Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Miya:8500245 Length = 491 Score = 172 bits (437), Expect = 2e-47 Identities = 135/436 (30%), Positives = 216/436 (49%), Gaps = 36/436 (8%) Query: 38 LVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNP 97 LVI AEG D DG LD S + G R+P++ AI+ QLD V H + Sbjct: 51 LVIGAAEGNRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGSE 110 Query: 98 YQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA-----------KWSTNRKMFIA 146 +ELA +L IAP + R VF S+SG+ + E ALKIA R F++ Sbjct: 111 PSIELAARLAAIAPQGLTR-VFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFLS 169 Query: 147 FIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINR 206 A+HG T G ++L + S P + V P YR P+G E I Sbjct: 170 LRNAYHGDTVGAVAL-GGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSCERECITH 228 Query: 207 VIDYIEEYLFEHYVPAEEVAGIFFEP-IQGEGGYVVPPKNFFKELKKLADKHGILLIDDE 265 + E LF + E+ EP +QG G ++ P + + +++L D+HG+ L+ DE Sbjct: 229 M-----ETLFARH--GHELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADE 281 Query: 266 VQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGG-IPIGATIFRADLDFGV--------SG 316 V +G G+TG ++A E + PD + +AK + GG +P+ AT+ + G + Sbjct: 282 VAVGFGKTGTLFACEQEGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTF 341 Query: 317 VHSNTFGGNTVAAAAALAVIEEL-QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLG 375 H +T+ GN +A AAA+A ++ + ++E Q RL+ +++ +GD+R G Sbjct: 342 FHGHTYTGNPLACAAAIASLDVFEEERVMERLQPKIARLAARLDTLRD-LPHVGDIRQRG 400 Query: 376 LAWGVEFVKDRKTKE---YATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEAK 432 + G+E V++R TKE A + + +EA +RG+ + G + L+PPL I+++E Sbjct: 401 VMTGIEMVRNRATKEAYDLALRVGHRVTLEARRRGVIIRPLGDVMV-LMPPLSITDDEID 459 Query: 433 MGLDIFEEAIKVVSER 448 + + EAI+ V+ER Sbjct: 460 LLVGATGEAIRAVTER 475 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: 489 Number of extensions: 28 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: 491 Length adjustment: 33 Effective length of query: 421 Effective length of database: 458 Effective search space: 192818 Effective search space used: 192818 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