Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__SynE:Synpcc7942_0031 Length = 424 Score = 193 bits (490), Expect = 9e-54 Identities = 136/403 (33%), Positives = 212/403 (52%), Gaps = 37/403 (9%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNL-YYN 77 P+ +V G+GAR+ +G E ID ++ VN+ GH H +VEA+ +Q L H + + Sbjct: 20 PLKVVSGKGARLTLADGRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSH 79 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF-----TGCTKFIAFEGGFH 132 EP A L + P+ L +VFF ++G+ +VE A+K+A ++ ++ +AF+G +H Sbjct: 80 EPAERLAMELCKILPEKLTRVFFSDNGSTAVEVALKMALQYWHNLDQPRSRILAFDGAYH 139 Query: 133 GRTMGALSATWKPEFREPFEPLVPEFEHVPY-----GD----------VNAVEKAID-DD 176 G T GA+S + F PFE L+ E +PY GD + AVE+A+ D Sbjct: 140 GDTFGAMSVGERSLFNAPFEKLLFSVEFLPYPETWWGDETVEAKEAAAIAAVEQALAAGD 199 Query: 177 TAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHED 235 AAVI+EP VQG G+R+ FL++L G LLI DEV +G GRTG +FA + Sbjct: 200 VAAVIIEPLVQGAGGMRMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQRAG 259 Query: 236 VLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAA 288 + PD++CL+KGL GG +P+ T+A E + + F G+ HG ++ NPL CAA A+ Sbjct: 260 IQPDLICLSKGLTGGFLPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAAIAS 319 Query: 289 VSTVLE-ENLPEAAERKGKLAMRILSEAEDVVEEVRGRGLMMGVEVGD-----DERAKDV 342 + +L+ E + + E + +L++ V G+ V D D V Sbjct: 320 LELLLDSEAIVQGLEDAHLPGLELLAQHPKVTRPRLTGGIAACDLVSDRGGYLDPIGLRV 379 Query: 343 AREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADAL 385 + + RG L+ G+V+ L+PP + EL+ A +AD L Sbjct: 380 RQAAIARGLLLR-PLGNVLYLLPPYCLTPTELQDIYAAIADLL 421 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: 416 Number of extensions: 19 Number of successful extensions: 8 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: 424 Length adjustment: 31 Effective length of query: 358 Effective length of database: 393 Effective search space: 140694 Effective search space used: 140694 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