Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 225 bits (574), Expect = 2e-63 Identities = 156/430 (36%), Positives = 233/430 (54%), Gaps = 63/430 (14%) Query: 26 MATTTNDPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDL 85 +A TT+ P + IE+AEG+Y G +D SGIGV NVG R+PKV++AI+ QLD Sbjct: 11 LAQTTDFP--LLIEIEKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDK 68 Query: 86 VLHA-AGTDYYNPYQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMF 144 +H +Y Q +LAK L + P ++ V+L NSG+EA E ALK+AK T R+ Sbjct: 69 YMHLMVYGEYVQSPQTQLAKALTDTLPKKLDN-VYLVNSGSEAVEGALKLAKRYTGRREI 127 Query: 145 IAFIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELI 204 ++ + A+HG +HG +S+ ++ +R+ P +PG+ H+ + PD+L Sbjct: 128 LSCVNAYHGSSHGALSVGGNEIFKRAYR-PLLPGIRHLDF-------------NEPDQL- 172 Query: 205 NRVIDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDD 264 D I EE A I E +QGE G V K +FK L+ D+ G LLI D Sbjct: 173 ----DQI----------TEETAAIMVETVQGEAGIRVGTKEYFKALRHRCDETGTLLILD 218 Query: 265 EVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGGIPIGA--------TIFRADLDFGVSG 316 E+Q G GRTG+ WA +H+DIVPDIV AK +GGG+PIGA ++F+ + G Sbjct: 219 EIQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGGGMPIGAFIAPQSIMSVFKNNPLLG--- 275 Query: 317 VHSNTFGGNTVAAAAALAVIEELQN-GLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLG 375 H TFGG+ V+ AAALA I+ L++ LI++ ++ LF++ L K I ++R G Sbjct: 276 -HITTFGGHPVSCAAALATIDILRDEKLIQHVERKANLFKKHLNHPK-----IQEIRNKG 329 Query: 376 LAWGVEFVKDRKTKEYATKERGEIVVEALKRGLA---LLGCGKSAIRLIPPLIISEEEAK 432 L V+F K I+ A++ G+ L C + ++R+ PPL I++EE + Sbjct: 330 LMMAVKFEAFEVLK--------PIIDRAIELGIITDWFLFC-EDSMRIAPPLTITDEEIE 380 Query: 433 MGLDIFEEAI 442 I ++I Sbjct: 381 KACAIILQSI 390 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: 432 Number of extensions: 27 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: 393 Length adjustment: 32 Effective length of query: 422 Effective length of database: 361 Effective search space: 152342 Effective search space used: 152342 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: 50 (23.9 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