Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_043768728.1 U743_RS12545 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000733765.1:WP_043768728.1 Length = 456 Score = 173 bits (439), Expect = 8e-48 Identities = 122/417 (29%), Positives = 193/417 (46%), Gaps = 56/417 (13%) Query: 22 LPIV-ISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA-F 79 LP+V + +AEG W+ P G RY+D +S++ GHRHP I+ L Q + + A F Sbjct: 29 LPLVPVERAEGAWLYGPNGERYLDAVSSWWTNIFGHRHPHIVERLKTQLDTLDHAMLAGF 88 Query: 80 HSDQLGPWYEKVAKLTNKEMVLPM--NTGAEAVETAIKTARRWAYDVKKVEANRAEIIVC 137 + E++A +T + M + G+ A+E A+K + Y V + R I Sbjct: 89 THPPVVELSERLAAITPGGLSRCMYADNGSSAIEVALKMSHH--YWVNSGQPQRTRFIAL 146 Query: 138 EDNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIP------------------------- 172 ++HG TMGA+++SS Y+ + +L IV+ Sbjct: 147 SGSYHGETMGALAVSSTGLYRDAYKALLMEPIVVQAPDCGVMDPGTRAPGVSWEDHARRT 206 Query: 173 YGDLEALKAAITPNTAAFILEP-IQGEAGINIPPAGFLKEALEVCKKENVLFVADEIQTG 231 + ++EA A TAA I+EP +Q G+ + P +LK E C + V +ADEI TG Sbjct: 207 FKEMEAALEAHAHETAAVIVEPMLQCAGGMRMWPPIYLKLLREACDRHGVHLIADEIATG 266 Query: 232 LGRTGKVFACDWDNVTPDMYILGKALGGGVFPISCAAANRDILGVF-------EPGSHGS 284 RTGK+FAC+W ++ PD L K L GG P++ N + F + H Sbjct: 267 FCRTGKLFACEWADIEPDFLCLSKGLTGGTLPLAVCMTNEQVYRAFYDDYSSGKAFLHSH 326 Query: 285 TFGGNPLACAVSIAALEVLEEEKLTERSLQLGEKLVGQLKEID-NPMITEVRGKGLFIGI 343 ++ GNPL C ++A L++LEE +LG+ L Q+ E+ +P + +VR +G + I Sbjct: 327 SYTGNPLTCTAALATLDILEERDWPAHVRKLGQHLWNQVSELTRHPHVADVRQQGFVLAI 386 Query: 344 EL--------------NEPARPYCEQLKAAGLLCKETHENVIRIAPPLVISEEDLEW 386 +L R Y L LL N + PP ++EE+++W Sbjct: 387 DLAADGPGRVPYPAGERRGLRVYQHGLSQGALL--RPLGNTVYFMPPYCVTEEEIDW 441 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: 495 Number of extensions: 31 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: 396 Length of database: 456 Length adjustment: 32 Effective length of query: 364 Effective length of database: 424 Effective search space: 154336 Effective search space used: 154336 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