Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013092327.1 BC1002_RS22675 aspartate aminotransferase family protein
Query= curated2:Q8TUE8 (395 letters) >NCBI__GCF_000092885.1:WP_013092327.1 Length = 442 Score = 177 bits (450), Expect = 4e-49 Identities = 132/404 (32%), Positives = 197/404 (48%), Gaps = 55/404 (13%) Query: 34 PLVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAENL-----IHVSN 88 P +L KG + G+E +D AG+ N GH +V AI Q L + + Sbjct: 27 PRLLESAKGMYYRSTDGREILDGCAGLWCVNAGHSRDEIVAAITQQLSTLDFAPTFQMGH 86 Query: 89 LYYTEIQAEFAETLASITGMERVFFCNSGAESVEAAMKLA------RVATGKSAFVAAEH 142 E + AE + G++R+FF NSG+ESV+ A+K+A R ++ + E Sbjct: 87 PLAFEAATKVAELMPE--GLDRIFFTNSGSESVDTALKIALAYHRARGEGQRTRLIGRER 144 Query: 143 SFHGRTIGALSVTHKSMYRDPFMPPVSSETTFVPYSD------------------AEAIR 184 +HG G +SV + R F + +P++ AE + Sbjct: 145 GYHGVGFGGISVGGIAPNRKTFSGALLPAVDHLPHTHNLEHNAFSKGQPAWGAHLAEELE 204 Query: 185 QAIS----ENTAAVILEPIQGEGGINIPDPGYLKEVREICDETGALLIFDEVQTGFGRTG 240 + ++ AAVI+EP+ G G+ IP GYL+++REIC + G LLIFDEV TGFGR G Sbjct: 205 RIVALHDASTIAAVIVEPVAGSTGVLIPPQGYLQKLREICTKHGILLIFDEVITGFGRLG 264 Query: 241 TWFCKEQFGVEPDIMSMSKAI-GGGFPMGAIAAHNGIN---FGRGQ-------HASTFGG 289 E FGV PD+++M+KAI PMGA+AA I+ G G H T+ Sbjct: 265 KATASEHFGVTPDLITMAKAINNASIPMGAVAASRTIHDTVVGSGAPGAIELFHGYTYSA 324 Query: 290 GPLACAAALASVKVIREEKLLERSKEMGAYFMKKLAGM-VRDDVVEVRGKGLMIGVEIKY 348 P A AAA+A++ + R ++L ER+ + F G+ V +VR GL+ G+E++ Sbjct: 325 HPAAAAAAIATLNLYRRDQLFERAASLAPTFEAAAHGLRGAKHVKDVRNLGLVAGIELES 384 Query: 349 PCG-----KFVDFAR--EQGVLVNCTSDSVLRLVPPLVITKEQI 385 G + F + E GVL+ T D +L PPL+I +EQI Sbjct: 385 RDGAPGARAYEAFVKCFEAGVLIRFTGD-ILAFSPPLIIDEEQI 427 Lambda K H 0.319 0.135 0.391 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: 388 Number of extensions: 16 Number of successful extensions: 4 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: 395 Length of database: 442 Length adjustment: 32 Effective length of query: 363 Effective length of database: 410 Effective search space: 148830 Effective search space used: 148830 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 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