Align [LysW]-aminoadipate kinase; EC 2.7.2.- (characterized)
to candidate Dsui_1309 Dsui_1309 acetylglutamate kinase
Query= SwissProt::O50147 (269 letters) >FitnessBrowser__PS:Dsui_1309 Length = 293 Score = 122 bits (306), Expect = 9e-33 Identities = 85/274 (31%), Positives = 141/274 (51%), Gaps = 16/274 (5%) Query: 2 IVVKVGGAEGINY---EAVAKDAASLWKEGVKLLLVHGGSAETNKVAEALGHPPRFLTHP 58 IVVK GG + + A+D L G+ +++VHGG + + +G F+ Sbjct: 28 IVVKYGGNAMTDEHLKQCFARDVVLLKLVGMNVVVVHGGGPQIENMLGRVGKKGEFI--- 84 Query: 59 GGQVSRLTDRKTLEIFEMVYCGLVNKRLVELLQKEGANAIGLSGLDGRLFVGRRKTAVKY 118 Q R+TD +T+E+ EMV G VNK +V L+ + G A+GL+G DG + + +K + Sbjct: 85 --QGMRVTDAETMEVVEMVLGGQVNKDVVNLINRAGGKAVGLTGKDGGM-IRAKKLLLPN 141 Query: 119 VENGKVKVHRGDYTGTVEEVNKALLDLLLQAGYLPVLTPPALSYENEAINTDGDQIAALL 178 EN + G G + +++ +L+ L AG++PV+ P + + E N + D +A + Sbjct: 142 KENPDDLIDVGQ-VGDIVQIDPSLIGNLEGAGFIPVIAPIGVGKDGETYNINADVVAGKV 200 Query: 179 ATLYGAEALVYLSNVPGLLARYPDEASLVREIPVERIEDPEYLALAQGRMKRKVMGAVEA 238 A + AE LV L+N PG+L + L+ I ++I+D G M K+ A++A Sbjct: 201 AEVLKAEKLVLLTNTPGVLDK---AGQLITGITPKQIDDMVEDGTLSGGMLPKISSALDA 257 Query: 239 VRGGVKRVVFADARVENPIRRAL---SGEGTVVR 269 R GVK V D RVE+ + + G GT+++ Sbjct: 258 ARNGVKSVHIIDGRVEHALLLEILTDHGVGTMIK 291 Lambda K H 0.317 0.137 0.385 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: 231 Number of extensions: 22 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: 269 Length of database: 293 Length adjustment: 26 Effective length of query: 243 Effective length of database: 267 Effective search space: 64881 Effective search space used: 64881 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 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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