAASAAVAITTTDLVSKSVAIESQVGGSTIRIGGMAKGS 230 D ++P L L + G A AI TTD K + ++ G T+ + GMAKG+ Sbjct: 135 AMDKWAAAVPALAADLGNK--GPEDFAKAIMTTDAFPKFASRTVELSGGTVTLVGMAKGA 192 Query: 231 GMIHPNMATMLGVVTTDAVVACDVWRKMVQISVDRSFNQITVDGDTSTNDTVIALSSGLS 290 GMI PNMATML V DA V W+ + + +VD +FN++TVDGDTSTNDTV L++G S Sbjct: 193 GMICPNMATMLATVLCDADVEPAAWQALFRDAVDATFNRVTVDGDTSTNDTVFGLANGAS 252 Query: 291 GFNSNIISSLKSREAGQLQECLDVVMQGLAKSIAWDGEGATCLIEITVSGASTEAEAAKV 350 G + + + L L V+ +A + DGEGAT +I I V+GA +A+A Sbjct: 253 GV------AARGADLTVLGAALTGVLGDVAYMLVKDGEGATKVIHINVAGARDDADAELA 306 Query: 351 ARSVAGSSLVKSAIYGRDPNWGRIAAAAGYAGVPFDQMKLKVSLGNILLMDGGEPQSFDR 410 AR+V S LVK+A+YGRD NWGRI AA G +G F+ + VSL + L GG+P + D Sbjct: 307 ARTVGHSQLVKTAMYGRDANWGRIVAALGRSGATFNPAAVIVSLCGVELFRGGQPTNLDF 366 Query: 411 AAASNYLRRAGETHDTVRIFISIGDGQGEGRAWGCDLSYDYVKINAEY 458 A L+ D V + I +G+G G R DL++DY+ NA+Y Sbjct: 367 DA---LLKEPLAGRDIV-VNIMLGNGPGSYRLLASDLTHDYISCNADY 410 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: 461 Number of extensions: 20 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: 460 Length of database: 412 Length adjustment: 32 Effective length of query: 428 Effective length of database: 380 Effective search space: 162640 Effective search space used: 162640 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 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