Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 Length = 430 Score = 283 bits (724), Expect = 8e-81 Identities = 149/413 (36%), Positives = 236/413 (57%), Gaps = 16/413 (3%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+VI+R +G ++DVDG + DF G+GV+N+GH+HP+VV A++ Q +K +H Y Sbjct: 28 PLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKISHACFQVVAY 87 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 + + LA++L E+ G K + SGAEA E A+K+ + T R +AF FHGRT Sbjct: 88 KPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHTNRSAVIAFRGGFHGRTL 147 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 +LT + F P P V H PYPN YR + L ++E + Sbjct: 148 LGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGV-----------TSAMALQALDELLA 196 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 V P + AI EP+QG+GG++ P F + L+ ++GI+L DE+Q G GRTGK++ Sbjct: 197 TQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWF 256 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335 +H G++PDL+ K++ GGLPL+GV+ +A+I PG T+GGN ++ AA + V+ Sbjct: 257 GFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVI 316 Query: 336 EIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393 E ++LL + +G+ L + L + +Y IGD RG G A+E++K E + +L Sbjct: 317 EAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEARTPDADL 376 Query: 394 RDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444 R++ E+ GL+++ CG N +RF+ PL+ ++ +ID A++I + AL L Sbjct: 377 NQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALARVL 429 Lambda K H 0.320 0.141 0.418 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: 485 Number of extensions: 30 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: 445 Length of database: 430 Length adjustment: 32 Effective length of query: 413 Effective length of database: 398 Effective search space: 164374 Effective search space used: 164374 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 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