Align ornithine aminotransferase; EC 2.6.1.13 (characterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme
Query= CharProtDB::CH_122124 (454 letters) >FitnessBrowser__Burk376:H281DRAFT_04057 Length = 394 Score = 221 bits (564), Expect = 2e-62 Identities = 136/393 (34%), Positives = 211/393 (53%), Gaps = 19/393 (4%) Query: 38 VVFARAQGTSVWDPEGRHYLDFLSAYSAVNQGHCHPKLVAALVDQASRLTLSSRAFYNDV 97 +VF +G+ ++D G+ YLDF+ ++ GHC ++ AL QA L S AFYN+ Sbjct: 20 IVFTHGKGSWLYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPSPAFYNEP 79 Query: 98 FPKFAEMVTKYFGFDMVLPMNTGAEAVETGIKIARKWGYKVKGIPENEAIILSAENNFHG 157 K A ++T++ FD V N+GAEA E IK+ARKWG K K + I++ +++FHG Sbjct: 80 MAKLAALLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFK---DGAFEIITFDHSFHG 136 Query: 158 RTMAAISLSSDPESRENYGPYVPNIGCTIPGTEKPITYNDKAALREAFEKAGSNLAAFLV 217 RT+A +S S P Y P VP ND A++ + + A ++ Sbjct: 137 RTLATMSASGKPGWDTIYAPQVPGF--------PKADLNDIASVEKLI---NAKTVAVML 185 Query: 218 EPIQGEAGIIVPDDDYLQLARSLCDQHNVLLICDEIQTGIARTGKLLCHEWSGIKPDMVL 277 EPIQGE G+I +++Q R L +HNVLLI DE+Q+G R G L +E SG++PD++ Sbjct: 186 EPIQGEGGVIPATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMT 245 Query: 278 LGKAISGGMYPVSCVLGRKDVMLTVEPGTHGSTYGGNPLACAVAIRALEVVQEENMVERA 337 LGK I GG+ P++ +L + +V + E G G TY GNPL AV + + +E Sbjct: 246 LGKGIGGGV-PLAALLAKAEVAV-FEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGV 303 Query: 338 EKLGQAFRSG-LEAIQNPIIQTVRGKGLLNAIVIDESKTNGHTAWDLCMLMKEKGLLAKP 396 G+ R+ LE + + RG+GLL A+++ K G+ + M+ GLL Sbjct: 304 RARGEYLRAKLLELSEERGFKGERGEGLLRALLL--GKDIGNQIVEKARDMQPDGLLLNA 361 Query: 397 THQNIIRLAPPLVITEEEIAKALEIIKAAVAEL 429 N++R P L +T EEI + + ++++ + L Sbjct: 362 ARPNLLRFMPALNVTNEEIDQMMAMLRSILDTL 394 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: 386 Number of extensions: 15 Number of successful extensions: 4 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: 394 Length adjustment: 32 Effective length of query: 422 Effective length of database: 362 Effective search space: 152764 Effective search space used: 152764 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 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