Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_034272173.1 AMYHA_RS15990 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000504245.1:WP_034272173.1 Length = 393 Score = 249 bits (636), Expect = 9e-71 Identities = 148/349 (42%), Positives = 200/349 (57%), Gaps = 15/349 (4%) Query: 8 LRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDE 67 L LVRG+G V+D G YLDL+ GI VN LGHAHP V +S Q+ + ++ + Sbjct: 20 LELVRGDGATVFDADGNAYLDLVGGIAVNALGHAHPAVVEAVSEQVATLGHTSNLYINPV 79 Query: 68 REEMLEELSHWVDYE-YVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLS 126 + E L V NSG EAVEAAIK RL TG+S++VA FHGRT+G+LS Sbjct: 80 ALSLAETLLDIAGLSGKVLFCNSGAEAVEAAIKITRL-TGKSKLVACDGGFHGRTMGALS 138 Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFVK 186 T + RE F PL+PG H+PF + A + A+ +TAAV EP+ GEGG+VPA + F++ Sbjct: 139 VTGQPSKREPFEPLLPGVTHVPFGDTAALESAVDGDTAAVFVEPVLGEGGVVPAPDGFLR 198 Query: 187 TLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL--- 242 R++ GALL+ DEVQ+G+ R G + A + GV PD++T+ KG+G G P+ + Sbjct: 199 AAREIATAAGALLVLDEVQTGIGRLGSWFAFQQAGVTPDVITLAKGLGGGLPLGAVIGIG 258 Query: 243 -TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRL---VEKAGEKF----MEFSGERV 294 T + G+HG+TFGGNP+AC A +R +R L VE G+ + V Sbjct: 259 QTGELLKPGQHGTTFGGNPIACAAGHAVIRTIREQGLLDHVETLGKDLAAGVRKLDHPLV 318 Query: 295 VKTRGRGLMIGIVLRRP-AGNYVKALQERGILVNTAGNRVIRLLPPLII 342 + RG GL+ GI L +P A A Q G L+N VIRL PPLII Sbjct: 319 SEVRGAGLLQGIGLTKPVAPTVATAAQRAGYLINPVQPDVIRLAPPLII 367 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: 363 Number of extensions: 16 Number of successful extensions: 7 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: 393 Length adjustment: 30 Effective length of query: 332 Effective length of database: 363 Effective search space: 120516 Effective search space used: 120516 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 Jul 26 2024. The underlying query database was built on Jul 25 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