Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_021560695.1:WP_027490801.1 Length = 444 Score = 351 bits (901), Expect = e-101 Identities = 188/437 (43%), Positives = 263/437 (60%), Gaps = 11/437 (2%) Query: 10 LPGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVG 69 LPGPKA+ +I R+ + ++ + P + P V+ G G V+DVDGN F DF +G+ V G Sbjct: 14 LPGPKAQAMIARDAEVISPSY--PRDYPFVMSHGRGTEVWDVDGNRFLDFMAGIAVCATG 71 Query: 70 HSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANE 129 H+HP+VV+A++ A KF H S +D+++E L E+L +AP SG EA E Sbjct: 72 HAHPQVVKAVQDAAAKFLHIS-SDYWHEEMTGLGERLAAVAPLGAPAMSFICQSGTEAVE 130 Query: 130 AAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYR 189 A+KL +Y TGR +F+ F FHGRT LS T+SK+ QQ GF PT+ GVTH+PYPNPYR Sbjct: 131 GALKLARYVTGRPRFIGFLGGFHGRTFGSLSFTSSKYTQQKGFSPTLAGVTHVPYPNPYR 190 Query: 190 NTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKAL 249 + D+ VLD+I R VPP E+ AI EP+QGEGGY+ PP GF L Sbjct: 191 PLFA------GDDQGAAVLDYIRMLFQRSVPPSEVAAILIEPMQGEGGYLTPPDGFLAGL 244 Query: 250 KKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI 309 + DE+GILL DEVQ GIGRTG+ +A EH+GV+PD+I K +G GLP+ VI + I Sbjct: 245 RALCDEHGILLIFDEVQSGIGRTGRMFACEHWGVQPDIITSAKGLGSGLPIGAVIAKKSI 304 Query: 310 TFD-KPGRHATTFGGNPVAIAAGIEVVEIVK-ELLPHVQEVGDYLHKYLEEFKEKYEVIG 367 K G H T+GGNPV AA +++V+ L+ + VGD+ L E + Y IG Sbjct: 305 MSQWKRGAHGNTYGGNPVTCAAANATLDLVRGGLMDNAARVGDHFMARLRELQRDYPCIG 364 Query: 368 DARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKE 427 + RG GL +E+++ K L + +V+ + GL+LL CG +++RF+PPL V+ Sbjct: 365 EVRGKGLWIGMELIEDDGKKTPATALCEAVVQRAFHNGLLLLSCGTSTVRFMPPLNVSVG 424 Query: 428 EIDVAMEIFEEALKAAL 444 E+D A+ + +L AL Sbjct: 425 EVDEAIALLRSSLDQAL 441 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: 530 Number of extensions: 35 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: 444 Length adjustment: 32 Effective length of query: 413 Effective length of database: 412 Effective search space: 170156 Effective search space used: 170156 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 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