Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_013537136.1 THEAM_RS01940 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::Q5JFW1 (330 letters) >NCBI__GCF_000185805.1:WP_013537136.1 Length = 349 Score = 232 bits (592), Expect = 9e-66 Identities = 147/346 (42%), Positives = 198/346 (57%), Gaps = 25/346 (7%) Query: 2 IKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRGLDLRFTNTKE 61 +K +VGASGY G EL+RLL++HP +T +TSR+F G++V ++ P+L + E Sbjct: 9 VKVGIVGASGYTGAELLRLLSIHPNATVTYLTSRQFRGKQVKEIFPHLIRSPFEELSFDE 68 Query: 62 FD-------ADVIFLAVPHGTSMEIIDDYLGSA---KIIDMSADFRLRE-DLYREYYG-E 109 F+ DV+F +PH S + + ++ K+ID SADFR + Y YG E Sbjct: 69 FNPERAVELCDVVFCCLPHRASFPAVKALMEASSKVKVIDFSADFRFNSFETYESVYGVE 128 Query: 110 HKRPELIEEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFREL----TDE-AIVD 164 H EL +E VYGLPEL R++I+++ LVANPGC T+ ILALYP E TD +VD Sbjct: 129 HGARELFKEAVYGLPELFREQIKRSRLVANPGCYPTSAILALYPAVEAGAVDTDHPVVVD 188 Query: 165 LKVSSSAGGRRENVASIHPERSHVVRVYKPYHHRHEGEVIQETGVKAA-FTVHSVDIIRG 223 K S GR+E+V E + R Y HRH E+ ++ G+K+ FT H V + RG Sbjct: 189 SKSGVSGAGRKESVTFTFCEVNEDFRAYSVDGHRHGPEIAEKLGLKSVRFTPHLVPMNRG 248 Query: 224 LLATIYFRFEGSTRELLRKLLV-YKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGFAH 282 +L T YF+ E S EL YK E FVR+ T P V G+NF DI Sbjct: 249 ILTTAYFKTELSKEELQHLYENRYKGEFFVRVRTSP------PRTHDVAGTNFCDIYVTK 302 Query: 283 DEENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVY 328 D+E+ A+V+SAIDNL KG S QAVQNMNLMFGL E GL + ++ Sbjct: 303 DKESGLAVVVSAIDNLGKGASSQAVQNMNLMFGLPEEAGLKLFSLW 348 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: 298 Number of extensions: 16 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: 349 Length adjustment: 28 Effective length of query: 302 Effective length of database: 321 Effective search space: 96942 Effective search space used: 96942 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