Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 162 bits (409), Expect = 3e-44 Identities = 135/427 (31%), Positives = 211/427 (49%), Gaps = 33/427 (7%) Query: 44 EGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPYQVE-L 102 +G Y ID +G LD S G V +G + +VI A+++Q+ L A T + E L Sbjct: 20 DGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGK-LAFAHTGFLTSEPAEAL 78 Query: 103 AKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKW------STNRKMFIAFIGAFHGRTH 156 A L+ APGD+ R F+S G+EA EAA+K+A+ T R+ IA ++HG T Sbjct: 79 ADLLISQAPGDLHRVYFVSG-GSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNTL 137 Query: 157 GTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLF 216 G ++ +R + P + + H+ Y + DG E+ + RV + +E + Sbjct: 138 GALA-AGGNAWRRQQFAPLLIDISHIAPCYEYVDRG--DG-ESRYDYGQRVANELEAEIL 193 Query: 217 EHYVPAEEVAGIFFEPIQGEGGYVVPP-KNFFKELKKLADKHGILLIDDEVQMGMGRTGR 275 + E V EP+ G VP + +FK ++++ D++G+LLI DEV GMGRTG Sbjct: 194 R--LGPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGH 251 Query: 276 MWAIEHFDIVPDIVTVAKALGGGI-PIGATIFRADLDFGVSG-----VHSNTFGGNTVAA 329 ++A E + PDI+ +AK LG G PIGA + + + G H +T+ G+ VA Sbjct: 252 LFACEADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVAT 311 Query: 330 AAALAVIEE-LQNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKT 388 AA LAV+ L GL++ + ++ L ++ +GD+RG GL G+E V DR++ Sbjct: 312 AAGLAVVRALLDRGLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRES 371 Query: 389 K---EYATKERGEIVVEALKRGLALL-------GCGKSAIRLIPPLIISEEEAKMGLDIF 438 K + G++ A + GL G I L PP I+SE++ D Sbjct: 372 KTPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKL 431 Query: 439 EEAIKVV 445 E A+ V Sbjct: 432 EVALDQV 438 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: 451 Number of extensions: 30 Number of successful extensions: 5 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: 440 Length adjustment: 33 Effective length of query: 421 Effective length of database: 407 Effective search space: 171347 Effective search space used: 171347 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 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