Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_019866214.1 METMI_RS0110330 aspartate aminotransferase family protein
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000384075.1:WP_019866214.1 Length = 463 Score = 228 bits (581), Expect = 3e-64 Identities = 150/394 (38%), Positives = 212/394 (53%), Gaps = 51/394 (12%) Query: 28 KAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINAL-----IDQANRVTLTSRAFHSD 82 +A G ++ D G Y+DLLS + G HP +I+AL ++ N V L S Sbjct: 43 RAVGQYLYDQNGTEYLDLLSGFGVFAIGRNHPTVISALQETLTLELPNLVQLDVSVL-SG 101 Query: 83 QLGPWYEKVAKLT--NKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCEDN 140 LG +++ K T N + N+G EAVE AIK AR Y K R +I+ CE Sbjct: 102 LLG---QEIVKTTPENLNKIFFCNSGTEAVEAAIKFAR---YTTK-----REKIVFCEHG 150 Query: 141 FHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITP-NTAAFILEPIQGEA 199 +HG TMG++S++ ++ GFGP+LPG IP+ DL AL+AA++ + AAFI+EPIQG+ Sbjct: 151 YHGLTMGSLSLNGENIFREGFGPLLPGCSAIPFNDLGALEAALSQKDVAAFIVEPIQGK- 209 Query: 200 GINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALGG 259 G+N+P +L E +CK+ LFVADE+QTGLGRTGK +A D NV+PDM + KAL G Sbjct: 210 GVNLPDDNYLPEVERLCKQYGTLFVADEVQTGLGRTGKFWAVDHWNVSPDMICMAKALSG 269 Query: 260 GVFPISCAAANRDILGVF-----EPGSHGSTFGGNPLACAVSIAALEVLEEEKLTERSLQ 314 G P+ A + I+ HGSTF N +A A +A L VL EEKL + + Sbjct: 270 GFVPVGAVAITQKIMDTVYNRMDRAVVHGSTFSKNNMAMAAGLATLHVLAEEKLVDNCAK 329 Query: 315 LGEKLVGQLKEIDN--PMITEVRGKGLFIGIELNEP----ARPYCEQLKAA--GLLC--- 363 +G ++ L + + E RGKG+ I IE P + L+AA GL C Sbjct: 330 VGTDIINSLNAMSGKYEFLKEARGKGMMIAIEFKSPKSLTLKAAWAMLEAANKGLFCQMI 389 Query: 364 -----KETH---------ENVIRIAPPLVISEED 383 KE H NV+++ PPL ++++D Sbjct: 390 TIPLFKEHHILTQVAGHGMNVVKLLPPLNLTQQD 423 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: 413 Number of extensions: 20 Number of successful extensions: 7 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: 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