Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= curated2:Q89RB7 (404 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 229 bits (584), Expect = 1e-64 Identities = 140/370 (37%), Positives = 196/370 (52%), Gaps = 7/370 (1%) Query: 25 VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQ 84 +V + G G W+ D G RYLD + ++ GH HP I+ A+ QA +L S AF+N+ Sbjct: 23 LVFAEGRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFYNEP 82 Query: 85 LAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHG 144 +AA + +V ++GAEA E AIK RKWG + KG EII A FHG Sbjct: 83 SLKLAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKG---GAHEIITFAGGFHG 139 Query: 145 RTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVII 204 RTL + S P F P PGF D ++ I TVA ++EPIQGE GV+ Sbjct: 140 RTLATMSASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIMLEPIQGEGGVVP 199 Query: 205 PPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYP 264 A + +R++C ++L++DE+QTG+GRTGKL A QH GIE D+ LGK + GG P Sbjct: 200 ASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGG-VP 258 Query: 265 VSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGL 324 +SA+L+ V G G T+ GNPL AV A + VL G + A +G L GL Sbjct: 259 LSALLAKESVC-CFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGAGL 317 Query: 325 KDIRANT-VREVRGRGLMLAVELHPEAGRARRYCEALQG-KGILAKDTHGHTIRIAPPLV 382 + + +R RG+GL+ A+ L E G A +G +G+L H +R P L Sbjct: 318 QRLSDRLGLRGERGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRPHLLRFMPSLT 377 Query: 383 ITSDEVDWAL 392 ++ +E+D L Sbjct: 378 VSREEIDQML 387 Lambda K H 0.319 0.136 0.405 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: 406 Number of extensions: 21 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: 404 Length of database: 396 Length adjustment: 31 Effective length of query: 373 Effective length of database: 365 Effective search space: 136145 Effective search space used: 136145 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. 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