Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_014518834.1 CA_RS02090 aspartate aminotransferase family protein
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000008765.1:WP_014518834.1 Length = 426 Score = 308 bits (789), Expect = 2e-88 Identities = 171/412 (41%), Positives = 247/412 (59%), Gaps = 20/412 (4%) Query: 38 LVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNP 97 L + R EG Y DG +LDF+SG+ V N+G NP VI+A K+Q+D ++H Y Sbjct: 22 LGVVRGEGAYLYTEDGRKVLDFASGVAVCNLGHNNPAVIKAAKEQMDKLIHGGHNVVYYE 81 Query: 98 YQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHG 157 V+LA+K+VE+ + V+ SNSG EANE A+K+AK+ T R+ I+F G+FHGRT Sbjct: 82 SYVKLAEKIVELTGN--KTMVYFSNSGAEANEGAIKLAKYITKRQAIISFKGSFHGRTLA 139 Query: 158 TMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFE 217 T S+T S R +P V YP +R P+ +N + I E+ +F+ Sbjct: 140 TTSITGSSSKYRKNYEGLLPSVYFAEYPYCFRCPYK----QNKESCNMECISQFED-MFK 194 Query: 218 HYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMW 277 + E VA I EP+QGEGGY+VPPK F K ++++ DK+GI LI DEVQ G GRTG+++ Sbjct: 195 KLIEPESVAAIIMEPVQGEGGYIVPPKKFLKAVREICDKYGICLIFDEVQCGFGRTGKIF 254 Query: 278 AIEHFDIVPDIVTVAKALGGGIPIGATIFRADL-DFGVSGVHSNTFGGNTVAAAAALAVI 336 A E+F++ PDI T AKA+ G P+ A I + +L + +G H TFGGN VA AA+LA I Sbjct: 255 AHENFEVEPDIFTCAKAIASGFPLSAVIGKKELMEKWPAGAHGGTFGGNPVACAASLATI 314 Query: 337 EELQNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKEYATKER 396 +EL++G+++NA + +E L ++K+KY IGD+RG+GL G+EF K+ + Sbjct: 315 KELESGVLDNANNMGNYLKEELLKLKDKYACIGDIRGIGLMIGMEFCKENNNPD------ 368 Query: 397 GEIVV----EALKRGLALLGCG--KSAIRLIPPLIISEEEAKMGLDIFEEAI 442 G+IV A+ L LLGCG + +R I PL + + E M + I E+ I Sbjct: 369 GDIVTFIREVAVNNNLILLGCGTEHNVLRFIAPLTVEKSEIDMAISIVEKGI 420 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: 523 Number of extensions: 24 Number of successful extensions: 4 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: 426 Length adjustment: 32 Effective length of query: 422 Effective length of database: 394 Effective search space: 166268 Effective search space used: 166268 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 Jul 25 2024. The underlying query database was built on Jul 25 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