Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_068458903.1 APY04_RS00380 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_001541235.1:WP_068458903.1 Length = 398 Score = 226 bits (575), Expect = 1e-63 Identities = 137/372 (36%), Positives = 200/372 (53%), Gaps = 22/372 (5%) Query: 13 GEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEML 72 G+G ++ +G RYLD AGI VN LG++HP V + RQ K+ ++ E + Sbjct: 19 GDGAWLTTIEGDRYLDFGAGIAVNALGYSHPHVVAALERQGRKLWHLSNVYRIAGAERLA 78 Query: 73 EELSHWVDYEYVYMGNSGTEAVEAAIKFARL---ATGRSE---IVAMTNAFHGRTLGSLS 126 E L+ + + NSG EA E AIK AR A G+ E I+ AFHGRTL +++ Sbjct: 79 ERLTEACFADVAFFANSGAEANECAIKIARRNQHACGKPERWRIITFAGAFHGRTLATMA 138 Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFVK 186 A +KY +GFGP V GF P ++ A + A+ +TAA++ EP+QGEGGI +F++ Sbjct: 139 AGGNRKYLDGFGPAVDGFDLCPLEDIAAVRNAVGAQTAAIMIEPVQGEGGIRQVSFQFLR 198 Query: 187 TLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLTDL 245 LR+L ++ G LLI DE+Q GL RTG A + V PDI+T+ KG+G GFP+ L Sbjct: 199 QLRELCDEQGLLLIFDEIQCGLGRTGYLFAHQEAEVAPDIMTLAKGLGGGFPIGACLATR 258 Query: 246 E----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSGE--------- 292 + G HGSTFGGNPLA L I++ D + + K E Sbjct: 259 HAGEGMTPGSHGSTFGGNPLAVAVANAVLDIVQSDEFLAEVRRKGDLMRAELAAVASRFP 318 Query: 293 -RVVKTRGRGLMIGIVLRRPAGNYVKALQERG-ILVNTAGNRVIRLLPPLIIEGDTLEEA 350 VV+ RG G+M+GI PA +AL+ G +L A + + R+LPPLI+ + + Sbjct: 319 NMVVEIRGCGMMLGIKCALPAPQIAEALRVHGKVLTIPASDDITRILPPLIVTDGEIRQF 378 Query: 351 RKEIEGVLNDIL 362 + ++ L ++ Sbjct: 379 AQRLQLALGAVV 390 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: 360 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: 398 Length adjustment: 30 Effective length of query: 332 Effective length of database: 368 Effective search space: 122176 Effective search space used: 122176 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