Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 238 bits (608), Expect = 2e-67 Identities = 143/367 (38%), Positives = 201/367 (54%), Gaps = 21/367 (5%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEM 71 +GEG ++ GRR+LD AG+ VN LGHAHP V + Q K+ ++ +E + Sbjct: 19 QGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPGQERV 78 Query: 72 LEELSHWVDYEYVYMGNSGTEAVEAAIKFARL---ATGRSE---IVAMTNAFHGRTLGSL 125 E L + + N+G EA+E IK AR GR E IVA T +FHGRT+ +L Sbjct: 79 AERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGSFHGRTIATL 138 Query: 126 SATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFV 185 +A KY EGFGP+ GF H+P+ ++EAA+ AI TAA++ EP+QGEGGI PAD ++ Sbjct: 139 AAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAIGSNTAALLVEPVQGEGGIRPADPAYL 198 Query: 186 KTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLTD 244 + LR L + G LL+ DEVQ+G+ RTGK A E G+ PD++ + KG+G GFPV L Sbjct: 199 RGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMGLAKGLGGGFPVGAVLAT 258 Query: 245 LE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSGE-------- 292 + + G HG TFGGNPLA L + +E+ G Sbjct: 259 EKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAVAALLRGRLDDLARRY 318 Query: 293 --RVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEA 350 + + RG+GLM+G+ + L G+L AG+ V+RL+PPLII +E A Sbjct: 319 PGAIAQVRGQGLMLGLKTVPVNTEFNAKLFAAGLLAVGAGDNVVRLVPPLIIGEAEVERA 378 Query: 351 RKEIEGV 357 + I+GV Sbjct: 379 VEIIDGV 385 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: 385 Number of extensions: 20 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: 388 Length adjustment: 30 Effective length of query: 332 Effective length of database: 358 Effective search space: 118856 Effective search space used: 118856 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