Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_019557719.1 F612_RS0110440 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000381085.1:WP_019557719.1 Length = 392 Score = 233 bits (595), Expect = 5e-66 Identities = 135/373 (36%), Positives = 208/373 (55%), Gaps = 24/373 (6%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEM 71 +G+G + D +G+ YLD I+GI V LGHAHP + +Q ++++ ++ +++ + Sbjct: 18 KGDGATLQDSEGKMYLDAISGIAVTSLGHAHPFISEAICKQSQQLIHTSNLYHIKKQQML 77 Query: 72 LEELSHWVDYEYVYMGNSGTEAVEAAIKFAR-----LATGRSEIVAMTNAFHGRTLGSLS 126 ++L E V+ NSG EA EAAIK A+ IV M N+FHGRT+ +LS Sbjct: 78 ADQLIELSGMEQVFFCNSGAEANEAAIKIAKKFGHQQGITNPTIVVMENSFHGRTMATLS 137 Query: 127 ATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAIT--KETAAVIFEPIQGEGGIVPADEEF 184 AT K EGF PLV GF +PF+NV AA EA++ ++ A++ EPIQGEGG+ + + Sbjct: 138 ATGNPKVHEGFQPLVGGFTRVPFDNV-AAVEALSDNRDIVAILVEPIQGEGGVYVPQKGY 196 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL- 242 +K LR + + LL+ DE+Q+G+ RTG++ A +H + PD++T+ K +GNG P+ + Sbjct: 197 LKALRKICDANNWLLMIDEIQTGMGRTGQWFAFQHENITPDVLTLAKALGNGVPIGACIA 256 Query: 243 ----TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEK----FMEFSG--- 291 TD+ P G HG+TFGGNPLAC + +L+ + +K +F Sbjct: 257 NNKATDVLAP-GNHGTTFGGNPLACAVGLAVIEVLKTHNYIPAIAKKGALLLNQFKSALT 315 Query: 292 --ERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEE 349 + RG+G MIGI L RP VK ERG+L+N +RLLP ++ +E Sbjct: 316 QQPGISSIRGQGYMIGIQLDRPCAELVKMALERGLLINVTRGDTVRLLPSFVMSQQQTDE 375 Query: 350 ARKEIEGVLNDIL 362 ++ ++ D L Sbjct: 376 LVTKLSQLIIDFL 388 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: 328 Number of extensions: 18 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: 392 Length adjustment: 30 Effective length of query: 332 Effective length of database: 362 Effective search space: 120184 Effective search space used: 120184 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