Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 276 bits (707), Expect = 6e-79 Identities = 139/373 (37%), Positives = 237/373 (63%), Gaps = 10/373 (2%) Query: 20 VTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCS--NLYYN 77 + + EG ++ +G +YIDL++GI V+ +GH HP V++A+++Q+++ +H Y Sbjct: 21 IEIEKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMHLMVYGEYVQ 80 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFTGCTKFIAFEGGFHGRTMG 137 PQ + A+ L + PK L+ V+ NSG+E+VE A+KLA+++TG + ++ +HG + G Sbjct: 81 SPQTQLAKALTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYTGRREILSCVNAYHGSSHG 140 Query: 138 ALSATWKPEFREPFEPLVPEFEHVPYGDVNAVEKAIDDDTAAVIVEPVQGEAGVRIPPEG 197 ALS F+ + PL+P H+ + + + +++ I ++TAA++VE VQGEAG+R+ + Sbjct: 141 ALSVGGNEIFKRAYRPLLPGIRHLDFNEPDQLDQ-ITEETAAIMVETVQGEAGIRVGTKE 199 Query: 198 FLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGGVPVGATI 257 + + LR CDE G LLI+DE+Q+G GRTG+F+AF+H D++PDIV AKG+GGG+P+GA I Sbjct: 200 YFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGGGMPIGAFI 259 Query: 258 AREEVAEAFEPG---DHGSTFGGNPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSE 314 A + + F+ H +TFGG+P++CAA A + + +E L + ERK L + L+ Sbjct: 260 APQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVERKANLFKKHLNH 319 Query: 315 AEDVVEEVRGRGLMMGVEVGDDERAKDVAREMLDRGALVN--VTSGDVIRLVPPLVIGED 372 + ++E+R +GLMM V+ E K + ++ G + + + D +R+ PPL I ++ Sbjct: 320 PK--IQEIRNKGLMMAVKFEAFEVLKPIIDRAIELGIITDWFLFCEDSMRIAPPLTITDE 377 Query: 373 ELEKALAELADAL 385 E+EKA A + ++ Sbjct: 378 EIEKACAIILQSI 390 Lambda K H 0.318 0.137 0.405 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: 376 Number of extensions: 22 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: 389 Length of database: 393 Length adjustment: 31 Effective length of query: 358 Effective length of database: 362 Effective search space: 129596 Effective search space used: 129596 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