Align [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate Echvi_3847 Echvi_3847 N-acetyl-gamma-glutamyl-phosphate reductase, common form
Query= BRENDA::Q5JFW1 (330 letters) >FitnessBrowser__Cola:Echvi_3847 Length = 322 Score = 166 bits (419), Expect = 9e-46 Identities = 119/335 (35%), Positives = 176/335 (52%), Gaps = 37/335 (11%) Query: 2 IKAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRG-LDLRFTN-T 59 IK A++GA+GY GGEL+R+L HP E+ I S G+K+ +VHP+L G DL FT+ Sbjct: 4 IKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFTDEV 63 Query: 60 KEFDADVIFLAVPHGTSMEII--DDYLGSAKIIDMSADFRLREDLYREYYGEHKRPELIE 117 K D +FL +PHG + + + + IID+S DFR + Sbjct: 64 KTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFR----------------DESN 107 Query: 118 EFVYGLPELHRKEIRKAELVANPGCNATATILALYP--FRELTDEAIVDLKVSSSAG-GR 174 F+YGLPE++ + +A+ +ANPGC AT LAL P L I ++ S G G+ Sbjct: 108 GFLYGLPEVNASQTGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGK 167 Query: 175 RENVASIHPERSHVVRVYKPYHHRHEGEVIQETG-VKAAFTVHSV------DIIRGLLAT 227 + + + +R+ V VYK + H+H E+ Q G ++ F H + + RG+ T Sbjct: 168 KLSETTHFSQRNQNVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVT 227 Query: 228 IYFRFEGSTRELLRKLLVYKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGFAHDEENS 287 YF FEGS E + +Y D F + ++ D K V+ +N + +E Sbjct: 228 AYFPFEGSLEEAYK---IYHD--FYQNAAFTHVSEKDIDLKQVVSTNKCIVHL--KKEAG 280 Query: 288 RAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGL 322 + ++ SAIDNL+KG SGQAVQN NL FGL+E+ GL Sbjct: 281 QLVIYSAIDNLLKGASGQAVQNYNLAFGLNEKEGL 315 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: 301 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: 322 Length adjustment: 28 Effective length of query: 302 Effective length of database: 294 Effective search space: 88788 Effective search space used: 88788 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: 48 (23.1 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