Align Arginine biosynthesis bifunctional protein ArgJ, chloroplastic; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate WP_015411128.1 MM_RS02540 glutamate synthase
Query= SwissProt::Q3C251 (460 letters) >NCBI__GCF_000007065.1:WP_015411128.1 Length = 395 Score = 286 bits (731), Expect = 1e-81 Identities = 175/416 (42%), Positives = 241/416 (57%), Gaps = 27/416 (6%) Query: 50 KQIDGGVTAAKGFKAAGLYGGLRAKGEKPDLALVTCDVDAISAGAFTKNVVAAAPVLYCK 109 KQI+GG+ A +G A G+ G K +A++ + A AG FT+N V AAPV + Sbjct: 2 KQIEGGICAVRGVSAYGIKPG------KMGIAVIRAEGPA--AGVFTRNKVVAAPVTLSR 53 Query: 110 KALDISETARAVLINAGQANAATGDAGYQDVIECVNNLSKILQIRPEEILVESTGVIGHR 169 + ++ AV+ N+G ANA TGD G+ D +E + +++ L + P+ + V STGVIG R Sbjct: 54 ERIETEHRLSAVIANSGNANAFTGDDGFLDAMEMASMVAENLGLDPDNVAVASTGVIGRR 113 Query: 170 IKKDALLNSLPQLVRSLSSSVGGAASAAVAITTTDLVSKSVAIESQVGGSTIRIGGMAKG 229 + + LP+++ L SS + +AA AI TTD K A+E G +RIG +AKG Sbjct: 114 LDVSFIKEHLPEVLEGLGSSPECSRAAAKAIMTTDRALKESAVELDCG---VRIGAIAKG 170 Query: 230 SGMIHPNMATMLGVVTTDAVVACDVWRKMVQISVDRSFNQITVDGDTSTNDTVIALSSGL 289 SGMI PNM TML TDA V DV ++I+VD++FN + VDGDTSTND V+ S+ Sbjct: 171 SGMIEPNMGTMLCFAYTDAKVPADVLDAALKIAVDKTFNMVVVDGDTSTNDMVLFTSTCK 230 Query: 290 SGFNSNIISSLKSREAGQLQECLDVVMQGLAKSIAWDGEGATCLIEITVSGASTEAEAAK 349 SG + L E G L V LAK +A DGEGAT LIE V+GA +A Sbjct: 231 SGVKP-CLDCLDDFEEG-----LVCVFTDLAKKMAKDGEGATKLIEARVTGAKKYEDARL 284 Query: 350 VARSVAGSSLVKSAIYGRDPNWGRIAAAAGYAGVPFDQMKLKVSLGNILLMDGGEPQSFD 409 VA+++ S LVKSAI+G+DPNWGR+ AAAGY+G +Q +L +S GGE Sbjct: 285 VAKTIVRSPLVKSAIFGKDPNWGRVVAAAGYSGAELEQERLTLSFSG-----GGEEVELV 339 Query: 410 RA-----AASNYLRRAGETHDTVRIFISIGDGQGEGRAWGCDLSYDYVKINAEYTT 460 +A A+ L + +D + I + + G+ AWGCDL+YDYV+INAEYTT Sbjct: 340 KAGEISTASDLSLLKKIMANDEIIINLDLAMGEESATAWGCDLTYDYVRINAEYTT 395 Lambda K H 0.316 0.131 0.375 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: 402 Number of extensions: 19 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: 460 Length of database: 395 Length adjustment: 32 Effective length of query: 428 Effective length of database: 363 Effective search space: 155364 Effective search space used: 155364 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 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