Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_027179082.1 G496_RS0109520 aspartate aminotransferase family protein
Query= curated2:O30156 (375 letters) >NCBI__GCF_000429985.1:WP_027179082.1 Length = 460 Score = 218 bits (555), Expect = 3e-61 Identities = 143/388 (36%), Positives = 211/388 (54%), Gaps = 41/388 (10%) Query: 26 EGCYVYDVNGKRYLDLVAGIATVSIGHCNSHLVERLKEQLE-KLIHISNLYYTTPQVELA 84 +G Y+ D NG+R LD +AG +IG + H+ E LK+ L+ K + + + LA Sbjct: 45 QGAYLTDENGRRVLDFLAGFGVYNIGRNHPHVAEVLKDVLDAKTASLVQMDVSPLCGMLA 104 Query: 85 EKLSEIA--GMDRFFFCNSGAEAVEAALKFARRATGRKKFVSFTGDFHGRTMGALSVTHK 142 EKL+ +A ++ FF NSG E+VE ALKFAR+A+G+ K V FHG T+GALSV Sbjct: 105 EKLASLAPGDLEAVFFTNSGTESVEGALKFARQASGKHKVVHCEHAFHGLTLGALSVNGN 164 Query: 143 EKFRKPFEPLVSPVEFAEFNNPESLEKVVDE-ETAAVIVELVQGEAGVYPADREFVKAIE 201 ++FR+ EPL+ FN+ +LE V E + A I+E VQG+ GV+ + ++ + Sbjct: 165 KEFRERNEPLLPDCVRIPFNDLAALEAVFREGDVGAFIMETVQGK-GVFIPEDGYLAGVR 223 Query: 202 ELREKYGFLLIVDEVQTGFGRTGRWFAKDHYGIEPDMITMAKAMGSG-VPIGCCALKEEV 260 EL +KY LLI DEVQ G GRTG+ FA DH+GI+PD++ ++KA+ G VP+G E+ Sbjct: 224 ELCDKYEVLLIADEVQCGMGRTGKMFAVDHWGIKPDIMAVSKALSGGYVPVGAIITTREL 283 Query: 261 AEKI-----QVGDHGSTFGGNPLACTAALATIEVIEREGLVENSARMGEYF------VKR 309 ++ + H +TFG N LA A LATIEV+E+E LVEN+AR+G+ + + Sbjct: 284 HSRVFDSMERCFAHSNTFGQNDLAMAAGLATIEVLEKENLVENAARIGDKIKAGLIELSK 343 Query: 310 LKESFENVIGVGLMIGFDVGDAAEFVRKC-------LENGLL-----------------V 345 E + G+GLMIG + K + N L V Sbjct: 344 RYEMLSEIRGIGLMIGMQFSEPKSLGLKASWKLLHKMNNDLFCQMITMPLLDKHNILTQV 403 Query: 346 NNTSERRIRLVPPLVITEREVDKAVEIM 373 ++++PPL IT+ + DK + M Sbjct: 404 AGHGLDTVKILPPLTITDEDADKFLTAM 431 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: 421 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 460 Length adjustment: 31 Effective length of query: 344 Effective length of database: 429 Effective search space: 147576 Effective search space used: 147576 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 10 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