Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate SMc02138 SMc02138 acetylornithine transaminase
Query= SwissProt::P38021 (401 letters) >FitnessBrowser__Smeli:SMc02138 Length = 399 Score = 243 bits (620), Expect = 7e-69 Identities = 135/366 (36%), Positives = 207/366 (56%), Gaps = 8/366 (2%) Query: 20 NNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKITLTS 79 + Y P+ G W+ +G Y+D + + + GH HP +++ALK QADK+ S Sbjct: 9 DTYLRAPLRFERGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQADKVWHLS 68 Query: 80 RAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIA 139 + + ++T + + N+GAEA+E A+K ARR+ + KG + + +I Sbjct: 69 NLYEIAGQESLARRLTQVTFADRVFFTNSGAEALECAIKTARRYHF-AKGHVE-KFHVIT 126 Query: 140 CVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFEPIQ 199 G FHGRT+ ++ +++Y GFGP PG +P+GD+ A++ AI TAA L EPIQ Sbjct: 127 FEGAFHGRTLATIAAGGQQKYIEGFGPKAPGFYQVPFGDIGAVKNAINEETAAILVEPIQ 186 Query: 200 GEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKA 259 GE GI + F+Q +C E +L I DE+Q+G+GRTGK FA +W GI PD+ + K Sbjct: 187 GEGGIRTASKEFMQGLRELCDEFGLLLILDEVQSGVGRTGKLFAHEWAGIKPDIMAVAKG 246 Query: 260 LGGGVFPI-SCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRSLEL 318 +GGG FP+ +C+A + G+ G+HGST+GGNPLA AV A L+V+ E D+ E+ Sbjct: 247 IGGG-FPLGACLATEAAAAGMV-AGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLDQVREV 304 Query: 319 GEYFKSELESIDS---PVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKETHDTVIR 375 F+ L S+ VI+E+RG GL +G++ + + ++ E LL + V+R Sbjct: 305 ALVFRQGLASLKDRFPDVIEEIRGDGLMLGIKAKVPSADLLKAIRAEKLLVVPAGENVLR 364 Query: 376 FAPPLI 381 PPLI Sbjct: 365 LLPPLI 370 Lambda K H 0.318 0.136 0.401 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: 383 Number of extensions: 14 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: 401 Length of database: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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 (21.7 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