Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_013643724.1 METBO_RS00600 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000191585.1:WP_013643724.1 Length = 390 Score = 269 bits (688), Expect = 8e-77 Identities = 137/369 (37%), Positives = 221/369 (59%), Gaps = 14/369 (3%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R ++ LV+G+ VWD G Y+D +AGI VN +GH++P+ + Q++K++ ++ Sbjct: 20 RHKIALVKGKDTTVWDADGNSYIDCVAGIAVNNVGHSNPKVGEAICNQVKKLIHTSNLYY 79 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGS 124 +E+ + + L ++ + NSG EA E AIK AR +G+ EI+ M N+FHGRT+ + Sbjct: 80 TEEQVTLAKLLVDVSPHQKAFFCNSGAEANEGAIKLARKHSGKGEIITMINSFHGRTITT 139 Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEF 184 ++AT + KY++GF PL PGFK+ P+ ++EA KE I+ TAAV+ EP+QGE G++ E + Sbjct: 140 ITATGQPKYQKGFEPLTPGFKYAPYGDIEAVKEMISPSTAAVLVEPVQGESGVIVPPEGY 199 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLT 243 +K L+++ ED LLI DEVQ+G RTG+ A + +GV PDI ++ K I GFP+ L Sbjct: 200 LKQLKEVCEDSNVLLIFDEVQTGFGRTGEMFASQTFGVTPDITSLAKAIAGGFPMGAVLA 259 Query: 244 DLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEF---------S 290 + ++ G H +TFGGNPL C A ++ + ++L++K+ E F Sbjct: 260 NNDVAESFVPGDHAATFGGNPLGCAAAKASINFILEEKLLDKSKENGSYFVEKLLKLQNQ 319 Query: 291 GERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEA 350 E + + RG+GLM+G+ ++ G V L + GI+VN A V+R +PPL I + ++ Sbjct: 320 HELINEVRGKGLMVGVEMKTDCGCMVDELFKEGIIVNCAAGNVLRFVPPLTITKEQIDTV 379 Query: 351 RKEIEGVLN 359 + VL+ Sbjct: 380 TAALNNVLS 388 Lambda K H 0.320 0.140 0.410 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: 341 Number of extensions: 17 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: 362 Length of database: 390 Length adjustment: 30 Effective length of query: 332 Effective length of database: 360 Effective search space: 119520 Effective search space used: 119520 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: 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