Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= curated2:P36839 (385 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 266 bits (680), Expect = 7e-76 Identities = 152/381 (39%), Positives = 229/381 (60%), Gaps = 17/381 (4%) Query: 4 LFQTYGRWDIDIKKAKGTYVEDQNGKTYLDFIQGIAVSNLGHCHEAVTEAVKKQLDSVWH 63 LF Y +DI+I K +G V D+NG YLD G AV ++GH H E + Q+ ++ Sbjct: 3 LFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGF 62 Query: 64 VSNLFQNSLQEQAAQKLAAHSAGD--LVFFCNSGAEANEGAIKLARKATGKTKIITFLQS 121 SN N LQ+Q A++L S + +F NSGAEANE A+KLA G+TK+I+F ++ Sbjct: 63 YSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKA 122 Query: 122 FHGRTYAGMAATGQDKIKTGFGPMLGGFH--YLPYNDPSAFKALGEEGDIAAVMLETVQG 179 FHGRT + AT I P+ H YLP ND A K +GD+ AV++E +QG Sbjct: 123 FHGRTSLAVEATNNPTI---IAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQG 179 Query: 180 EGGVNPASAEFLSAVQSFCKEKQALLIIDEIQTGIGRTGKGFAYEHFGLSPDIITVAKGL 239 GG+ + EF+ ++ C E +LI+DEIQ+G GR+GK FA+++ + PDIITVAKG+ Sbjct: 180 VGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGI 239 Query: 240 GNGFPVGAVIGKKQLGEAFTP--GSHGTTFGGNMLAMAAVNATLQIVFQPDFLQEAADKG 297 GNGFP+ V+ + F P G GTTFGGN LA +A A + ++ Q + ++ A G Sbjct: 240 GNGFPMAGVL----ISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVG 295 Query: 298 AFLKEQLEAELKSPFVKQIRGKGLMLGIECDGPVADIIAEL-QTLGLLVLPAGPNVIRLL 356 +L E+L+ K P +K++RG+GLM+G+E + P+ ++ + L + +G NV+RLL Sbjct: 296 DYLLEELK---KFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGTNVLRLL 352 Query: 357 PPLTVTKDEIAEAVSKLKQAI 377 PPL ++ +E E +++ K+ + Sbjct: 353 PPLCLSMEEADEFLARFKRVL 373 Lambda K H 0.318 0.135 0.390 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: 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: 385 Length of database: 373 Length adjustment: 30 Effective length of query: 355 Effective length of database: 343 Effective search space: 121765 Effective search space used: 121765 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 (21.7 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