Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_078717746.1 B5D49_RS10955 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_900167125.1:WP_078717746.1 Length = 394 Score = 271 bits (694), Expect = 2e-77 Identities = 167/399 (41%), Positives = 232/399 (58%), Gaps = 12/399 (3%) Query: 3 VPRGFSYAGVHCRIKRK-RKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSG 61 +P+G++YA K+K R DLG+I S P AGVFTTN+ +AAPV L + + Sbjct: 4 LPKGYTYAVAAAGFKKKDRLDLGLIVSGPPAVCAGVFTTNLFQAAPVRVCRNALASSAT- 62 Query: 62 IRAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVES 121 +RAI VNSG ANACTGEQG+ + + +P VL +STGVIG +L +E + Sbjct: 63 VRAIVVNSGQANACTGEQGVRDCETVRGMVGDLAGVPARDVLPASTGVIGPRLKLELWRA 122 Query: 122 GIEEAVKNLSK-DPVPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMAT 180 + ++L + P A+A+MTTDT+ K+ S+ V + G + +LG+AKG+GMI PNMAT Sbjct: 123 ALPALQESLGQAGPEDVAQAMMTTDTRHKVASRVVELSGGRVRLLGMAKGAGMIGPNMAT 182 Query: 181 MLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAG-NAPIQEE 239 MLSF+ DA V +L D S+N + VDGDTSTND + LANG +G NA + Sbjct: 183 MLSFLVCDAQVDAAWWSGVLSREADRSFNRVIVDGDTSTNDTSLALANGASGVNADSAAD 242 Query: 240 TDGFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVK 299 + L +AV +V LA ++V D EG TKV + V A A L+ARA+ +S LVK Sbjct: 243 RE---ILAQAVRDVLHALAYELVRDAEGGTKVARICVTGAASDADAELVARAVGTSPLVK 299 Query: 300 TAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDT-AKKI 358 TA++G+DANWGRV+ AAG SGA F P++L L F G + V G+ D D + + Sbjct: 300 TALFGQDANWGRVVCAAGRSGAVFPPEKLTLRF----GDVLVFAQGRPESGDLDALLEPV 355 Query: 359 LSEKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 + + I +D+ G DLT +YV IN YR+ Sbjct: 356 MKASDIPIAIDLGAGTGSFEVLASDLTREYVSINADYRS 394 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: 367 Number of extensions: 18 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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