Align ornithine aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= CharProtDB::CH_122124 (454 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 238 bits (608), Expect = 2e-67 Identities = 151/388 (38%), Positives = 208/388 (53%), Gaps = 23/388 (5%) Query: 38 VVFARAQGTSVWDPEGRHYLDFLSAYSAVNQGHCHPKLVAALVDQASRLTLSSRAFYNDV 97 V+F + +G + +GR +LDF + + GH HP+LVAAL QA +L S + Sbjct: 15 VIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPG 74 Query: 98 FPKFAEMVTKYFGFDMVLPMNTGAEAVETGIKIARKWGYKVKGIPENEAIILSAENNFHG 157 + AE + K D NTGAEA+E IKIAR++ + G PE I+ + +FHG Sbjct: 75 QERVAERLIKASFADTAFFCNTGAEAMELVIKIARRY-HHCAGRPERNRIV-ACTGSFHG 132 Query: 158 RTMAAISLSSDPESRENYGPYVPNIGCTIPGTEKPITYNDKAALREAFEKAGSNLAAFLV 217 RT+A ++ + P+ E +GP + Y D A R A GSN AA LV Sbjct: 133 RTIATLAAAGTPKYLEGFGPVAQGFD--------HVPYGDLEAARGAI---GSNTAALLV 181 Query: 218 EPIQGEAGIIVPDDDYLQLARSLCDQHNVLLICDEIQTGIARTGKLLCHEWSGIKPDMVL 277 EP+QGE GI D YL+ R+L DQ +LL+ DE+QTGI RTGKL HEWSGI PD++ Sbjct: 182 EPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMG 241 Query: 278 LGKAISGGMYPVSCVLGRKDVMLTVEPGTHGSTYGGNPLACAVAIRALEVVQEENMVERA 337 L K + GG +PV VL + + PGTHG T+GGNPLA AVA L+ V +ER Sbjct: 242 LAKGLGGG-FPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERV 300 Query: 338 EKLGQAFRSGLEAIQN---PIIQTVRGKGLLNAIVIDESKTNGHTAWDLCMLMKEKGLLA 394 + + R L+ + I VRG+GL+ + T + + GLLA Sbjct: 301 QAVAALLRGRLDDLARRYPGAIAQVRGQGLMLGLKTVPVNTEFNAK------LFAAGLLA 354 Query: 395 KPTHQNIIRLAPPLVITEEEIAKALEII 422 N++RL PPL+I E E+ +A+EII Sbjct: 355 VGAGDNVVRLVPPLIIGEAEVERAVEII 382 Lambda K H 0.316 0.133 0.392 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: 430 Number of extensions: 21 Number of successful extensions: 5 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: 388 Length adjustment: 32 Effective length of query: 422 Effective length of database: 356 Effective search space: 150232 Effective search space used: 150232 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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