Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 226 bits (576), Expect = 1e-63 Identities = 147/406 (36%), Positives = 216/406 (53%), Gaps = 17/406 (4%) Query: 41 ERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPYQV 100 +RAE DV+G DF+ GI V+N G R+P+V++A+ QL+ H A V Sbjct: 27 DRAENATLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFTHTAYQIVPYESYV 86 Query: 101 ELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMS 160 LA+++ + P D +K L +G EA E A+KIA+ T R IAF G FHGRT M+ Sbjct: 87 ALAERINALVPIDGLKKTALFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTLLGMA 146 Query: 161 LTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFEHYV 220 LT + P + H P+P G+ ++ L E LF+ + Sbjct: 147 LTGKVAPYKVGFGPFPSDIYHAPFPCDLH---GVSTEQSIQAL---------ESLFKTDI 194 Query: 221 PAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMWAIE 280 + VA I EP+QGEGG+ P +F + L+ L DKHGILLI DEVQ G GRTG+++A+ Sbjct: 195 DPQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMS 254 Query: 281 HFDIVPDIVTVAKALGGGIPIGATIFRAD-LDFGVSGVHSNTFGGNTVAAAAALAVIEEL 339 H+ + PD++T+AK+L GG+P+ A RA +D + G T+ GN +A AAA AVIE + Sbjct: 255 HYPVAPDLITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGNPLAVAAAHAVIETI 314 Query: 340 -QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKEYATKERGE 398 Q L E A L + L++ + I D+RGLG VEF D T + + + Sbjct: 315 EQERLCERATALGKQLKAALQQASQTCPGIADIRGLGSMVAVEF-HDPATGQPSAELAKR 373 Query: 399 IVVEALKRGLALLGCGK--SAIRLIPPLIISEEEAKMGLDIFEEAI 442 + + A++ GL LL CG + IR + PL I + + L + + + Sbjct: 374 VQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVLTKVL 419 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: 460 Number of extensions: 21 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: 424 Length adjustment: 32 Effective length of query: 422 Effective length of database: 392 Effective search space: 165424 Effective search space used: 165424 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