Align Glutamate 5-kinase; EC 2.7.2.11; Gamma-glutamyl kinase; GK (uncharacterized)
to candidate Dsui_2134 Dsui_2134 aspartate kinase, monofunctional class
Query= curated2:Q7U842 (357 letters) >FitnessBrowser__PS:Dsui_2134 Length = 407 Score = 47.8 bits (112), Expect = 5e-10 Identities = 54/199 (27%), Positives = 88/199 (44%), Gaps = 19/199 (9%) Query: 1 MTLWVVKLGTSLLRGDTAATIAGFAAGIAAAFARGDRVVLVSSGAVGLGCQRLQLPQRPE 60 M L V K G + + + I A +A A G VV+V S G + + L + Sbjct: 1 MALIVQKYGGTSV--GSTERIKNVAKRVARWKAMGHDVVVVPSAMSGETNRLIGLAKEIS 58 Query: 61 TVVA---LQAAAATGQGQLMALYERALANHGIAVAQI------LVTRSDLADRRRYQNAS 111 + L A+TG+ + L A+ G+ ++T S R Q Sbjct: 59 ATPSPRELDVIASTGEQVTIGLLAMAIQEEGLKAKSYTGSQVRVLTDSTFTKARILQIDD 118 Query: 112 GTLQQLLQWGVLPVV------NENDAISPAELRFGDNDTLSALVAAAVGADQLILLTDVD 165 +++ L G + VV +EN I+ L G +DT + +AAA+ AD+ + TDVD Sbjct: 119 ERMRKDLAEGNVVVVAGFQGADENGNITT--LGRGGSDTSAVALAAALKADECQIYTDVD 176 Query: 166 RLYSADPRLVVDARPISDV 184 +Y+ DPR+V +AR + + Sbjct: 177 GVYTTDPRVVPEARKLDTI 195 Lambda K H 0.320 0.135 0.396 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: 183 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 357 Length of database: 407 Length adjustment: 30 Effective length of query: 327 Effective length of database: 377 Effective search space: 123279 Effective search space used: 123279 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: 50 (23.9 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