Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Koxy:BWI76_RS14020 Length = 461 Score = 230 bits (587), Expect = 6e-65 Identities = 150/425 (35%), Positives = 222/425 (52%), Gaps = 20/425 (4%) Query: 33 PENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLT 92 P LP+ I + EG+ + D D + D +G G + +GH+HP V+++I+ Sbjct: 38 PRKLPLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTL 97 Query: 93 DFFYENAIILAEKLIELAPGDIERKVVY--GNSGAEANEAAMKLVKYGTGRKQFLAFYHA 150 D +E L+ L PG+ + + G SGA+A EAA+KL K TGR ++F Sbjct: 98 DLTTPLKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFSGG 157 Query: 151 FHGRTQAVLSLTA--SKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVL 208 +HG T LS+T S +G MP V +PYP+ YR GI G LT Sbjct: 158 YHGMTHGALSVTGNLSPKAAVNGM---MPEVQFMPYPHQYRCPLGIGGEAGVKALTYYFE 214 Query: 209 DFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMG 268 + I + P A+ E +QGEGG P + + ++K E+GILL DEVQ G Sbjct: 215 NLINDVESGVRKP---AAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAG 271 Query: 269 IGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAI 328 RTGKF+A EH G+EPD+I KA+GGGLPLA + + +PG H TF GN +A+ Sbjct: 272 FARTGKFFAFEHAGIEPDIIVMSKAVGGGLPLAVLGIKKQFDAWEPGHHTGTFRGNQLAM 331 Query: 329 AAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKET 386 A G+ + +K+ + G++L L E +++Y VIG RGLGL +EIVK E Sbjct: 332 ATGLTTLRHLKDNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGLMIGIEIVKPNEA 391 Query: 387 KEK---YP---ELRDRIVKESAKRGLVLLGCGDNS--IRFIPPLIVTKEEIDVAMEIFEE 438 + YP EL + K+ + GL+L G + +R +P L+++ E+++ + FE+ Sbjct: 392 PDHMGCYPADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELEIFFDKFEQ 451 Query: 439 ALKAA 443 AL AA Sbjct: 452 ALLAA 456 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: 537 Number of extensions: 26 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: 461 Length adjustment: 33 Effective length of query: 412 Effective length of database: 428 Effective search space: 176336 Effective search space used: 176336 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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