Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_012537583.1 AFE_RS14090 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::Q5JFW1 (330 letters) >NCBI__GCF_000021485.1:WP_012537583.1 Length = 344 Score = 211 bits (537), Expect = 2e-59 Identities = 141/349 (40%), Positives = 190/349 (54%), Gaps = 25/349 (7%) Query: 1 MIKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRG-LDLRFTNT 59 MI+A +VG +GY G EL+RLL HPEVE+ AITSR AGQ+V + PNLRG +L +T Sbjct: 1 MIRAGIVGGTGYTGVELLRLLLPHPEVELVAITSRAEAGQRVDEHFPNLRGHCNLSYTAP 60 Query: 60 KEF---DADVIFLAVPHGTSMEIIDDYLG-SAKIIDMSADFRLRE-DLYREYYG-EHKRP 113 DV+F A PHG +M+ L +IID+ ADFRL + +++ ++YG H+ P Sbjct: 61 DPAILGTLDVVFFATPHGVAMDSAPKLLAEGVRIIDLGADFRLPDAEVFAQWYGMAHRAP 120 Query: 114 ELIEEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFRE----LTDEAIVDLKVSS 169 E++ E YGLPE +R +I +A L+ANPGC TA IL L P D I D K Sbjct: 121 EVLGEACYGLPEYYRTKISEARLIANPGCYPTAVILGLAPLLAEGLLQEDTLIADCKSGV 180 Query: 170 SAGGRRENVASIHPERSHVVRVYKPYHHRHEGEV------IQETGVKAAFTVHSVDIIRG 223 S GR V I PE + V Y HRH E+ I T ++ FT H + +IRG Sbjct: 181 SGAGRSAKVGLILPETADSVSAYGVGGHRHRPEIEAVLSDISGTPLELQFTPHLMPMIRG 240 Query: 224 LLATIYFRF-EGSTRELLRKLLV--YKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGF 280 + AT+Y R + + L+ L Y EPFV ++ P + V G+N I Sbjct: 241 IHATLYGRLAQPMSDAALQDLFATRYASEPFVDVLP----FGSHPATRSVRGANMCLIA- 295 Query: 281 AHDEENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVYP 329 H + +VLS IDNL+KG +GQA+QNMN +F L E GL + P Sbjct: 296 VHQPRPGQVVVLSVIDNLVKGAAGQAIQNMNRLFSLAEDAGLMQIALLP 344 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: 351 Number of extensions: 14 Number of successful extensions: 7 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: 344 Length adjustment: 28 Effective length of query: 302 Effective length of database: 316 Effective search space: 95432 Effective search space used: 95432 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 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