Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_015739795.1 ADEG_RS09255 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= SwissProt::Q9K8V3 (411 letters) >NCBI__GCF_000024605.1:WP_015739795.1 Length = 399 Score = 393 bits (1009), Expect = e-114 Identities = 208/396 (52%), Positives = 266/396 (67%), Gaps = 2/396 (0%) Query: 16 GSVTSAKGFSAVGIHTGVKRKRKDLGAIVCEVPASSAAVYTLNKVQAAPLKVTQESIAVE 75 G VT+ KGF A G+ G+KR +KDL +V EVPA++A V+T N+V+AAP+ +TQ +A E Sbjct: 6 GGVTAPKGFLANGVAAGIKRYKKDLALVVSEVPAAAAGVFTTNRVKAAPVLLTQSRVA-E 64 Query: 76 GKLQAMIVNSGIANACTGKRGLDDAYTMRAVGAETFHIPEHYVAVTSTGVIGEFLPMDVI 135 G+ QA+IVNSG ANACTG GL DA M AE +PE V V+STG+IGE LP++ I Sbjct: 65 GQAQAVIVNSGNANACTGLEGLADARLMARAAAEALSLPEEMVLVSSTGIIGERLPVEKI 124 Query: 136 TNGIRQLKPEATIEGAHAFNEAILTTDTVEKHTCYQTIVNGKTVTVGGVAKGSGMIHPNM 195 + +L EG A EAI+TTDTV K + ++ G T +GG+AKGSGMIHP M Sbjct: 125 LKALPELVKGLGREGHRAAAEAIMTTDTVPKEAAVEFLLEGFTCRIGGMAKGSGMIHPCM 184 Query: 196 ATMLSFVTTDANIDHGHLQGALSAITNETFNRITVDGDTSTNDMVVVMASGLAENEALTP 255 ATML+F+TTD I L+ AL + +TFN ITVDGDTSTNDMV+V+A+G A N + Sbjct: 185 ATMLAFLTTDVAITPELLKLALREVVEDTFNLITVDGDTSTNDMVLVLANGQASNPMIEK 244 Query: 256 EHPDWANFYKALQLACEDLAKQIARDGEGATKLIEVEVTGAANDQEAGMVAKQIVGSDLV 315 E P +A F +AL LA+QIARDGEGAT+LIEV+V GA +EA A+ + S+LV Sbjct: 245 EGPAYATFKQALYEVAASLARQIARDGEGATRLIEVQVEGACTKEEARRAARAVAASNLV 304 Query: 316 KTAIYGADANWGRIICAIGYSGCEVNQETIDIAIGPIVTLKQSEPTGFSEEEATAYLKEA 375 K A++G D NWGRI+CA+GYSG + E + + +GP+ + + + T F EEEA A L Sbjct: 305 KAAVFGKDPNWGRIVCALGYSGARFDPEKVAVWLGPVQVVAEGKGTSFDEEEARAAL-ST 363 Query: 376 DPVKISVNLHIGNGTGKAWGCDLTYDYVRINAGYRT 411 DPV I VNL G AWGCDLTYDYVRINA YRT Sbjct: 364 DPVIIRVNLGAGEARATAWGCDLTYDYVRINAHYRT 399 Lambda K H 0.315 0.131 0.373 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: 424 Number of extensions: 13 Number of successful extensions: 3 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: 411 Length of database: 399 Length adjustment: 31 Effective length of query: 380 Effective length of database: 368 Effective search space: 139840 Effective search space used: 139840 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: 42 (22.0 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