Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_073039302.1 BUB04_RS11050 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_900129305.1:WP_073039302.1 Length = 397 Score = 269 bits (688), Expect = 8e-77 Identities = 146/370 (39%), Positives = 213/370 (57%), Gaps = 21/370 (5%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEM 71 RG G +WD +G+ Y+D +AGI V LGH+HPE + Q K+V +F + E+ Sbjct: 25 RGAGCRLWDTEGKEYMDFLAGIAVCNLGHSHPEVARVVCEQARKLVHVSNLFYTRPQVEL 84 Query: 72 LEELSHWVDYEYVYMGNSGTEAVEAAIKFAR------LATGRSEIVAMTNAFHGRTLGSL 125 L + V+ NSG EA EAAIK AR GR I+ M ++FHGRTL +L Sbjct: 85 AARLIERSFADKVFFANSGAEANEAAIKLARKYSRDKYGPGRFHIITMKDSFHGRTLATL 144 Query: 126 SATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFV 185 SAT ++K +GF PLV GF+ +P+N+++A +EA+T++T AV+ EPIQGEGG+ P D ++ Sbjct: 145 SATGQEKVHKGFDPLVEGFRFVPYNSIQAVEEAVTEKTCAVLVEPIQGEGGVRPGDPDYF 204 Query: 186 KTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLTD 244 + LR+L LLI DEVQ+G+ RTG A E GV PD++T+ K +GNG P+ L Sbjct: 205 RALRELCTAKDLLLIFDEVQTGMGRTGSLFAYEQLGVTPDVMTLAKALGNGLPIGAMLAT 264 Query: 245 LEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSG--------- 291 E R G H STFGG PL A A L I+ ++ + EK F G Sbjct: 265 EEAARAFTPGSHASTFGGTPLVTAASAKVLEIISKEDFLADVREKGRYFLGRLQDLQKKH 324 Query: 292 -ERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEA 350 ++++ RGRGLM+G+ L RP V E+G ++N + V+R +PPLI+ + ++ Sbjct: 325 PDKILDARGRGLMLGLELSRPGKTVVDRCLEQGFVINCTHDTVLRFVPPLIVTREEIDRL 384 Query: 351 RKEIEGVLND 360 + ++ VL + Sbjct: 385 METLDAVLKE 394 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: 348 Number of extensions: 16 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