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 WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= metacyc::MONOMER-18314 (387 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 248 bits (632), Expect = 3e-70 Identities = 136/399 (34%), Positives = 218/399 (54%), Gaps = 23/399 (5%) Query: 3 LIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISI 62 ++ YG + I +GE VWD EG+ YLDF GI LGH +P+++ + Q++ + Sbjct: 29 VMNTYGRFPIAIERGEGCRVWDTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQIKRLHH 88 Query: 63 LSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRK------KI 116 +S + P++ E+ Q L ++ D A NSG EA E A+K ARK K I Sbjct: 89 VSNLYYIPVQGELAQWL--IQHSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIENPTI 146 Query: 117 IAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNI-------EDLSKIDNETA 169 + +FHGRT +++ T KY + F PL+ ++ +N+I E+L K + A Sbjct: 147 LTAHASFHGRTLATMTATGQPKYHKGFSPLMPGFYYVPYNDIAAIESAIEELDKDKRQVA 206 Query: 170 AVIVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVP 229 A+++E +QGE G+ P ++ + K ++E G LLI DE+Q G GR+GK+W Y++ I P Sbjct: 207 AIMLEALQGEGGIRPGDMTYFKRIREICNEKGILLILDEVQAGMGRSGKIWGYENLGIEP 266 Query: 230 DILTAGKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVV 289 DI T+ K +GGG P+ + H + E G H ST+GGNP A A A C +E+EN++ Sbjct: 267 DIFTSAKGLGGGIPIGAMLCKSH-CDVFEPGSHASTFGGNPFACAVALAVCHTLEQENLL 325 Query: 290 EQANQKGQQFSNILVKNLADL--KVVREVRGKGLMIGIDIR----FQPGQVLKYLQEKGI 343 Q+G + I +K +AD + EVRG GL+ G+++ ++K +G+ Sbjct: 326 ANVQQRGDEL-RIELKAIADKYPNLFSEVRGWGLINGLELNATATLTSIDIVKAAMNEGL 384 Query: 344 LAVKAGSTVIRFLPSYLITYENMEEASNVLREGLLKIEN 382 L V AG V+RF+P ++T ++EA ++L + + N Sbjct: 385 LIVPAGPKVLRFVPPLIVTETEVKEAMDLLAKAIANTVN 423 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: 386 Number of extensions: 20 Number of successful extensions: 6 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: 423 Length adjustment: 31 Effective length of query: 356 Effective length of database: 392 Effective search space: 139552 Effective search space used: 139552 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 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