Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_022947828.1 H035_RS0104615 aspartate aminotransferase family protein
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000421465.1:WP_022947828.1 Length = 463 Score = 226 bits (577), Expect = 8e-64 Identities = 150/409 (36%), Positives = 215/409 (52%), Gaps = 57/409 (13%) Query: 29 AEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINAL-----IDQANRVTLTSRAFHSDQ 83 A G ++ D E N Y+DLLS + G HP I +AL +D + V + Sbjct: 44 ARGPYLYDQEDNEYLDLLSGFGVFALGRNHPTIQSALREVLDLDLPDLVQMDVSILS--- 100 Query: 84 LGPWYEKVAKLTNKEM--VLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCEDNF 141 G EK+ ++T + + + N+GAEAVE AIK AR R+ I+ CE F Sbjct: 101 -GLLAEKLVQVTPEPLTKLFFCNSGAEAVEAAIKFAR--------YTTGRSRILYCEHAF 151 Query: 142 HGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPN-TAAFILEPIQGEAG 200 HG T+GA+S++ E +++GFGP+LP IP+ DLEAL+ A+ TAAFI+EPIQG+ G Sbjct: 152 HGLTLGALSLNGEEVFRQGFGPLLPDCDAIPFNDLEALERALKEQPTAAFIVEPIQGK-G 210 Query: 201 INIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALGGG 260 +N+P +L EA +C+K LF+ADEIQ GLGRTG+++A + V PDM ++ KAL GG Sbjct: 211 VNLPDDDYLTEAARLCRKYGALFIADEIQAGLGRTGRLWAIEHWGVEPDMLLMAKALSGG 270 Query: 261 VFPISCAAANRDILG-VFEPGS----HGSTFGGNPLACAVSIAALEVLEEEKLTERSLQL 315 P+ A ++ VF HGSTF N A A +A L V+EEEKL + + Sbjct: 271 FVPVGAVAMTAHVMDKVFNRMDRAVVHGSTFSKNNPAMAAGLATLSVIEEEKLLANAARQ 330 Query: 316 GEKLVGQLKEIDNP--MITEVRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHE----- 368 GE L+G L + + VRGKGL + +E +P +LK A L + ++ Sbjct: 331 GEALIGGLNALTDKYEFFQAVRGKGLMLALEFGKPRSL---KLKTAWSLLETANKGLFSQ 387 Query: 369 ---------------------NVIRIAPPLVISEEDLEWAFQKIKAVLS 396 NV++ PPLVI +D+EW + VL+ Sbjct: 388 MVTIPLFKRHRILSQVAGHGMNVVKFLPPLVIGAKDVEWIVSAMDDVLA 436 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: 452 Number of extensions: 22 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 396 Length of database: 463 Length adjustment: 32 Effective length of query: 364 Effective length of database: 431 Effective search space: 156884 Effective search space used: 156884 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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