Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein
Query= curated2:Q58131 (398 letters) >FitnessBrowser__Pedo557:CA265_RS15205 Length = 378 Score = 277 bits (709), Expect = 3e-79 Identities = 160/370 (43%), Positives = 224/370 (60%), Gaps = 27/370 (7%) Query: 26 VEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQAETLIHTS--NIYYTIPQ 83 V KG+ +YD KK++D +AGIGV+NVGHCHP VV+AI++QAET +H Y PQ Sbjct: 5 VRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMHLMVYGEYVQTPQ 64 Query: 84 IKLAKKLVEL--SGLDRAFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISMYNAFHGR 141 + AK L ++ L +F NSG EA EGA+K A++Y GR+G I+ NA+HG Sbjct: 65 VNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYT----GRKG--FIACKNAYHGS 118 Query: 142 TLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAITDKTAAIMIEPVQGEGGIHVA 201 T + Y G+ P P ++ N++ L E IT++ AA+ IEP+QGE GI V+ Sbjct: 119 TQGAESLMESDFYSSGYGPFLPHVSFIEHNNLADL-EKITNEIAAVFIEPIQGEAGIRVS 177 Query: 202 DKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVEPDILTLAKALGGGVPIG 261 D Y++A+R C + +LIFDE+Q G GR+G+MFAFEHY V PD+L LAK +GGG+PIG Sbjct: 178 DLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGGMPIG 237 Query: 262 AVVLKEEIAKALSYG---DHGTTFGGNPLACSAALASVEVIEELIKDDKVIEKGKYFIRK 318 A + EI LS+ H TTFGG+P+ C+A LA++ + + D+V EKG+ F + Sbjct: 238 AFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQLFKQL 297 Query: 319 LENLIEKYNFIKEVRGLGLMIGAELEFNGADIVKKMLEKGFLINCTSDTVL------RFL 372 L+ + IKE+RG GLM+ +EF +I KK+++ L SD L R Sbjct: 298 LQ-----HPAIKEIRGKGLMLA--VEFENFEINKKIIDACILDGVLSDWFLHCSNSMRIA 350 Query: 373 PPLIVEKEHI 382 PPLI+ KE I Sbjct: 351 PPLIITKEEI 360 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: 402 Number of extensions: 19 Number of successful extensions: 7 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: 378 Length adjustment: 30 Effective length of query: 368 Effective length of database: 348 Effective search space: 128064 Effective search space used: 128064 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