Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= curated2:O30156 (375 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 252 bits (643), Expect = 1e-71 Identities = 150/368 (40%), Positives = 213/368 (57%), Gaps = 14/368 (3%) Query: 11 ILQTYTRQKVVIERGEGCYVYDVNGKRYLDLVAGIATVSIGHCNSHLVERLKEQLEKLIH 70 + Y + I + G V+D N ++YLDL G A +SIGH N H V RL +QL K+ Sbjct: 3 LFDVYPLNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGF 62 Query: 71 ISNLYYTTPQVELAEKLSEIAGMDRF--FFCNSGAEAVEAALKFARRATGRKKFVSFTGD 128 SN QV+LAEKL E++G F F CNSGAEA E ALK A GRKK ++FTG Sbjct: 63 YSNSVKIPLQVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGA 122 Query: 129 FHGRTMGALSVTHKEKFRKPFEPLVSPVEFAEFNNPESLE---KVVDEETAAVIVELVQG 185 FHGRT A++VT K P + + F FNN +LE K E +AVI+E +QG Sbjct: 123 FHGRTSLAVAVTDNPKIVAPVNQTENVI-FLPFNNEIALEETFKAQGNEISAVIIEGIQG 181 Query: 186 EAGVYPADREFVKAIEELREKYGFLLIVDEVQTGFGRTGRWFAKDHYGIEPDMITMAKAM 245 G+ A + F++ I L ++Y + I D VQ G+GRTG +++ D+ G+E D+ TMAK M Sbjct: 182 VGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKGM 241 Query: 246 GSGVPIGCCALKEEVAEKIQVGDHGSTFGGNPLACTAALATIEVIEREGLVENSARMGEY 305 G+G P+ ++ + K G+ G+TFGGN LAC AALA +EV+E++ L++N+ +G Y Sbjct: 242 GNGFPVAGISIASKF--KPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNY 299 Query: 306 FVKRLKESFENVI---GVGLMIGFDVGDAAEFVRKCL--ENGLLVNNTSERRIRLVPPLV 360 + LK+ FE V+ G GLMIG ++ V+K L + + IRL+P L Sbjct: 300 LIAELKK-FEQVVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVIRLLPALN 358 Query: 361 ITEREVDK 368 +T+ D+ Sbjct: 359 LTKAHADE 366 Lambda K H 0.320 0.138 0.398 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: 334 Number of extensions: 18 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: 375 Length of database: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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 (21.8 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