Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_086509812.1 BZY95_RS10115 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::P9WQ77 (449 letters) >NCBI__GCF_002151265.1:WP_086509812.1 Length = 422 Score = 83.6 bits (205), Expect = 1e-20 Identities = 83/273 (30%), Positives = 120/273 (43%), Gaps = 21/273 (7%) Query: 117 PALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLS 176 P L H+FF + G++ +E A+K A + + PA ++L L A+HG + ++ Sbjct: 93 PGLEHVFFSDSGSVGMEVAMKMAVQYHHLRGK-----PAKH-RMLSLMKAYHGDTSGCMA 146 Query: 177 LTNTKPTITARFPKFDWPRIDAPYMRPGLDE-PAMAALEAEALRQARAAFETRPHDIACF 235 + + + + + F + AP R D P A + ALR + E +IA Sbjct: 147 VCDPEEGMHSLFSGYLPRHHFAPAPRAPYDAGPDEVARDLAALR---SVLERHHGEIAAL 203 Query: 236 VAEPI-QGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPD 294 + EP+ Q GG P + + R+LCDEFD LL+FDEV TG G TG +A V PD Sbjct: 204 LMEPLLQAAGGLNMTSPLYLSGARQLCDEFDVLLVFDEVATGFGRTGKLFAADHAGVTPD 263 Query: 295 IVAFGKKTQ--VCGVMAGRRVDEVADNVFAVPSRLNS-----TWGGNLTDMVRARRILEV 347 I+ K G A D V D F S L++ T+ GN A L V Sbjct: 264 IMVLSKGLTGGYLGHAATLATDRVHD-AFVGESPLHAFMHGPTFMGNPLACRVALESLAV 322 Query: 348 IEAEGLFERAVQHGKYLRARL--DELAADFPAV 378 E E ++ + LR L DE P V Sbjct: 323 FEEERYLDKIAKLNGVLREELLEDEALRRHPEV 355 Lambda K H 0.323 0.137 0.412 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: 442 Number of extensions: 14 Number of successful extensions: 2 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: 449 Length of database: 422 Length adjustment: 32 Effective length of query: 417 Effective length of database: 390 Effective search space: 162630 Effective search space used: 162630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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