Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= curated2:Q9RW75 (429 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 148 bits (374), Expect = 3e-40 Identities = 112/363 (30%), Positives = 173/363 (47%), Gaps = 41/363 (11%) Query: 25 KHDVVMVRGQGATVWDENGRSYIDCVVGYGV--ATLGHSHPDVVKAVQEQAGKLMVMPQT 82 K +++V G+G T+ D NG+ Y+D G GV +G+ + +AV EQ + T Sbjct: 33 KGPMIVVEGEGLTLRDINGKEYLDATSG-GVWCVNVGYGRERIARAVYEQMKAMPYYAAT 91 Query: 83 VPNDKRAEFLQELVGVLPQGLDRVFLCNSGTEAMEAAKKFAITAT------GRSRFVSMK 136 N EF Q+L+ +P GL R +L NSG+EA E A K + + + + Sbjct: 92 AGNIPYIEFAQKLLAHMP-GLTRAYLSNSGSEANEKAYKMVRSLAHLSGNPAKKKILFRA 150 Query: 137 RGFSGRSLGALSFTWEPKYREPFGDAVDNKSVDFV-----------TYGNLDELRAAVTE 185 R + G +LGALS T + + +E FG V V+F TY D A E Sbjct: 151 RDYHGTTLGALSSTGQAERKEWFGPLVPG-FVEFPHACCYRCAFNKTYPGCDIDCARAVE 209 Query: 186 Q---------TAAVIMEPVQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTG 236 + +I+EP+ GGV P AE+ I R G LLI+DE+ G RTG Sbjct: 210 RIIEQEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGRTG 269 Query: 237 KMFACEHFGVIPDGMTLAKAIAGG---------TPTAAFAMMSEVADRMPAGGHGTTFGG 287 MF +H+GV PD +T+AK +A T A +++ AD+M +T+GG Sbjct: 270 TMFGYQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTYGG 329 Query: 288 NPLSMAAGVASLRAMKREGLAEQAREKGAYMMDKLRAI-QSPKIREVRGLGLMIGVELKE 346 +A + ++ ++ E L + G Y++ L+ + P + +VRG GL+ G+EL + Sbjct: 330 CAAGCSAALENMAIIEEEKLLDNVNAMGDYLLAGLKELGDLPYVGDVRGKGLLCGIELVQ 389 Query: 347 KSA 349 A Sbjct: 390 DKA 392 Lambda K H 0.317 0.132 0.380 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: 414 Number of extensions: 18 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: 429 Length of database: 459 Length adjustment: 32 Effective length of query: 397 Effective length of database: 427 Effective search space: 169519 Effective search space used: 169519 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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