Align Arginine biosynthesis bifunctional protein ArgJ, chloroplastic; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_012408920.1 NPUN_RS11840 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q9ZUR7 (468 letters) >NCBI__GCF_000020025.1:WP_012408920.1 Length = 413 Score = 445 bits (1144), Expect = e-129 Identities = 238/414 (57%), Positives = 310/414 (74%), Gaps = 8/414 (1%) Query: 59 WKQIAGGVTAAKGFKAAGMYAGLRAAGKKPDLALVTCDVEAVAAGVFTTNVVAAAPVVYC 118 W++I GG+TA +G++AAG+ AGL+ +G PDLAL+ +VEA+AAGVFTT+ V AA V YC Sbjct: 4 WQRITGGITAPRGYQAAGITAGLKPSGL-PDLALIFSEVEAIAAGVFTTSQVKAACVEYC 62 Query: 119 KKVLETSKTARAVLINAGQANAATGDAGYQDMLDCVGSIATLLKVKPEEVLIESTGVIGQ 178 ++ L+ +ARA+L NAGQANAATG+ GY D L+ +IA L + E VL+ STGVIGQ Sbjct: 63 RQRLQAKPSARAILCNAGQANAATGNQGYLDTLESSLAIAHALNISSESVLLASTGVIGQ 122 Query: 179 RIKKEELLHALPTLVNSRSDSVEEADSAAVAITTTDLVSKSVAVESQVGGIKIRVGGMAK 238 RIK + L +P +V + S + +D+AA AI TTDLV+KS+A+E+ VG +R+GG+AK Sbjct: 123 RIKMDALRSGIPKVVAALSAT--GSDAAAGAIITTDLVTKSIALETIVGERPVRIGGIAK 180 Query: 239 GSGMIHPNMATMLGVITTDALVESDIWRKMVKVAVNRSFNQITVDGDTSTNDTVIALASG 298 GSGMIHPNMATML +T DA+V +W++M+ A +RSFN ITVDGDTSTND++IALA+G Sbjct: 181 GSGMIHPNMATMLAFVTCDAVVSPALWQQMLARAADRSFNSITVDGDTSTNDSLIALANG 240 Query: 299 LSGSPSISSLNCKEAAQLQACLDAVMQGLAKSIAWDGEGATCLIEVTVKGTETEAEAAKI 358 S +P+I EA +L+A L AV Q LAK+IA DGEGATCLIEV V G E A +I Sbjct: 241 QSRTPAIIEWGA-EAEKLEAMLTAVCQHLAKAIARDGEGATCLIEVEVTGAHDELSARQI 299 Query: 359 ARSVASSSLVKAAVYGRDPNWGRIAAAAGYAGVSFQMDKLKISLGEFSLMESGQPLPFDR 418 A+++A SSLVK+A++GRDPNWGRIAAAAG AG+ F+ + L+I LG F ++E+GQPL FDR Sbjct: 300 AKTIAGSSLVKSAIFGRDPNWGRIAAAAGRAGIPFEQENLQIKLGNFLMLENGQPLTFDR 359 Query: 419 DGASNYLKK--TGEV--HGTVTIDISVGDGAAIGKAWGCDLSYDYVKINAEYTS 468 AS YLKK TG TV I ++VG+G +GKAWGCDLSYDYV+INAEYT+ Sbjct: 360 AAASAYLKKAATGAYLQDDTVLISVNVGNGNGVGKAWGCDLSYDYVRINAEYTT 413 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: 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: 468 Length of database: 413 Length adjustment: 32 Effective length of query: 436 Effective length of database: 381 Effective search space: 166116 Effective search space used: 166116 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