Align Alpha-aminoadipate--LysW ligase LysX; AAA--LysW ligase LysX; EC 6.3.2.43 (characterized)
to candidate YP_004144858.1 Mesci_5758 ATP-dependent carboxylate-amine ligase
Query= SwissProt::Q5SH23 (280 letters) >NCBI__GCF_000185905.1:YP_004144858.1 Length = 406 Score = 53.1 bits (126), Expect = 1e-11 Identities = 56/189 (29%), Positives = 85/189 (44%), Gaps = 29/189 (15%) Query: 80 PEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWG--- 136 P IE C DK+ LA+AG+P P +AT+ + G PV+LKP +G+ Sbjct: 102 PTSIERCCDKFVQRQLLAEAGVPIPAYRVATNVADVESSAAEIGLPVILKPAVGTGSQGV 161 Query: 137 RLLAKVTDRAAAEALLEHKEVLGGFQH-----QLFYIQEYVEKPGRDIRVFVVGERAI-- 189 RL + + L EH L G +H ++E+ E P V+G I Sbjct: 162 RLCRNIHE------LAEHTTYLLGGKHIWRSPPRILVEEFAEGP--HYITHVMGHEVIGI 213 Query: 190 -AAIYRRSAHWITNTARGGQAENCPLTEEVAR------LSVKAAEAVGGGVVAVDLFESE 242 AA + R H++ RGG PLT++ + LS A ++G G ++L ++ Sbjct: 214 EAADFDRPPHFV---FRGG-IFPAPLTDDEHKRIIDTSLSCLQALSLGWGPTCIELRWTK 269 Query: 243 RGLLVNEVN 251 G +V EVN Sbjct: 270 CGPVVIEVN 278 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: 235 Number of extensions: 8 Number of successful extensions: 1 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: 406 Length adjustment: 28 Effective length of query: 252 Effective length of database: 378 Effective search space: 95256 Effective search space used: 95256 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: 49 (23.5 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