Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900115975.1:WP_092482996.1 Length = 396 Score = 240 bits (613), Expect = 5e-68 Identities = 146/410 (35%), Positives = 221/410 (53%), Gaps = 50/410 (12%) Query: 42 RGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAII 101 RGEG R++D DG F DF G+ V ++GH HP VV AI++QA + H S ++ E Sbjct: 27 RGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVSNL-YYIEPQAR 85 Query: 102 LAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK------YGTGRKQFLAFYHAFHGRT 155 LAE L++ + D +V + NSGAEANE A+KL + +G + + + +FHGRT Sbjct: 86 LAELLVQNSCCD---RVFFCNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGRT 142 Query: 156 QAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215 A ++ T QQ GF P PG ++P+ +P D +E Sbjct: 143 LAAITATGQPKYQQ-GFEPLPPGFKYVPFNDP---------------------DALE--- 177 Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275 R + PH A+ EP+QGEGG + +++ D G+LL DEVQ G+GRTG+F Sbjct: 178 -RAIGPHTC-AVMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEF 235 Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAAGIEV 334 A +H+ VEPD+I KA+GGG P+ ++ + + PG HATTFGGNP+A AAG+ Sbjct: 236 LAYQHYDVEPDIITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAA 295 Query: 335 VEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPE 392 ++ + ++ + + VG Y + L++ KY+ I + RGLGL +E+ + Sbjct: 296 MQTMLGDGVMQNCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRP--------- 346 Query: 393 LRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKA 442 IV ++GL++ +N +RF PPL++ EE+D A+E E L A Sbjct: 347 -GGDIVNRCREKGLLINCVNNNVLRFTPPLVIGTEEVDRALETVEAVLIA 395 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: 492 Number of extensions: 27 Number of successful extensions: 8 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 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