Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase
Query= curated2:Q58131 (398 letters) >FitnessBrowser__azobra:AZOBR_RS19590 Length = 405 Score = 288 bits (738), Expect = 1e-82 Identities = 160/394 (40%), Positives = 229/394 (58%), Gaps = 8/394 (2%) Query: 7 IDLEKKYHLQIYGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKK 66 I E + Y L VVL G+G+ V+D +G +YLD L+ N GHCHPK++EA+ + Sbjct: 9 IGTEHRLGAHNYKPLDVVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQ 68 Query: 67 QAETLIHTSNIYYTIPQIKLAKKLVELSGLDRAFFCNSGAEANEGAIKFARKYVSKVLG- 125 QA L TS + ++L L+G + NSGAEA E AIK RK+ +V G Sbjct: 69 QASKLTLTSRAFRNDQLALFYEELAALTGSHKILPMNSGAEAVESAIKTVRKWGYEVRGV 128 Query: 126 -REGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAITDKT 184 EII + FHGRT++ ++ + P + GF P PGF+ VPF D AL+ A+T T Sbjct: 129 PENQAEIIVCSDNFHGRTISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALEAALTPNT 188 Query: 185 AAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVE 244 A+++EP+QGE G+ + YL+ VRDLC ++N+V+I DE+Q G+GRTG++ A EH GVE Sbjct: 189 VAVLLEPIQGEAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVE 248 Query: 245 PDILTLAKALGGG-VPIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVEVIEELI 303 D+ + KAL GG P+ AV+ E+ L G HG+TFGGNPLAC+ A A++ V+ E Sbjct: 249 ADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAMRVLVEEG 308 Query: 304 KDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAEL--EFNGA-DIVKKMLEKGFL 360 D +G YF+ +L + + N I+E RG GLM+ EL E GA + + +G L Sbjct: 309 MIDNAAAQGAYFLEQLGAI--RSNVIREARGRGLMLAVELHPEAGGARRYCEALRARGVL 366 Query: 361 INCTSDTVLRFLPPLIVEKEHIDALINALDEVFT 394 T D +R PPL++ +E +D + D V T Sbjct: 367 AKDTHDHTIRIAPPLVITREQVDWALEQFDAVLT 400 Lambda K H 0.320 0.141 0.409 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: 361 Number of extensions: 21 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: 398 Length of database: 405 Length adjustment: 31 Effective length of query: 367 Effective length of database: 374 Effective search space: 137258 Effective search space used: 137258 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: 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