Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__PV4:5208066 Length = 405 Score = 242 bits (617), Expect = 2e-68 Identities = 149/388 (38%), Positives = 213/388 (54%), Gaps = 19/388 (4%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y ++ VRG+G+RVWD EGNE++D GG V LGH +P +V A+K Q E + + Sbjct: 20 YAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLANV 79 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK------KFVAAM 137 + L E +V+ NSG EANEAALK AR + K + +A Sbjct: 80 MTNEPALALATKLVEATFAE--KVYFANSGAEANEAALKLARRYALDKFGAEKDQIIAFD 137 Query: 138 RGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGE 197 + F GRT ++SV + Y + F P + + +P+ND+ AL+ V ++T A++LEP+QGE Sbjct: 138 KAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDIAALEAEVSDKTCAIMLEPLQGE 197 Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257 GG+ A PEFLRA R + + AL+I DE+QTG+GR G+ +A+ + PDILT AKALG Sbjct: 198 GGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVTPDILTTAKALG 257 Query: 258 GGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWF 317 GG P+ A + E+A + G HG+T+GGNPLA A G A + + + + Sbjct: 258 GGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEVLDGVKRREQLL 317 Query: 318 MEKLRAIPSP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIR 371 + L I EVRG GL++G L E ++ ++ E ++ L AGP VIR Sbjct: 318 RDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVAGTSE-GLMCLIAGPNVIR 376 Query: 372 FLPPLVIEKED----LERVVEAVRAVLA 395 F P LVI + D L R AV V+A Sbjct: 377 FTPSLVIPEADIAEGLARFERAVAKVVA 404 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: 390 Number of extensions: 25 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: 395 Length of database: 405 Length adjustment: 31 Effective length of query: 364 Effective length of database: 374 Effective search space: 136136 Effective search space used: 136136 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