Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_007473232.1 CMTB2_RS01220 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:O30156 (375 letters) >NCBI__GCF_000170735.1:WP_007473232.1 Length = 420 Score = 148 bits (373), Expect = 3e-40 Identities = 104/325 (32%), Positives = 173/325 (53%), Gaps = 24/325 (7%) Query: 22 IERGEGCYVYDVNGKRYLDLVAGIATVSIGHCNSHLVERLKEQLEKLIHISNLYYTTPQV 81 IE+GEG Y++D+ G +YLD + + GHC+ + E ++K +S T +V Sbjct: 32 IEKGEGAYIFDIEGNKYLDYIQSWGPLIFGHCDKDTQNAIIEAVKK--GVSFGAPTKVEV 89 Query: 82 ELAEKLSEI-AGMDRFFFCNSGAEAVEAALKFARRATGRKKFVSFTGDFHGRTMGAL--S 138 ELA+++ E+ ++ F NSG EA +A++ AR TG+ + F G +HG + L + Sbjct: 90 ELAKEVLELFPHLNLIRFVNSGTEATMSAIRLARGYTGKDDIIKFEGCYHGHSDSLLVSA 149 Query: 139 VTHKEKFRKPFEPLVSPVEF------AEFNNPESLEKVVDE-ETAAVIVELVQGEAGVYP 191 + F P P V P +F A++N+ ES++K + + VI+E + G + P Sbjct: 150 GSGAATFGVPSSPGV-PADFTKHTLLAKYNDIESVKKCFENGDVGCVIIEPIAGNMSLVP 208 Query: 192 ADREFVKAIEELREKYGFLLIVDEVQTGFGRTGRWFAKDHYGIEPDMITMAKAMGSGVPI 251 ++EF+ + E+ YG +LI DEV +GF R + D YGI+ D++T K +G G+P+ Sbjct: 209 GEKEFLGELREICNHYGAVLIFDEVMSGF-RASLRGSFDIYGIKADIVTFGKVIGGGMPV 267 Query: 252 GCCALKEEVAEKIQ-VGD--HGSTFGGNPLACTAALATIEVIER-----EGLVENSARMG 303 G A K+E+ EK+ VG T GNP+A +A L I+ ++ + L + + ++ Sbjct: 268 GAFAGKKEIMEKLSPVGPVYQAGTLSGNPVAMSAGLTVIKKLKENPEIYKELEDKAKKLM 327 Query: 304 EYFVKRLKES--FENVIGVGLMIGF 326 E F + KE+ N +G M GF Sbjct: 328 EGFSEISKENNIDFNYNVIGSMFGF 352 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: 391 Number of extensions: 17 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: 375 Length of database: 420 Length adjustment: 31 Effective length of query: 344 Effective length of database: 389 Effective search space: 133816 Effective search space used: 133816 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