Align Arginine biosynthesis bifunctional protein ArgJ, chloroplastic; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate Synpcc7942_1896 Synpcc7942_1896 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein
Query= SwissProt::Q9ZUR7 (468 letters) >FitnessBrowser__SynE:Synpcc7942_1896 Length = 414 Score = 436 bits (1120), Expect = e-127 Identities = 233/417 (55%), Positives = 301/417 (72%), Gaps = 8/417 (1%) Query: 56 QGSWKQIAGGVTAAKGFKAAGMYAGLRAAGKKPDLALVTCDVEAVAAGVFTTNVVAAAPV 115 Q +W++I+GG+TA +GF+AAG+ AGL+A+G+ PDLAL+ + +A+AA VFTT+ V AA V Sbjct: 2 QAAWQEISGGLTAPRGFQAAGITAGLKASGQ-PDLALIVSESDAIAAAVFTTSQVRAACV 60 Query: 116 VYCKKVLETSKTARAVLINAGQANAATGDAGYQDMLDCVGSIATLLKVKPEEVLIESTGV 175 + ++ L+ + ARA+L N+GQANAATGD G+ D ++ +A L++ +VL+ STGV Sbjct: 61 DFSRQQLDGNSIARAILCNSGQANAATGDQGWSDAVESAEQLAQALQIPSHQVLVASTGV 120 Query: 176 IGQRIKKEELLHALPTLVNSRSDSVEEADSAAVAITTTDLVSKSVAVESQVGGIKIRVGG 235 IGQRIK E L +P + + S E +AA AI TTDLV+K +A+E +G +R+GG Sbjct: 121 IGQRIKMEALRTGIPQAIAALSP--EGGPAAAQAILTTDLVAKQIALELPLGDRTVRIGG 178 Query: 236 MAKGSGMIHPNMATMLGVITTDALVESDIWRKMVKVAVNRSFNQITVDGDTSTNDTVIAL 295 +AKGSGMIHPNMATML IT DA V +W++M+ AV+RSFNQITVDGDTSTND V AL Sbjct: 179 IAKGSGMIHPNMATMLSFITCDAAVSPQLWQEMLSRAVDRSFNQITVDGDTSTNDCVFAL 238 Query: 296 ASGLSGSPSISSLNCKEAAQLQACLDAVMQGLAKSIAWDGEGATCLIEVTVKGTETEAEA 355 A+G S +P+I+ A QL+A L AV Q LAK+IA DGEGATCLIEV VKGT +A A Sbjct: 239 ANGQSRTPAITERG-PIADQLEAMLTAVCQHLAKAIARDGEGATCLIEVQVKGTADDAAA 297 Query: 356 AKIARSVASSSLVKAAVYGRDPNWGRIAAAAGYAGVSFQMDKLKISLGEFSLMESGQPLP 415 IAR++A SSLVK+A++GRDPNWGRIAAAAG AGV F + L + LGEF L+ +GQPLP Sbjct: 298 RAIARTIAGSSLVKSAIFGRDPNWGRIAAAAGRAGVQFNSENLGVRLGEFELLRNGQPLP 357 Query: 416 FDRDGASNYLKKTGE----VHGTVTIDISVGDGAAIGKAWGCDLSYDYVKINAEYTS 468 FDR+ AS YL+ TV I + VG G G AWGCDLSYDYV+INAEYT+ Sbjct: 358 FDRNAASQYLRDRAAGAYLQDDTVLIQVDVGAGTGQGVAWGCDLSYDYVRINAEYTT 414 Lambda K H 0.315 0.129 0.364 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: 504 Number of extensions: 15 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: 468 Length of database: 414 Length adjustment: 32 Effective length of query: 436 Effective length of database: 382 Effective search space: 166552 Effective search space used: 166552 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