Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= SwissProt::P38021 (401 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 219 bits (557), Expect = 1e-61 Identities = 138/382 (36%), Positives = 215/382 (56%), Gaps = 32/382 (8%) Query: 24 PLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADK---ITLTSR 80 PL I I +A G ++ P+G +Y+D++S N GHRHPK+++A++DQ DK + + Sbjct: 18 PLLIEIEKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMHLMVYGE 77 Query: 81 AFHNDQLGPFYEKTAKLTGK-EMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIA 139 + Q T L K + + +N+G+EAVE A+K A+R+ + EI++ Sbjct: 78 YVQSPQTQLAKALTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYT--------GRREILS 129 Query: 140 CVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFEPIQ 199 CV +HG + A+S+ E +KR + P+LPGI+ + + + + L Q IT TAA + E +Q Sbjct: 130 CVNAYHGSSHGALSVGGNEIFKRAYRPLLPGIRHLDFNEPDQLDQ-ITEETAAIMVETVQ 188 Query: 200 GEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKA 259 GEAGI + + + + C E L I DEIQ G GRTGK +A IVPD+ + K Sbjct: 189 GEAGIRVGTKEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKG 248 Query: 260 LGGGVFPISCIAADREILGVF--NP-GSHGSTFGGNPLACAVSIASLEVLEDEKLADRSL 316 +GGG+ PI A + I+ VF NP H +TFGG+P++CA ++A++++L DEKL Sbjct: 249 MGGGM-PIGAFIAPQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVE 307 Query: 317 ELGEYFKSELESIDSPVIKEVRGRGLFIGV--ELTEAARPYCERLKEEG------LLCKE 368 FK L + P I+E+R +GL + V E E +P +R E G L C++ Sbjct: 308 RKANLFKKHL---NHPKIQEIRNKGLMMAVKFEAFEVLKPIIDRAIELGIITDWFLFCED 364 Query: 369 THDTVIRFAPPLIISKEDLDWA 390 + +R APPL I+ E+++ A Sbjct: 365 S----MRIAPPLTITDEEIEKA 382 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: 414 Number of extensions: 34 Number of successful extensions: 6 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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