Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_041466176.1 CPAR_RS07660 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000020505.1:WP_041466176.1 Length = 402 Score = 230 bits (587), Expect = 4e-65 Identities = 134/376 (35%), Positives = 205/376 (54%), Gaps = 20/376 (5%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R L + +G +++ G RYLD+IAGIGVN +G+ ++ Q K + +F Sbjct: 21 RLPLDIAYAKGSFLYTSGGDRYLDMIAGIGVNAIGYGDQRLEHAITEQAAKYIHVSNLFM 80 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLA------TGRSEIVAMTNAFH 118 + ++ L V+ NSGTEA+EAAIK AR T +++++++TN FH Sbjct: 81 QKPQFDLAATLLEISGMSKVFFCNSGTEAIEAAIKLARRFAARNGDTSKTQVLSLTNCFH 140 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GRT G+LS T K KY GF PLVP I FNN+E + ++ TAAV E +QGEGGI Sbjct: 141 GRTYGALSLTAKPKYVGGFEPLVPETGMIDFNNIEDLERKVSSRTAAVFVEFVQGEGGIH 200 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237 E F+ L++L + L++ADE+Q+G RTG F + + ++PD+V + K +G G P Sbjct: 201 KVSEAFIARLKELAAEHDFLIVADEIQAGCGRTGSFFSYMPFDIQPDLVCVAKPLGGGLP 260 Query: 238 VSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGE--------- 284 + + ++ G HG+TFGGNP+AC A + ++ D+L+E A E Sbjct: 261 LGAIIGTEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAIKADKLMENAIETGAMMRAAF 320 Query: 285 KFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEG 344 + M ++++ R GLMIGI + R A YV +R +LVN VIRLLPPL I Sbjct: 321 EKMAEKHAQILEIRQYGLMIGITVNREAKYYVDEALKRNVLVNATSQNVIRLLPPLSISK 380 Query: 345 DTLEEARKEIEGVLND 360 + + ++ + ++ Sbjct: 381 EEAQLCLDTLDAIFSE 396 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: 296 Number of extensions: 14 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: 402 Length adjustment: 30 Effective length of query: 332 Effective length of database: 372 Effective search space: 123504 Effective search space used: 123504 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