Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__Keio:17148 Length = 459 Score = 264 bits (674), Expect = 4e-75 Identities = 158/373 (42%), Positives = 218/373 (58%), Gaps = 18/373 (4%) Query: 41 DAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGEFYRTLTAIL 100 D +G E+IDC+GG+G+ N+GH NP VV AV+ Q Q L P+R +TL A+ Sbjct: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 Query: 101 PPELNRVFPVNSGTEANEAALKFARAHT---GRKKFVAAMRGFSGRTMGSLSVTWEPKYR 157 P +L F NSGTE+ EAALK A+A+ G+ F+A F G+++G+LS T + +R Sbjct: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFR 197 Query: 158 EPFLPLVEPVEFIPYNDVEALKRAVDE------ETAAVILEPVQGEGGVRPATPEFLRAA 211 +PF+PL+ +P+ ++EA++ A++E + AAVILEP+QGEGGV P +L A Sbjct: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257 Query: 212 REITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGV-PLGAAVMREE 270 R++ E GAL+ILDE+QTGMGRTGK FA EH + PDIL LAKALGGGV P+GA + EE Sbjct: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEE 317 Query: 271 VARSMPKGG--HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIP--- 325 V + H TTFGGNPLA AA +A I L L +A + G ++ R + Sbjct: 318 VFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREY 377 Query: 326 SPKIREVRGMGLMVGLELKEKAAPYIARLEK-EHRVLALQA--GPTVIRFLPPLVIEKED 382 ++E RG G+++ +E + Y E RVL IR PPL + E Sbjct: 378 PDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQ 437 Query: 383 LERVVEAVRAVLA 395 E V++A R LA Sbjct: 438 CELVIKAARKALA 450 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: 404 Number of extensions: 19 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: 459 Length adjustment: 32 Effective length of query: 363 Effective length of database: 427 Effective search space: 155001 Effective search space used: 155001 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: 51 (24.3 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