Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 216 bits (549), Expect = 1e-60 Identities = 138/391 (35%), Positives = 210/391 (53%), Gaps = 16/391 (4%) Query: 1 MKLIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENI 60 M+L +Y + I K VWD ++YLD + G V +GH NP + L +QL + Sbjct: 1 MQLFDVYPLNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKV 60 Query: 61 SILSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFK 120 S S P++ ++ + L +V K L NSG EA E ALK A GRKK+IAF Sbjct: 61 GFYSNSVKIPLQVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFT 120 Query: 121 NAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNN---IEDLSKID-NETAAVIVEPI 176 AFHGRT+ +++VT N K P V FL FNN +E+ K NE +AVI+E I Sbjct: 121 GAFHGRTSLAVAVTDNPKIVAPVNQTEN-VIFLPFNNEIALEETFKAQGNEISAVIIEGI 179 Query: 177 QGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGK 236 QG G+ A+ F++ ++ + ++ I D +Q G+GRTG +++ + + D+ T K Sbjct: 180 QGVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAK 239 Query: 237 AIGGGFPVSVVFLPDHIANKLE--EGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQ 294 +G GFPV+ + IA+K + G+ G+T+GGN +A AA A +V+EK+N+++ A + Sbjct: 240 GMGNGFPVAGI----SIASKFKPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEE 295 Query: 295 KGQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQPGQVLK-YLQEKGILAVKAGSTVI 353 G N L+ L + V EVRG+GLMIGI++ + V K L I +A VI Sbjct: 296 VG----NYLIAELKKFEQVVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVI 351 Query: 354 RFLPSYLITYENMEEASNVLREGLLKIENKA 384 R LP+ +T + +E + + + KA Sbjct: 352 RLLPALNLTKAHADEFLAAFEKAVKGVGQKA 382 Lambda K H 0.317 0.136 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: 364 Number of extensions: 25 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: 387 Length of database: 382 Length adjustment: 30 Effective length of query: 357 Effective length of database: 352 Effective search space: 125664 Effective search space used: 125664 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: 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