Align Alpha-aminoadipate--LysW ligase LysX; AAA--LysW ligase LysX; EC 6.3.2.43 (characterized)
to candidate WP_084544898.1 H566_RS23860 RimK family alpha-L-glutamate ligase
Query= SwissProt::Q5SH23 (280 letters) >NCBI__GCF_000482785.1:WP_084544898.1 Length = 370 Score = 117 bits (293), Expect = 4e-31 Identities = 81/218 (37%), Positives = 112/218 (51%), Gaps = 12/218 (5%) Query: 63 LAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLM--- 119 L L ALG+PV N P IE DK ATS+ L +A +P P T + EA R++ Sbjct: 110 LGVLHALVALGVPVYNDPRAIERAVDKAATSLLLHQAAIPTPPTWVTESAAEAERIVMRE 169 Query: 120 EAFGYPVVLKPVIGSWGRLLAKVTDRAAAEALLEHKEVLGGFQHQLFYIQEYVEKP---G 176 A G+ VV+KP+ GS G+ + V A + G +L Y+Q +V +P G Sbjct: 170 SAAGHAVVVKPLFGSQGKGIELVGRVDGAHVPMPDLRHFG----RLAYLQRFVPQPRTPG 225 Query: 177 RDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEVARLSVKAAEAVGGGVVAV 236 D RV VVG +A+ A+ R SAHWI N ARG + + C LT +A L+ +A+ A+G V Sbjct: 226 HDWRVMVVGGKAVTAMKRVSAHWIHNVARGAKCQRCELTPALAVLAERASAALGLDYAGV 285 Query: 237 DLFES--ERGLLVNEVNHTMEFKNSVHTTGVDIPGEIL 272 D+ S GL V EVN ++ T DI I+ Sbjct: 286 DIVPSAVAGGLQVIEVNGVAAWRGLQRVTDFDIAARIV 323 Lambda K H 0.319 0.136 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: 243 Number of extensions: 10 Number of successful extensions: 2 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: 280 Length of database: 370 Length adjustment: 28 Effective length of query: 252 Effective length of database: 342 Effective search space: 86184 Effective search space used: 86184 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 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