Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_051305361.1 G494_RS0103960 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000429965.1:WP_051305361.1 Length = 466 Score = 171 bits (434), Expect = 3e-47 Identities = 132/438 (30%), Positives = 211/438 (48%), Gaps = 48/438 (10%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASG-VGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 ++I G+G+ V D+ GN + D SG V + VG+ + EA+ Q +K +++ F Sbjct: 39 MIIVEGQGLMVKDIRGNEYLDATSGGVWSVMVGYGRDSIAEAVCAQLKKMPYFAGV-FGN 97 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGT-------GRKQFLAFYH 149 +I A+KL+E P KV + NSG+EANE A K+V+ + G+ + + Sbjct: 98 VPSIKFAQKLLEKLPR--MDKVYFSNSGSEANEKAFKIVRQASRISPERKGKYKIMYRDR 155 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIP----YPNPYRNTWGIDGYEEPDELTN 205 +HG T +S T +QD F P + G P Y P+ T+G E E Sbjct: 156 DYHGTTIGAMSATGQAQRKQD-FGPFVEGFVEFPHCACYRCPHDKTYG----ECNIECAR 210 Query: 206 RVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEV 265 +V D I + IGA+ EPI GG + P ++ L++ +Y I + DEV Sbjct: 211 KVEDIILKE-----GADTIGAMIVEPITAGGGILKPVPEYYPILQEICKKYDIWMIMDEV 265 Query: 266 QMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVI----HRADITFDKPG------ 315 G GRTGKFW EHF V+PD++ K + H D+ + P Sbjct: 266 VCGFGRTGKFWGHEHFDVDPDIVTMAKGLASSYEALSATVVKQHVYDVFLNDPANEDDRL 325 Query: 316 ---RHATTFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDAR 370 R +T+GG A+ A +E I+++ L+ + +E+G Y+ LEE K K++ +GD R Sbjct: 326 NYFRDISTYGGCTSAMTAALESTRIIEDENLVENSREIGAYMISKLEELK-KFDCVGDIR 384 Query: 371 GLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNS-------IRFIPPLI 423 G GL +E V ++ETKE E + + + V++G ++S + F P LI Sbjct: 385 GEGLFGGIEFVTNRETKEPITEGQMAALMGNVMAQGVIVGRTNSSFHGLNNIMNFAPCLI 444 Query: 424 VTKEEIDVAMEIFEEALK 441 +TKE++D + A++ Sbjct: 445 ITKEQVDTVVGAVAAAIE 462 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: 526 Number of extensions: 26 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: 466 Length adjustment: 33 Effective length of query: 412 Effective length of database: 433 Effective search space: 178396 Effective search space used: 178396 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