Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000025485.1:WP_043795594.1 Length = 392 Score = 264 bits (675), Expect = 3e-75 Identities = 152/373 (40%), Positives = 219/373 (58%), Gaps = 23/373 (6%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEM 71 RGEGV++WD G+RYLD ++GI V LGHAHP + Q +++ ++ E+E + Sbjct: 18 RGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLIHTSNIYGVAEQERL 77 Query: 72 LEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGR-----SEIVAMTNAFHGRTLGSLS 126 L+ + V+ NSG EA EAAIK ARL R I+ ++FHGRTL +LS Sbjct: 78 GALLTEQAGMDRVFFANSGAEANEAAIKLARLHAHRRGIENPAILVAEHSFHGRTLATLS 137 Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITK--ETAAVIFEPIQGEGGIVPADEEF 184 AT +K + GF PLV GF +P+++++A + A T A++ EPIQGEGGI +++ Sbjct: 138 ATGNRKVQAGFEPLVQGFVRVPYDDLDAIETAATNRPNIVAILIEPIQGEGGIRLPSDDY 197 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL- 242 + LR++ + G LL+ DE+Q+G+ RTG+ A +H G++PD+VT+ KG+GNG P+ L Sbjct: 198 LVRLREICDRSGWLLMLDEIQTGMGRTGRLFAFQHAGIQPDVVTLAKGLGNGMPIGACLA 257 Query: 243 ----TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAG-------EKFMEFSG 291 ++ P G HGSTFGGNPLACR L L + L E A + G Sbjct: 258 RGAAAEVFSP-GSHGSTFGGNPLACRVGRAVLETLIDENLTENAAAQGAYLLDSLRAALG 316 Query: 292 ER--VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEE 349 E +V+ RGRGLM+GI L RP G V + G+L+N RVIRLLPPLII+ ++E Sbjct: 317 ETHGLVEIRGRGLMVGIELDRPCGELVGRALDAGLLINVTAERVIRLLPPLIIDRAQIDE 376 Query: 350 ARKEIEGVLNDIL 362 + G+++ L Sbjct: 377 LVATLTGLIHGFL 389 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: 378 Number of extensions: 19 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: 362 Length of database: 392 Length adjustment: 30 Effective length of query: 332 Effective length of database: 362 Effective search space: 120184 Effective search space used: 120184 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 Jul 25 2024. The underlying query database was built on Jul 25 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