Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_078430602.1 BK574_RS25380 acetylornithine transaminase
Query= curated2:Q9X2A5 (385 letters) >NCBI__GCF_002019605.1:WP_078430602.1 Length = 405 Score = 309 bits (792), Expect = 8e-89 Identities = 159/387 (41%), Positives = 249/387 (64%), Gaps = 6/387 (1%) Query: 2 YLMNTYSRFPATFVYGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLI 61 YLM+TY+R P T G+G+ + D +G +YLD +G+AVNVLGHSHP +V+ IK+Q EK + Sbjct: 11 YLMSTYNRLPITIERGEGNRLIDTEGKSYLDLFTGLAVNVLGHSHPEIVKTIKEQGEKFL 70 Query: 62 HCSNLFWNRPQMELAELLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKKYRILS 121 H SN+F N+P ++LA+ L ++ GKVFF N+G EA EAA+K+ K+ K+ +++ ++ Sbjct: 71 HISNVFLNQPAIQLAQKLVNHSINGKVFFTNSGAEATEAALKLIHKWTKEGNKENRGVVV 130 Query: 122 AHNSFHGRTLGSLTATGQPKYQKPFEPL-VPGFEYFEFNNVEDLRRKM-SEDVCAVFLEP 179 SFHGRTLG+L T QP + F +P +E E +N+E L + +++ A+ +EP Sbjct: 131 LEKSFHGRTLGALKLTRQPGVYQDFPVTDMPVYE-VEPHNIEQLEEVIKTKNPAAILMEP 189 Query: 180 IQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKYGVVPDVLTTA 239 + G GI+P +E+L+E +L +Y L DE+Q G+GRTGKLFAYQ G+ PD++ A Sbjct: 190 VLGSGGILPLQEEYLQEVSRLAKQYGVLCCMDEIQTGIGRTGKLFAYQHAGITPDLILFA 249 Query: 240 KGLGGGVPIGAVIV-NERANVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEEK 298 KG+GGG+P+G +IV E +++ PGDHGTTF +PL+ G TV++ L ++G L++ + Sbjct: 250 KGVGGGLPLGGIIVAEELSHLFRPGDHGTTFAPSPLSAALGNTVLRVLLEDGELDQSVNR 309 Query: 299 GNYLMKKLQEMKEEY-DVVADVRGMGLMIGIQFREEVSN-REVATKCFENKLLVVPAGNN 356 NYL +KL E+KE++ ++ ++RG G+M+GI + +++ E+ LV Sbjct: 310 SNYLHEKLNELKEKHPHMITEIRGKGMMVGIVTSLKTEEAKDLQRNLLEDGYLVDVTQQT 369 Query: 357 TIRFLPPLTVEYGEIDLAVETLKKVLQ 383 +R LPPLT+ E++ V + LQ Sbjct: 370 IVRLLPPLTLTESEVNSFVGVFETNLQ 396 Lambda K H 0.318 0.138 0.402 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: 436 Number of extensions: 20 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: 405 Length adjustment: 31 Effective length of query: 354 Effective length of database: 374 Effective search space: 132396 Effective search space used: 132396 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 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