Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate Echvi_2790 Echvi_2790 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Cola:Echvi_2790 Length = 434 Score = 139 bits (350), Expect = 2e-37 Identities = 135/445 (30%), Positives = 206/445 (46%), Gaps = 50/445 (11%) Query: 23 HKYMATTTNDPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQ 82 H Y A + N LV+++A GV+ DG L+D S G + P + AI++Q Sbjct: 16 HPYTAASRPMDN---LVVKKASGVFLELEDGTRLIDGMSSWWSTIHGYQVPALNRAIQQQ 72 Query: 83 LDLVLHAAGTDYYNPYQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA------K 136 L+ + H + EL + L+E+ P ++ VF S+SG+ A E A+K+A K Sbjct: 73 LENMAHVMFGGITHRPAAELTQALLEVVPQGLKH-VFYSDSGSVAVEVAMKMALQYWHSK 131 Query: 137 WSTNRKMFIAFIGAFHGRTHGTMSL----TASKPVQRSRMFPTMPGVVHVPYPNPYRNPW 192 ++ F +HG T MS+ T + +R+ P + +P P + Sbjct: 132 GQGSKNRFATVRSGYHGDTWHDMSVCDPVTGMHSIFNNRLSPQ----IFLPAPQSTFH-- 185 Query: 193 GIDGYENPDELINRVIDYIEEYLFEHYVPAEEVAGIFFEPI-QGEGGYVVPPKNFFKELK 251 +LI ++ +E L H+ EE+A EPI QG GG ++ LK Sbjct: 186 --------GQLIPEELEEVERVLSSHH---EEIAAFILEPIVQGAGGMRFYHPDYLNSLK 234 Query: 252 KLADKHGILLIDDEVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGG-IPIGATIFRADL 310 +K+ ILLI DE+ G GRTG+++A EH I PDI+ + KAL GG + AT+ AD+ Sbjct: 235 THCEKYDILLIADEIATGFGRTGKLFACEHAAITPDIMCIGKALTGGYMSFAATLCTADV 294 Query: 311 DFGVSG------VHSNTFGGNTVAAAAALAVIE-ELQNGLIENAQKLEPLFRERLEEMKE 363 +S +H TF GN +A A ALA +E L Q +E + L + + Sbjct: 295 AHTISDGSPGVFMHGPTFMGNPLACATALASLELLLAKDWKAEIQAIESHLNDALAGL-Q 353 Query: 364 KYEIIGDVRGLGLAWGVEFVKDRKTKEYATKERGEIVVEALKRGLALLGCGKSAIRLIPP 423 E + +VR LG A GV +K A + I KRGL L GK I +PP Sbjct: 354 TLEAVKEVRVLG-AIGVVEMK-------AEVDMKAIQAALTKRGLWLRPFGK-LIYTMPP 404 Query: 424 LIISEEEAKMGLDIFEEAIKVVSER 448 +I+ E + + ++IK E+ Sbjct: 405 FVITPAELQQLTNAMVDSIKAYGEK 429 Lambda K H 0.319 0.139 0.410 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: 458 Number of extensions: 26 Number of successful extensions: 3 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: 454 Length of database: 434 Length adjustment: 32 Effective length of query: 422 Effective length of database: 402 Effective search space: 169644 Effective search space used: 169644 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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