Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate NP_349621.1 CA_C3020 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000008765.1:NP_349621.1 Length = 388 Score = 275 bits (703), Expect = 2e-78 Identities = 168/395 (42%), Positives = 237/395 (60%), Gaps = 18/395 (4%) Query: 3 VPRGFSYAGVHCRIKRKRKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGI 62 +P+GF G H IK+++ DLG+++SE C+AA VFT N P+I E + N + Sbjct: 6 IPKGFLCCGKHVGIKKRKLDLGVVYSEKLCSAAAVFTKNKFCGIPIIVGKENIKDNK--L 63 Query: 63 RAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESG 122 ++I V SGVAN TGE+G+ N R+ K + ELNI E++L SSTG+IG QLP++ + +G Sbjct: 64 QSIVVTSGVANVATGEEGLKNTYRILNKLSCELNIKSENILPSSTGIIGKQLPIDCIITG 123 Query: 123 IEEAVKNLSK-DPVPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATM 181 I +LSK + F AIMTTD ++KI S K+ + TVLGIAKGSGMI PNMATM Sbjct: 124 INGIKSSLSKYNWEEFNRAIMTTDKELKIKSCKIG----DATVLGIAKGSGMIEPNMATM 179 Query: 182 LSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETD 241 L++ TDA++ LK +LK +VD S+NMI +D DTST+D ILANG GN ++ Sbjct: 180 LAYFFTDASIKAVELKGILKRAVDKSFNMISIDHDTSTSDTAAILANGYVGNVNLEV--- 236 Query: 242 GFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTA 301 F K + ++ +A+ IV DGEG +K+IE V SA++IA++I++S LVK A Sbjct: 237 -FEKTFT---DMCIDMAKDIVRDGEGVSKLIEATVMGCSSFESAKVIAKSIINSPLVKIA 292 Query: 302 IYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKKILSE 361 IYG D NWGR+ A G S F+ D L E A + + G+ + + D ++ L + Sbjct: 293 IYGSDPNWGRIAMAIGKS---FEDDVDPLKIEIAFNSNVIYDKGKIYEENFDCIERYLRD 349 Query: 362 -KKVKIILDMKQGKELARAWGCDLTEKYVEINGRY 395 + KI ++ G A WG D TE Y+ IN Y Sbjct: 350 NNECKIQANLNVGDFAATVWGSDFTEDYIRINSYY 384 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: 396 Number of extensions: 18 Number of successful extensions: 6 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: 388 Length adjustment: 31 Effective length of query: 366 Effective length of database: 357 Effective search space: 130662 Effective search space used: 130662 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