Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_012384241.1 BIND_RS06310 aspartate aminotransferase family protein
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000019845.1:WP_012384241.1 Length = 444 Score = 160 bits (405), Expect = 8e-44 Identities = 121/406 (29%), Positives = 199/406 (49%), Gaps = 27/406 (6%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 ++ A+ +++ DG +LD ++G+ N G K+++AI+ Q + A + +P Sbjct: 32 IVASAKDMHYYTADGKPILDGTAGLWCCNAGHSRDKIVQAIQAQAAELDFAPPFQFGHPK 91 Query: 99 QVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA------KWSTNRKMFIAFIGAFH 152 LA ++ +APGD++ VF NSG+EA + ALKIA + +R I A+H Sbjct: 92 VFALAARIAALAPGDLDH-VFFGNSGSEAVDTALKIALAYHNIQGQGSRVRLIGRERAYH 150 Query: 153 GRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIE 212 G G ++ P R + GV H+P Y P E + D +E Sbjct: 151 GVGFGGGAV-GGIPGNRKAFGALLAGVDHLP--TTYNRAEQAFTKGEP-EWGGHLADELE 206 Query: 213 EYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGR 272 + + H A +A + EP+ G G + PPK + ++L+ + DK+GILLI DEV G GR Sbjct: 207 KLVALH--DASTIAAVIVEPMSGSTGVLPPPKGYLQKLRAICDKYGILLIFDEVICGYGR 264 Query: 273 TGRMWAIEHFDIVPDIVTVAKAL-GGGIPIGATIFRADL--------DFGVSGVHSNTFG 323 G +A E + +VPD++T AK + G +P+G + R + + V H T+ Sbjct: 265 LGYAFAAERYGVVPDMITFAKGITSGTVPMGGVLIRKPIYEAFMKGPELAVELTHGYTYS 324 Query: 324 GNTVAAAAALAVIE-ELQNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEF 382 G+ +A AA LA ++ + GL E A+KLEP++ + + +K I+ D+R +GL ++ Sbjct: 325 GHPLACAAGLATLDLYKEEGLFERARKLEPVWADAVHGLKSLPNIL-DIRTVGLTAAIDL 383 Query: 383 VKDRKTKEYATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISE 428 + K ++ +A L +I L PPLIISE Sbjct: 384 A---PIADAPGKRAFGVMDKAFHELDLLTRIAGDSIILTPPLIISE 426 Lambda K H 0.319 0.139 0.410 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: 528 Number of extensions: 27 Number of successful extensions: 3 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: 454 Length of database: 444 Length adjustment: 33 Effective length of query: 421 Effective length of database: 411 Effective search space: 173031 Effective search space used: 173031 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 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