Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_010960134.1 MCA_RS04000 aspartate aminotransferase family protein
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000008325.1:WP_010960134.1 Length = 462 Score = 239 bits (610), Expect = 1e-67 Identities = 151/409 (36%), Positives = 222/409 (54%), Gaps = 49/409 (11%) Query: 25 VISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRAFHSDQL 84 V +A+G ++ D + Y+DLLS + G HP+++ AL D + L Sbjct: 40 VYVRAQGPYLYDDQDREYLDLLSGFGVFALGRNHPQVVGALKDVLDAQLPDLVQMDVSLL 99 Query: 85 -GPWYEKVAKLTNKEM--VLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCEDNF 141 G EK+ + ++ + N+GAEAVE AIK AR Y K R +I+ CE F Sbjct: 100 SGLLSEKILQRCPGDLSRMFYCNSGAEAVEAAIKFAR---YTTK-----REKIVYCEHGF 151 Query: 142 HGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPN-TAAFILEPIQGEAG 200 HG T+GA+S++ + ++ GFGP+LP +P+ DL AL+AA+ N AAFI+EPIQG+ G Sbjct: 152 HGLTLGALSLNGEQVFRDGFGPLLPACKAVPFNDLGALEAALRHNDVAAFIVEPIQGK-G 210 Query: 201 INIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALGGG 260 +N+P G+L EA +C+K LFVADEIQTG+GRTGK +A + V PDM ++ KAL GG Sbjct: 211 VNLPDEGYLAEAARLCRKHGALFVADEIQTGIGRTGKFWAIEHWGVEPDMILMAKALSGG 270 Query: 261 VFPISCAAANRDIL-GVFEPGS----HGSTFGGNPLACAVSIAALEVLEEEKLTERSLQL 315 P+ A + I+ VF HGSTF N +A A IA LEVL EE+L E + +L Sbjct: 271 FIPVGAVAMKKHIMEAVFNRMDRAVVHGSTFSKNNMAMAAGIATLEVLAEERLVENAAKL 330 Query: 316 GEKLVGQLKEIDN--PMITEVRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHE----- 368 GE+++ ++ + + ++ VRGKG+ I +E P LKAA L + ++ Sbjct: 331 GEQIISGIRAMTDRYELLHAVRGKGMMIAVEFGAPK---SFSLKAAWSLLETANKGLFSQ 387 Query: 369 ---------------------NVIRIAPPLVISEEDLEWAFQKIKAVLS 396 NV++ PPLVI + D +W Q + V++ Sbjct: 388 MITIPLFKNHRILSQVAGHGMNVVKFLPPLVIGQRDADWILQAMDTVIA 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: 424 Number of extensions: 22 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: 462 Length adjustment: 32 Effective length of query: 364 Effective length of database: 430 Effective search space: 156520 Effective search space used: 156520 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