Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 6936060 Sama_0257 acetylglutamate kinase (RefSeq)
Query= BRENDA::A0A0H2X8L7 (447 letters) >FitnessBrowser__SB2B:6936060 Length = 262 Score = 108 bits (269), Expect = 3e-28 Identities = 82/259 (31%), Positives = 135/259 (52%), Gaps = 13/259 (5%) Query: 45 VVKVGGAVLRDDL--EALTSSLSFLQEVGLTPIVLHGAGPQLDAELSAAGIEKQTVNGLR 102 V+KVGGA+L+ ++ L + L E G +++HG G +D +L A G+E ++GLR Sbjct: 9 VLKVGGALLQCEMGMARLMDTARQLLEKGEQVVLVHGGGCLVDEQLKANGMETVKLDGLR 68 Query: 103 VTSPHALAIVRKVFQASNLKLVEALQQNGARATSITGGVFEAE------YLNRDTYGLVG 156 VT + I+ ++ KL LQ A+A ++ G+ + + + G+VG Sbjct: 69 VTPAEQMPIIAGALAGTSNKL---LQGAAAKAGVVSMGMSLCDANMVTAVIKDERLGMVG 125 Query: 157 EVKAVNLAPIEASLQAGSIPVITSLGETPSGQILNVNADFAANELVQELQPYKIIFLTGT 216 EV + +E L G +P+I+S+ G++LNVNAD AA+ L +L K++ L+ Sbjct: 126 EVSPKDAKALEFILAQGWLPIISSIAMGEDGELLNVNADQAASVLA-KLLGGKLVLLSDV 184 Query: 217 GGLLDAEGKLIDSINLSTEYDHLMQQPWINGGMRVKIEQIKDLLDRLPLESSVSITRPAD 276 G+LD +GKLI S+N S E D L++ I GM+VK+E ++ L V+ R + Sbjct: 185 SGVLDGKGKLIPSLN-SQEIDELVKLGVIEKGMKVKVEAALEVAQWLGQPVQVASWRDSG 243 Query: 277 LAKELFTHKGSGTLVRRGE 295 L + GT ++ E Sbjct: 244 QMAALIKGEAVGTQIQPQE 262 Lambda K H 0.318 0.134 0.383 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: 261 Number of extensions: 15 Number of successful extensions: 4 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: 447 Length of database: 262 Length adjustment: 29 Effective length of query: 418 Effective length of database: 233 Effective search space: 97394 Effective search space used: 97394 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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