Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_011033352.1 MM_RS07280 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000007065.1:WP_011033352.1 Length = 395 Score = 281 bits (718), Expect = 3e-80 Identities = 147/362 (40%), Positives = 227/362 (62%), Gaps = 11/362 (3%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R+ L L +G+G V D G+ Y+D +AGI VN +GH HP V + Q EK++ ++ Sbjct: 32 RQPLVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAEKLIHVSNLYY 91 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGS 124 + + E E L+ E V+ NSG EAVEAA+K AR+ATG+S VA ++FHGRT+G+ Sbjct: 92 TEIQAEFAETLASITGMECVFFCNSGAEAVEAAMKLARVATGKSAFVAAEHSFHGRTIGA 151 Query: 125 LSATWKKKYREGFGPLVPG-FKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEE 183 LS T K YR+ F P V +P+++ +A ++AI+++TAAV+ EPIQGEGG+ D Sbjct: 152 LSVTHKSMYRDPFMPPVSSKTSFVPYSDADAIRKAISEDTAAVVLEPIQGEGGVNVPDPG 211 Query: 184 FVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVS--L 240 ++K +R++ ++ G LLI DEVQ+G RTG + E +GV PDI++M K IG GFP+ Sbjct: 212 YLKEVREICDETGTLLIFDEVQTGFGRTGTWFCKEQFGVEPDIMSMAKAIGGGFPMGAIA 271 Query: 241 TLTDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGE-------KFMEFSGER 293 + L RG+H STFGG PLAC A +++ ++ ++L+E++ E K + + Sbjct: 272 ARSGLSFGRGQHASTFGGGPLACAAALASIQAIKEEKLLERSKEMGAYFTKKLSGMARDD 331 Query: 294 VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEARKE 353 +V+ RG+GLMIG+ ++ P G +V +E G+LVN + V+RL+PPL+I + ++ Sbjct: 332 IVEVRGKGLMIGVEIKYPCGKFVDFAREHGVLVNCTSDSVLRLVPPLVITKEQIDSVVDV 391 Query: 354 IE 355 +E Sbjct: 392 LE 393 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: 321 Number of extensions: 15 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: 395 Length adjustment: 30 Effective length of query: 332 Effective length of database: 365 Effective search space: 121180 Effective search space used: 121180 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