Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_093394523.1 BM091_RS06910 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q9X2A5 (385 letters) >NCBI__GCF_900114975.1:WP_093394523.1 Length = 432 Score = 162 bits (410), Expect = 2e-44 Identities = 131/393 (33%), Positives = 195/393 (49%), Gaps = 34/393 (8%) Query: 19 GSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCSNLFWNRPQMELAEL 78 G++I+DE GN Y+D+ +LGH+HP +V AIKD AE+ S + ++++AE Sbjct: 43 GAYIWDEDGNRYVDYVCSWGPLILGHAHPAVVSAIKDVAER--GTSYGIPTKLEVDMAEQ 100 Query: 79 LSKNTFGGK-VFFANTGTEANEAAIKIARKY-GKKKSEKKYRILSAHNSF----HGRTLG 132 + K + V F N+GTEA +A+++AR G+KK K H+ G + Sbjct: 101 VVKMVPSVEMVRFVNSGTEATMSALRLARAVTGRKKIVKFGGCYHGHSDCLLVSSGSGVV 160 Query: 133 SLTATGQPKYQKPFEPLVPGFEYFEFNNVEDLRRKMSEDVCAVFLEPIQGESGIVPATKE 192 +L G P + Y + VE + +M +++ AV +EP+ G G+VP K Sbjct: 161 TLGIPGSPGVPEEIVTHTVSLPYNNLSAVEKVFDEMGKEIAAVIVEPVAGNMGVVPPEKG 220 Query: 193 FLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKYGVVPDVLTTAKGLGGGVPIGAV- 251 FLE R LCD + ALL+FDEV G R A + Y V+PD+ K +GGG+P+GA Sbjct: 221 FLEGLRNLCDRWSALLIFDEVITGF-RLSPGGAQRYYNVMPDITCLGKIIGGGLPVGAYG 279 Query: 252 ----IVNERA---NVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEEKGNYLMK 304 I+ E A V + G T GNPLA AG+ +K L GF E++E+K YL K Sbjct: 280 GRSEIMREVAPSGKVYQAG----TLSGNPLAMAAGLATLKILETPGFYEDLEKKSAYLEK 335 Query: 305 KLQEMKEEYDVVADVRGMGLMIGIQFRE-EVSNREVATKCFENKLLVVPAG--NNTIRFL 361 L+E + V ++ +G M FR V N E A K N + G N I +L Sbjct: 336 GLREAVSDAGVEMVLQRVGSMGCGFFRSGAVKNFEDAIKSDTNAYALFWRGMLENGI-YL 394 Query: 362 PPLTVE---------YGEIDLAVETLKKVLQGI 385 P E Y ++D ++ +KVL+ + Sbjct: 395 APSQFEAFFVSSAHSYEDLDRTIDAARKVLKNM 427 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: 434 Number of extensions: 28 Number of successful extensions: 5 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: 432 Length adjustment: 31 Effective length of query: 354 Effective length of database: 401 Effective search space: 141954 Effective search space used: 141954 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