Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_084276125.1 B8779_RS08250 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900176045.1:WP_084276125.1 Length = 396 Score = 215 bits (547), Expect = 2e-60 Identities = 139/409 (33%), Positives = 222/409 (54%), Gaps = 50/409 (12%) Query: 42 RGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAII 101 +G+ ++YD G F DF SG+GV++VGH + R+ +AI QA+K H S + E + Sbjct: 24 KGKNAKLYDERGKEFIDFTSGIGVVSVGHGNKRLADAICDQAQKIIHISNL-YLIEPQAL 82 Query: 102 LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV-KYG-----TGRKQFLAFYHAFHGRT 155 LA++++EL+ D+ ++ + NSGAEANE A+K+ KYG R + + H+FHGRT Sbjct: 83 LAKRIVELSSYDM--RLFFANSGAEANEGAIKIARKYGEVDGKVKRYKIITLKHSFHGRT 140 Query: 156 QAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215 L T + + +F P DG+ D + +++ D I+++ Sbjct: 141 ITALKATGQEAMHT--YFGPFP-----------------DGFVYADSI-DQIPDLIDDHT 180 Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275 A+ E IQGEGG K + L K + +LL DEVQ GI RTG+F Sbjct: 181 V---------AVMIELIQGEGGVEPQDKEAVQNLAKLLKQKDVLLIIDEVQTGIYRTGEF 231 Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAIAAGIEVV 335 A + +EPD+I K +GGG+P+ V+ R F KPG H +TFGGN ++ A +EV+ Sbjct: 232 LASNLYEIEPDIITLAKGLGGGVPIGAVMTRLKDIF-KPGDHGSTFGGNYLSTRAALEVI 290 Query: 336 EIVKELLP--HVQEVGDYLHKYLEEFKEKYEVIGDAR-GLGLAQAVEIVKSKETKEKYPE 392 I++EL + E Y + L+E +KY + + G G+ + + + K E Sbjct: 291 AILEELKASGKLDEHFIYFEERLKEIAKKYAALFEKEVGFGMMRGL--------RAKSAE 342 Query: 393 LRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 ++ +I++E+ GL++L G N++RF+PPL +TKEE+D + FE+AL+ Sbjct: 343 IQGKIIEEAFNEGLLVLKAGRNTVRFLPPLTITKEEMDEGFKRFEKALE 391 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: 481 Number of extensions: 30 Number of successful extensions: 6 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: 396 Length adjustment: 32 Effective length of query: 413 Effective length of database: 364 Effective search space: 150332 Effective search space used: 150332 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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