Align lysine ε-aminotransferase (EC 2.6.1.36) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= metacyc::MONOMER-12388 (457 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 115 bits (289), Expect = 2e-30 Identities = 95/327 (29%), Positives = 146/327 (44%), Gaps = 29/327 (8%) Query: 124 RLFFVDGGALAVENALKAALDWKAQKLGLAEPDTDRLQVLHLERSFHGRSGYTMSLTNTE 183 R+FF + GA A E ALK A + + G + + ++ + +FHGR+ +T+S Sbjct: 98 RVFFCNSGAEANEAALKLARKFAHDRYG-----SHKSGIVAFKNAFHGRTLFTVSAG--- 149 Query: 184 PSKTARFPKFGWPRISSPALQHPPAEHTGANQEAERRALEAAREAFAAADGMIACFIAEP 243 G P S P + A A A D I EP Sbjct: 150 ----------GQPAYSQDFAPLPA--------DIRHAAYNDINSASALIDDSTCAVIVEP 191 Query: 244 IQGEGGDNHLSAEFLQAMQRLCHENDALFVLDEVQSGCGITGTAWAYQQLGLQPDLVAFG 303 IQGEGG S FLQ ++ LC+ ++AL + DEVQ+G G TG +AY G+ PDL+ Sbjct: 192 IQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTA 251 Query: 304 KKTQVCGVMGGGRIDEVPENVFAVSSRISSTWGGNLADMVRATRLLETIERTQVFDTVVQ 363 K +G E V V + +T+GGN A ++LE I ++ + V Q Sbjct: 252 KALGGGFPVGALLATEECARVMTVGTH-GTTYGGNPLASAVAGKVLELINTPEMLNGVKQ 310 Query: 364 RGKYFRDGLEDLAARHPSVVTNARGRGLMCAVDL-PDTRTRNEVLRLMYTEHQVIALPCG 422 R +F + L + R+ + + RG GL+ L D + + + + V+ L G Sbjct: 311 RHDWFVERLNTINHRY-GLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAG 369 Query: 423 GRSLRFRPALTIAEHEIDQALQALASS 449 G +RF PAL ++E E+ L A++ Sbjct: 370 GNVVRFAPALNVSEEEVTTGLDRFAAA 396 Lambda K H 0.320 0.135 0.403 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: 360 Number of extensions: 22 Number of successful extensions: 3 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: 457 Length of database: 406 Length adjustment: 32 Effective length of query: 425 Effective length of database: 374 Effective search space: 158950 Effective search space used: 158950 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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