Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate GFF1682 PGA1_c17050 N-acetyl-gamma-glutamyl-phosphate reductase ArgC
Query= BRENDA::Q5JFW1 (330 letters) >FitnessBrowser__Phaeo:GFF1682 Length = 342 Score = 222 bits (566), Expect = 9e-63 Identities = 146/346 (42%), Positives = 192/346 (55%), Gaps = 26/346 (7%) Query: 3 KAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRGLDLR-FTNTKE 61 K A++GASGY G ELVRL++ HP +EI A+++ R AG + +V P+LR L+L E Sbjct: 4 KVAILGASGYTGAELVRLISQHPTIEIAALSAERKAGMTMAQVFPHLRHLELPVLCKIGE 63 Query: 62 FD---ADVIFLAVPHGTSMEIIDDYLGSAKIIDMSADFRLRE-DLYREYYGE-HKRPELI 116 D D+ F A+PH TS E+I KI+D+SADFRLR+ D Y ++YG H Sbjct: 64 IDFTGIDLCFCALPHKTSQEVIAALPQDLKIVDLSADFRLRDPDEYEKWYGNPHAALAQQ 123 Query: 117 EEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFREL----TDEAIVDLKVSSSAG 172 +E VYGL E +R+EI+ A LVA GCNA AL P D+ I+DLK + S Sbjct: 124 KEAVYGLSEFYREEIKSARLVAGTGCNAATGQFALRPLIASGVIDLDDIILDLKCAVSGA 183 Query: 173 GRRENVASIHPERSHVVRVYKPYH-HRHEGEVIQETG------VKAAFTVHSVDIIRGLL 225 GR +H E S Y HRH GE QE VK FT H V RG+L Sbjct: 184 GRSLKENLLHAELSEGYHGYAVGGTHRHLGEFDQEFSKIAGRPVKVQFTPHLVPANRGIL 243 Query: 226 ATIYFRFEGSTRELLRKLLV--YKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGFAHD 283 AT+Y + + T + + L Y DEPF+ L+ P +++ GSNF IG A D Sbjct: 244 ATVYVKGDAQT---IHQTLATAYADEPFIELLP----FGEAPSTRHIRGSNFCHIGVAAD 296 Query: 284 EENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVYP 329 R IV++A+DNL KG SGQA+QN NLM G +E TGL P++P Sbjct: 297 RIEGRTIVIAALDNLTKGSSGQALQNANLMLGEEETTGLMMAPLFP 342 Lambda K H 0.321 0.140 0.404 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: 311 Number of extensions: 22 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: 330 Length of database: 342 Length adjustment: 28 Effective length of query: 302 Effective length of database: 314 Effective search space: 94828 Effective search space used: 94828 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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