Align ornithine aminotransferase; EC 2.6.1.13 (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= CharProtDB::CH_122124 (454 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 250 bits (638), Expect = 7e-71 Identities = 154/400 (38%), Positives = 222/400 (55%), Gaps = 19/400 (4%) Query: 33 YHPLPVVFARAQGTSVWDPEGRHYLDFLSAYSAVNQ-GHCHPKLVAALVDQASRLTLSSR 91 Y P VV +G VWD EGR Y+D L A AVN GH P LV ALV QA +L SS Sbjct: 22 YRPREVVLDHGKGARVWDTEGRDYVD-LGAGIAVNALGHQDPDLVDALVTQARKLWHSSN 80 Query: 92 AFYNDVFPKFAEMVTKYFGF-DMVLPMNTGAEAVETGIKIARKWGYKVKGIPENEAIILS 150 FY + AE + + GF + V N+G EA E IK+ RKW KG + +IL+ Sbjct: 81 VFYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKLVRKWAAS-KGRAPEQRVILT 139 Query: 151 AENNFHGRTMAAISLSSDPESRENYGPYVPNIGCTIPGTEKPITYNDKAALREAFEKAGS 210 +FHGRT+AA++ ++ P+ +ENY P +PG + + +ND A L AF A Sbjct: 140 FRGSFHGRTLAAVTATAQPKYQENYEP--------LPGGFRYLDFNDVAGLEAAF--AQG 189 Query: 211 NLAAFLVEPIQGEAGIIVPDDDYLQLARSLCDQHNVLLICDEIQTGIARTGKLLCHEWSG 270 ++AA ++EP+QGE G++ +++ AR LCD H LL+ DEIQ G+ RTG L H G Sbjct: 190 DVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDG 249 Query: 271 IKPDMVLLGKAISGGMYPVSCVLGRKDVMLTVEPGTHGSTYGGNPLACAVAIRALEVVQE 330 + PD+V L KA+ G +P+ +L V ++ G HG+T+GGNP+A AVA AL + Sbjct: 250 VTPDIVTLAKALGCG-FPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLAS 308 Query: 331 ENMVERAEKLGQAFRSGLEAIQN--PIIQTVRGKGLLNAIVIDESKTNGHTAWDLCMLMK 388 ++ K QA R GL AI + VRG+GL+ V+ E+ A ++ Sbjct: 309 AELMANVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKG--RAGEVLDHAA 366 Query: 389 EKGLLAKPTHQNIIRLAPPLVITEEEIAKALEIIKAAVAE 428 GLL +++R PPL IT+ ++A+ L ++AA+A+ Sbjct: 367 AHGLLVLQAGPDVLRFVPPLNITDADLAEGLARLRAALAD 406 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: 408 Number of extensions: 25 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: 454 Length of database: 411 Length adjustment: 32 Effective length of query: 422 Effective length of database: 379 Effective search space: 159938 Effective search space used: 159938 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 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