Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= curated2:Q8TUE8 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 197 bits (500), Expect = 7e-55 Identities = 138/410 (33%), Positives = 216/410 (52%), Gaps = 54/410 (13%) Query: 35 LVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAENLIHVSNLYYTEI 94 L + +G+G + D G+ Y+D ++ N GH +P + A++ Q + L HV +T Sbjct: 48 LPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHE 107 Query: 95 QA-EFAETLASIT--GMERVFFCNSGAESVEAAMKLA------RVATGKSAFVAAEHSFH 145 A E AE LA IT G+ERVF ++G+ ++E A+K++ + A K+ F+A S+H Sbjct: 108 PAIELAERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSYH 167 Query: 146 GRTIGALSVTHKSMYRDPFMP--------PVSSETTFVPYSDAEA-----------IRQA 186 G T+GALSV+ ++YR + P P P AEA + + Sbjct: 168 GETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLEQ 227 Query: 187 ISENTAAVILEP-IQGEGGINIPDPGYLKEVREICDETGALLIFDEVQTGFGRTGTWFCK 245 + T AVI+EP +Q GG+ + P YL +R +CDE G I DE+ GFGRTGT F Sbjct: 228 HAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFAC 287 Query: 246 EQFGVEPDIMSMSKAIGGGF-PMGAI--------AAHNGINFGRG-QHASTFGGGPLACA 295 EQ GV PD M +SK + GGF P+ A+ A + N G+ H+ ++ G PLAC Sbjct: 288 EQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLACR 347 Query: 296 AALASVKVIREEKLLERSKEMGAYFMKKLAGM-VRDDVVEVRGKGLMIGVEI-------- 346 AALA++ + R+E +LER++E+ A+ ++LA + V +VR G++ VE+ Sbjct: 348 AALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQVADVRQTGMIAAVELVRDKATRA 407 Query: 347 KYPCG-----KFVDFAREQGVLVNCTSDSVLRLVPPLVITKEQIDTVVDV 391 YP + E G L+ +V+ +PP V++ +++D +VDV Sbjct: 408 PYPSEERRGLRVYLHGLEHGALLR-PLGNVVYFMPPYVVSTDELDHLVDV 456 Lambda K H 0.319 0.135 0.391 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: 416 Number of extensions: 18 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: 395 Length of database: 467 Length adjustment: 32 Effective length of query: 363 Effective length of database: 435 Effective search space: 157905 Effective search space used: 157905 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 Aug 03 2021. The underlying query database was built on Aug 03 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