Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= curated2:C3P3K3 (396 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 250 bits (639), Expect = 4e-71 Identities = 135/378 (35%), Positives = 215/378 (56%), Gaps = 10/378 (2%) Query: 19 YHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA 78 Y+ P+ K EG W+ + +G R++DL + + GH HP ++ AL DQA + S Sbjct: 9 YNRAPLSFVKGEGAWLIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQAETLWHVSNL 68 Query: 79 FHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCE 138 +H Q +++ + + + V N+G E+ E A+K AR++ +D K + R EI+ Sbjct: 69 YHIPQQQALADRLVEHSFADTVFFTNSGTESCELAVKMARKYFHD--KGQPERVEILTFS 126 Query: 139 DNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPNTAAFILEPIQGE 198 +FHGR+ +S + +E+ GFGPMLPG + +GDL+ + AIT TAA ++EP+QGE Sbjct: 127 GSFHGRSSAGISAAGSEKMTAGFGPMLPGFKHLMFGDLDGVTDAITDQTAAILIEPVQGE 186 Query: 199 AGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALG 258 GI P LK ++C + +L + DE+Q G+GRTGK+FA +W +TPD+ ++ K +G Sbjct: 187 GGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMMVAKGIG 246 Query: 259 GGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALE-VLEEEKLTERSLQLG- 316 GG FP+ A + G+HGST+GGNPL CAV A ++ V + E L E S + G Sbjct: 247 GG-FPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVSRKAGL 305 Query: 317 --EKLVGQLKEIDNPMITE-VRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIRI 373 +KL G + +P + E VRG GL +G++ A ++ +NV+R+ Sbjct: 306 LRQKLEGLV--ASHPQVFEAVRGSGLMLGLKCVAANTDVVAAGYEAEVVTVPAADNVVRL 363 Query: 374 APPLVISEEDLEWAFQKI 391 PPL +++ED+ AF ++ Sbjct: 364 LPPLTLTDEDIAEAFARL 381 Lambda K H 0.317 0.136 0.402 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: 379 Number of extensions: 22 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: 396 Length of database: 394 Length adjustment: 31 Effective length of query: 365 Effective length of database: 363 Effective search space: 132495 Effective search space used: 132495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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