Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate YP_004144436.1 Mesci_5288 class III aminotransferase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000185905.1:YP_004144436.1 Length = 452 Score = 155 bits (393), Expect = 2e-42 Identities = 124/394 (31%), Positives = 197/394 (50%), Gaps = 51/394 (12%) Query: 10 LVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDERE 69 + + +G+++ D GRR++D G V+ LG+ HP V + +QL+++ A F + Sbjct: 56 IAKAQGIWIEDTAGRRFMDF-HGNSVHHLGYGHPRLVAAIKKQLDELCFAPRRFTCEPAV 114 Query: 70 EMLEELSHWV--DYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSA 127 E+ E+L+ + V G++A+E A+K AR ATGR + V+ +AFHG G+ S Sbjct: 115 ELAEKLAALAPGNLGKVLFTTGGSDAIEVALKIARAATGRFKTVSFWDAFHGAGFGAASV 174 Query: 128 TWKKKYREGF-GPLVPGFKHI--------PF--NNVEAAKEAIT----------KETAAV 166 + +R GP++ G +H+ P+ +++EA+ A ++ AAV Sbjct: 175 GGEATFRSHISGPMMTGTEHVAPWDGYRCPYGHDSLEASGLACANMIAYVLGCEQDVAAV 234 Query: 167 IFEPIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDI 225 + EP++ P F K +R+ + G LLI DEV +GL +TGKF A EH V PDI Sbjct: 235 VAEPMRATPN--PPPPGFWKRVREACDRHGTLLIFDEVPTGLGKTGKFFAHEHDDVTPDI 292 Query: 226 VTMGKGIGNG-FPVSLTLT--DLEIPRG--KHGSTFGGNPLACRAVATTLRILRRDRLVE 280 V +GK +G G P++ + DL++ G T NP+ RA TT+ I+ + LVE Sbjct: 293 VVLGKSLGGGVLPIAAIIARRDLDVTGGFAIGHYTHEKNPVTTRAALTTIDIILEEGLVE 352 Query: 281 KAGEKFMEFSGE---------RVVKTRGRGLMIGIVL------RRPAGNYVK----ALQE 321 +A E G V RGRGLM+G+ L R+PA + + A E Sbjct: 353 RAAELGRHMLGRMQHLMARSPHVGDVRGRGLMVGVELVEDRDTRQPARDLAERVFYACLE 412 Query: 322 RGILVNTAGNRVIRLLPPLIIEGDTLEEARKEIE 355 +G+ + V+ L PPL+I L+ A +E Sbjct: 413 QGLSFKISQGNVLTLSPPLVISKTDLDGALDIVE 446 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: 397 Number of extensions: 22 Number of successful extensions: 8 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: 452 Length adjustment: 31 Effective length of query: 331 Effective length of database: 421 Effective search space: 139351 Effective search space used: 139351 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