Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_028949958.1 Q385_RS0101465 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000619805.1:WP_028949958.1 Length = 457 Score = 218 bits (556), Expect = 2e-61 Identities = 151/448 (33%), Positives = 240/448 (53%), Gaps = 31/448 (6%) Query: 16 KEVIERNFKYLAM-TTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPR 74 KE+++ +Y + T N P + + EG +YD++G + D N G+++ R Sbjct: 4 KELLQLESEYCSFGDTVHYLNPPKIFAKSEGSYLYDLEGKQYLDLQMWYSACNFGYNNKR 63 Query: 75 VVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPG--DIERKVVYGNSGAEANEAAM 132 + + IK Q + + + F + I+L+ K+ + ++ +V + G++A E ++ Sbjct: 64 INDGIKNQMDTLGQLA-SQFLTKEKILLSYKIAKSVEDRFKVKGRVHFNVGGSQAIEDSL 122 Query: 133 KLVKYGTGRKQFLAFYHAFHGRTQAVLSLTAS-KWVQQDGFFPTMPGVTHIPYPNPYRNT 191 K+V+ T + AF +HGRT ++T+S ++ ++ G F IP+P +R Sbjct: 123 KIVRNYTKKNLNFAFMGGYHGRTIGATNITSSYRYRERYGHFSDR--AFFIPFPYCFRCP 180 Query: 192 WGIDGYEEPDELTNRVLD--FIEEYVFRHVPPH---EIGAIFFEPIQGEGGYVVPPKGFF 246 +G D E D + + F EY P E GA + EPIQG GGY++PPK +F Sbjct: 181 YGKDK-ETCDLYCAKEFEKLFESEYYTVCNPKTKNCEFGAFYIEPIQGTGGYIIPPKDYF 239 Query: 247 KALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGL-PLAGVIH 305 K +K DEY +LL DE+QMG RTGK W+IEHFGV PD+I FGK++ G+ PL+G+ Sbjct: 240 KKIKPVLDEYKVLLVSDEIQMGFYRTGKLWSIEHFGVVPDIIVFGKSLTNGMNPLSGLWA 299 Query: 306 RADITFDK---PGRHATTFGGNPVAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFK 360 + ++ + PG +TF NP+ + AG+EV +I+ K+ V+E G+ YL++ K Sbjct: 300 KEELINPEIFPPGSTHSTFSSNPIGVRAGLEVFKIIEEKDYEKIVKEKGEKFLNYLKDLK 359 Query: 361 EKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKR---------GLVL--L 409 +KY IGD GLGLA VEI + K+ +L D+IV+E K GLVL Sbjct: 360 KKYPFIGDVDGLGLALRVEICE-KDGYTPSKKLTDKIVEEGLKANLNLNEKTYGLVLDVG 418 Query: 410 GCGDNSIRFIPPLIVTKEEIDVAMEIFE 437 G N + P L +T EEI++A+E + Sbjct: 419 GYYKNVLTLAPSLDITDEEINLAVEFLD 446 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: 578 Number of extensions: 34 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: 457 Length adjustment: 33 Effective length of query: 412 Effective length of database: 424 Effective search space: 174688 Effective search space used: 174688 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 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