Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 209 bits (533), Expect = 8e-59 Identities = 138/373 (36%), Positives = 200/373 (53%), Gaps = 26/373 (6%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R L RG G + +G YLD +AGI N LGHAHP V + Q EK+ ++ Sbjct: 20 RAPLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNIYR 79 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATG---RSEIVAMTNAFH 118 E+EE+ + L + V+ NSGTEAVE A+K AR A G R +I +FH Sbjct: 80 IPEQEELADALCANSFADVVFFTNSGTEAVECALKTARKYHSANGQPERIDIYGFDGSFH 139 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAI-TKETAAVIFEPIQGEGGI 177 GRT +++A+ Y +GFGP +PG+ + F + +A K AI + TAA+I EP+QGEGG Sbjct: 140 GRTYAAVNASGNPSYVDGFGPRLPGYSQLTFGDHDAIKAAIASPTTAAIIVEPVQGEGGA 199 Query: 178 VPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIE-HYGVRPDIVTMGKGIGNG 235 + + LR L ++ G LLI DEVQ G+ RTGK A E G P I+ + K +G G Sbjct: 200 RSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAEGGEPHIMAVAKALGGG 259 Query: 236 FPVSLTLTDLEIPRG----KHGSTFGGNPLACRAVATTLRILRR----DRLVEKAGEKFM 287 FP+ L E +G HGSTFGGNPLA L I++ D + +G Sbjct: 260 FPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAALEIIKSPETLDNVKTVSGFFTQ 319 Query: 288 EFSG------ERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLI 341 + +G + +V RG+G++IG+ L +++ ++ +L+ G+ +RLLPPL Sbjct: 320 QLNGLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMVLARDEKLLIAGGGDNCVRLLPPLN 379 Query: 342 IEGDTLEEARKEI 354 + T+EEA + I Sbjct: 380 L---TIEEASEAI 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: 362 Number of extensions: 29 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 362 Length of database: 405 Length adjustment: 30 Effective length of query: 332 Effective length of database: 375 Effective search space: 124500 Effective search space used: 124500 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 09 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