Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013841660.1 DESRU_RS08285 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q97GH9 (387 letters) >NCBI__GCF_000215085.1:WP_013841660.1 Length = 432 Score = 140 bits (354), Expect = 5e-38 Identities = 100/307 (32%), Positives = 153/307 (49%), Gaps = 30/307 (9%) Query: 19 KGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHVSNYYWNENAMEL 78 +G G++++D DGNEYID+V LGH +P+++ A++ + + Y +EL Sbjct: 42 RGNGSRMWDVDGNEYIDYVCSWGPLILGHRHPAVMHAVQ----RCLERGITYGAPTDLEL 97 Query: 79 T---EILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKKEIIYMDNSFHGRT- 134 T ++ + V M NSGTEA + L+LAR Y + +I+ + +HG Sbjct: 98 TLARMVVEALPGVEMVRMVNSGTEATMSALRLARAYT------KRNKIVKFEGCYHGHHD 151 Query: 135 -------MGALSVTGQPKYQESFKPLIGAVKSVKFNDL---DDIKQKISSKTAAVIVEPI 184 GAL+ G P + + G + ++NDL + I ++ + AA+IVEP Sbjct: 152 SLLIKAGSGALT-HGVPTSPGVPENIAGNTINARYNDLPLLEKIMAEVGREVAAIIVEPA 210 Query: 185 QGEGGIIPAKKEYLKLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKFEVVPDIVCIAK 244 G G++PA + +L+ LR LC++ ALLIFDEV G R+ A + V PD+ C+ K Sbjct: 211 AGNMGLVPAAEGFLEGLRKLCNQYGALLIFDEVITGF-RLSYGGAQSYYNVTPDLTCLGK 269 Query: 245 ALGGGFPIGAMLAKESVASSFVPGD---HGNTYGGNPLACAVAIAVLKELVDKKVVEINV 301 +GGG P+GA + P T GNPLA IA L++L V E + Sbjct: 270 IIGGGMPVGAYGGVREIMQMISPAGPVYQAGTLSGNPLAMTAGIATLEQLQQPGVYE-EL 328 Query: 302 NEKSKYL 308 N KS L Sbjct: 329 NRKSALL 335 Lambda K H 0.318 0.137 0.395 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: 376 Number of extensions: 19 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: 387 Length of database: 432 Length adjustment: 31 Effective length of query: 356 Effective length of database: 401 Effective search space: 142756 Effective search space used: 142756 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