Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate GFF1085 PS417_05505 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__WCS417:GFF1085 Length = 464 Score = 219 bits (559), Expect = 1e-61 Identities = 148/434 (34%), Positives = 235/434 (54%), Gaps = 29/434 (6%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 + R EG Y D + LD +N G NP++ A+K+Q+D + A + Y + Sbjct: 36 IFSRCEGSYVWDTEDQAYLDLQMWYSAVNFGYANPRLNNALKQQIDTLPQIA-SQYLHKG 94 Query: 99 QVELAKKLVEIAPGD--IERKVFLSNSGTEANEAALKIAKWSTNRK-MFIAFIGAFHGRT 155 ++EL++ + A ++ +V + G+++ E +LK+ + +TN K + AF G +HGRT Sbjct: 95 KIELSEMIAVDAKKKFGLDGRVHFNVGGSQSIEDSLKVVRNATNGKSLMFAFEGGYHGRT 154 Query: 156 HGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIE-EY 214 G S+T+S +R R +P+P +R P G+ E + + E EY Sbjct: 155 LGASSITSSYRYRR-RYGHFGERAQFIPFPYHFRGPKGMTKEEYGSHCVQQFARLFETEY 213 Query: 215 --LFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGR 272 +++ V E A + EPIQG GGYV+PP NF++ELK + D+HGIL++ DE+QMG R Sbjct: 214 NGVWDPKVGQSEYAAFYVEPIQGTGGYVIPPMNFYRELKHVLDQHGILMVSDEIQMGFYR 273 Query: 273 TGRMWAIEHFDIVPDIVTVAKALGGGI-PIGATIFRADL----DFGVSGVHSNTFGGNTV 327 TG++W+IEHFD+ PD++ KAL G+ P+G R +L F HS TF N + Sbjct: 274 TGKLWSIEHFDVQPDVIVFGKALTNGLNPLGGIWAREELINPKIFPPGSTHS-TFASNPL 332 Query: 328 AAAAALAVIE---ELQNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVE--- 381 A L + + E+ G + A+ F E L+++++++ IIGDV GLGLA E Sbjct: 333 GTAVGLEMFKMTNEVDYGAMVMAK--GKFFLEGLQDLQKRFPIIGDVDGLGLALRCEICG 390 Query: 382 ---FVKDRKTKEYATKE--RGEIVVEALKRGLAL--LGCGKSAIRLIPPLIISEEEAKMG 434 F D+ T +Y +E +G++VV+ K GL L G K+ I L P L IS E ++G Sbjct: 391 PDGFTPDKATLDYMVEEGMKGDMVVDGQKLGLILDVGGYYKNVITLAPSLEISYPEIELG 450 Query: 435 LDIFEEAIKVVSER 448 L + E+ + ++R Sbjct: 451 LKLLEQLLVRATDR 464 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: 576 Number of extensions: 34 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: 464 Length adjustment: 33 Effective length of query: 421 Effective length of database: 431 Effective search space: 181451 Effective search space used: 181451 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