Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 8501786 DvMF_2502 glutamate-1-semialdehyde aminotransferase (RefSeq)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__Miya:8501786 Length = 425 Score = 129 bits (323), Expect = 2e-34 Identities = 97/293 (33%), Positives = 140/293 (47%), Gaps = 25/293 (8%) Query: 29 LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPM 88 L + +G+ + +G ++D V +G LGH +P V A+ + + P Sbjct: 35 LFVAHAKGSHLTTVDGTSFVDYVQSWGPMLLGHAHPVVASAIHAAVDR----GTSYGAPC 90 Query: 89 RGEFYRTLTAI-LPPELNRVFPVNSGTEANEAALKFARAHTGRKK---FVAAMRGFS--- 141 E I P + V VNSGTEA +AL+ AR TGR K FV G + Sbjct: 91 EDEVVLAEAVIDALPGVEMVRMVNSGTEATMSALRLARGVTGRNKVVKFVGCYHGHADAF 150 Query: 142 ----GRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD---EETAAVILEPV 194 G + +LS+ P E V PYND+ A+ ++ AA+I+EPV Sbjct: 151 LASAGSGVATLSIPGTPGVPEA---TVRDTLLAPYNDLTAVAELFTLHGKDIAAIIVEPV 207 Query: 195 QGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAK 254 G G+ FL+ R++ E GALLI DE+ TG R A + F I PD+ TL K Sbjct: 208 AGNMGLVLPMNGFLQGLRDLCTEHGALLIFDEVITGF-RVNYGGAQKRFDITPDLTTLGK 266 Query: 255 ALGGGVPLGAAVMREEVARSMPKGG---HGTTFGGNPLAMAAGVAAIRYLERT 304 +GGG+P+GA R ++ R + G T GNPLAMAAG+A + L+++ Sbjct: 267 IIGGGLPVGAYGGRADLMRRIAPCGEVYQAGTLSGNPLAMAAGIATLAELKKS 319 Lambda K H 0.319 0.137 0.402 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: 344 Number of extensions: 21 Number of successful extensions: 4 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: 395 Length of database: 425 Length adjustment: 31 Effective length of query: 364 Effective length of database: 394 Effective search space: 143416 Effective search space used: 143416 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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