Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012505186.1 PAES_RS02955 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000020625.1:WP_012505186.1 Length = 397 Score = 258 bits (658), Expect = 3e-73 Identities = 149/371 (40%), Positives = 217/371 (58%), Gaps = 23/371 (6%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R L + G+GVY++DE RYLD+I+GIGVN LG+ + + Q +KI+ A +F Sbjct: 20 RLPLAITHGKGVYLFDENSNRYLDMISGIGVNALGYGDERLIEAIHDQAKKIIHASNLFM 79 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAMTNAFH 118 + + ++ +L V+ NSGTEA+EAA+K +R +TG+ EI++++N FH Sbjct: 80 LEPQFKLASKLLDISGLSKVFFANSGTEAIEAAMKLSRKWASLSGSTGKKEILSLSNCFH 139 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GRT G++S T K KY EGF PL+PG I FN++E K IT TAAV E +QGEGGI Sbjct: 140 GRTYGAMSLTAKPKYLEGFDPLLPGTGSIAFNDIEDLKRKITSNTAAVFIEFVQGEGGIH 199 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237 EFV+ L+ L E L++ADE+Q+G RTGKF + H+ + PD+V + K +G G P Sbjct: 200 QISREFVEELKKLRETHNFLIVADEIQAGCGRTGKFFSYMHFDIDPDLVCVAKPLGGGLP 259 Query: 238 VSLTLTDLEI----PRGKHGSTFGGNPLACRAVATTLRILRRDRLVE---------KAGE 284 + + ++ G HG+TFGGNP+AC A + L +++E KA Sbjct: 260 LGAVIGSRKVQDVFAAGNHGTTFGGNPVACAAGHALIETLYSKKIMEHALATGSWIKAAL 319 Query: 285 KFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEG 344 + + ++ + R GLMIGI + R A YV+ +R +LVN VIRLLPPL I Sbjct: 320 TKLAETHTQIQEIRQYGLMIGITVNRDAAYYVQESLKRRVLVNATSQNVIRLLPPLTI-- 377 Query: 345 DTLEEARKEIE 355 T+EEA++ I+ Sbjct: 378 -TVEEAQQCID 387 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: 352 Number of extensions: 17 Number of successful extensions: 5 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: 397 Length adjustment: 30 Effective length of query: 332 Effective length of database: 367 Effective search space: 121844 Effective search space used: 121844 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