Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_028313185.1 G491_RS0100475 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000429905.1:WP_028313185.1 Length = 395 Score = 298 bits (764), Expect = 1e-85 Identities = 171/398 (42%), Positives = 250/398 (62%), Gaps = 17/398 (4%) Query: 5 RGFSYAGVHCRIKRKRK-DLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGI- 62 +GFS AG C +K+ K DLG+IF VP + AGVFT N V+AAPV+ D + + SG+ Sbjct: 10 QGFSAAGTACGLKKNGKPDLGMIFCSVPASVAGVFTRNKVQAAPVLLDKKNIS---SGVC 66 Query: 63 RAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESG 122 RA+ NSG AN CTG++G+ +A + L + E+VLV+STGVIG L +EK+ + Sbjct: 67 RAVVANSGCANCCTGKRGVDDAVETTRLASGNLGVDAENVLVASTGVIGKTLDVEKIRNA 126 Query: 123 IEEAVKNLSKDPV-PFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATM 181 V +LS D FA+AIMTTD K+ + + EG+ V+G+AKG+GMI P+MATM Sbjct: 127 FPRLVDSLSPDGFGAFAQAIMTTDNVPKVSAVQAEFEGQTFNVVGVAKGAGMIRPDMATM 186 Query: 182 LSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETD 241 L FI TD + + LK++L+ +VD S+N I +DGDTSTND V+++A+GL+ Q + Sbjct: 187 LCFICTDIQANPNTLKRVLRPAVDASFNRITIDGDTSTNDTVLLMASGLS-----QVAAN 241 Query: 242 GFWKLY-EAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKT 300 L+ +AV +V LA +V+DGEG KV+ ++++ A AR IA I S LVKT Sbjct: 242 RCMDLFQQAVDKVCLDLAHMLVKDGEGVNKVVTIDIQGADSDQDARQIADVIAHSPLVKT 301 Query: 301 AIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFD-EDTAKKIL 359 A +GEDANWGR++AAAG +G DP +D+FF +++ ++G G+D + E A +++ Sbjct: 302 AFFGEDANWGRLLAAAGRAGVPLDPYVVDIFF----NEVQMVKDGMGLDMEAEAMATEVM 357 Query: 360 SEKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 + + +D+K GK A CDL+ YV+IN YR+ Sbjct: 358 KLPEFTVKIDLKMGKGQASVLTCDLSYDYVKINADYRS 395 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: 427 Number of extensions: 13 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: 397 Length of database: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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