Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate SMa2400 SMa2400 diaminobutyrate--2-oxoglutarate aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Smeli:SMa2400 Length = 470 Score = 186 bits (473), Expect = 8e-52 Identities = 135/405 (33%), Positives = 200/405 (49%), Gaps = 69/405 (17%) Query: 10 LVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAG-PMFEHDER 68 L G V D GR YLD +AG G LGH HPE + L++++ +G P+ D Sbjct: 53 LKSASGCIVTDVDGRSYLDCLAGAGTLALGHNHPEVI----ETLQQVLGSGLPLHTLDLT 108 Query: 69 EEMLEELSHWV----------DYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFH 118 + + + + + + SGT+AVEAAIK A+ ATGR+++V+ A+H Sbjct: 109 TPVKDRFVSDIFGTLPAGLRDEAKIQFCSPSGTDAVEAAIKLAKTATGRTDLVSFRGAYH 168 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIP-----------------------FNNVEAA 155 G + GSLS + G LVPG P F Sbjct: 169 GMSQGSLSLMGSLGPKASVGQLVPGAHFFPYPYAYRCPFGRGGNETATLAAEYFERALRD 228 Query: 156 KEAITKETAAVIFEPIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFL 214 E AAVI E +QGEGG++PA E+++ +R +T D+G LI DEVQSG+ RTG F Sbjct: 229 PEGGINRPAAVILEAVQGEGGVIPAPVEWLRAVRRVTRDLGIPLIVDEVQSGVGRTGSFY 288 Query: 215 AIEHYGVRPDIVTMGKGIGNGFPVSLTL--TDLEIPR-GKHGSTFGGNPLACRAVATTLR 271 A + G+ PD+V + K IG G P+++ + DL++ + G H TF GN LA A + TL Sbjct: 289 AFQKAGIIPDVVVLSKAIGGGLPLAVVIYREDLDLWKPGAHAGTFRGNQLAMAAGSKTLE 348 Query: 272 ILRRDRLVEKA--GEKFMEFSGERVV-------KTRGRGLMIGIVLRRPAG--------- 313 I+ R+RLVE+A + + + ER+ + RG GLM+G+ + P G Sbjct: 349 IIERERLVERAAIAGRRLRANLERIAAQTPYIGEVRGEGLMLGVEVVDPEGLPDALGHPP 408 Query: 314 ---NYVKALQER----GILVNTAG--NRVIRLLPPLIIEGDTLEE 349 + +Q GI++ T G V+RLLPPL+I +++ Sbjct: 409 HGQEIARMIQHEMFRAGIILETGGRFGSVLRLLPPLVISDAEIDQ 453 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: 433 Number of extensions: 21 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: 470 Length adjustment: 31 Effective length of query: 331 Effective length of database: 439 Effective search space: 145309 Effective search space used: 145309 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