Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Caulo:CCNA_01648 Length = 420 Score = 166 bits (421), Expect = 9e-46 Identities = 127/386 (32%), Positives = 188/386 (48%), Gaps = 26/386 (6%) Query: 16 SRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCS-NL 74 +R P+ +V GAR+ ++G E +D +A G+ HP + A+++Q+E + H Sbjct: 24 ARPPLPVVATRGARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHVMFGG 83 Query: 75 YYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKFT------GCTKFIAFE 128 +EP A+ LA P DL+ VFF SG+ +VE A+K+A ++ G T+F+AF Sbjct: 84 LAHEPAYRLAKRLARLLPGDLDHVFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFR 143 Query: 129 GGFHGRTMGALSATWKPE-FREPFEPLVPEFEHVPYGDVNAVEKAID-------DDTAAV 180 GG+HG T+ ++ E F ++P A E A+D + AA+ Sbjct: 144 GGYHGDTLATMTVCDPEEGMHSLFAGVMPAQVIADLPRDPASEAALDALLAARGHEIAAM 203 Query: 181 IVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPD 239 +VEP +QG G+ P LR LR L D+HG+LLI DE+ +G GRTG FA + V PD Sbjct: 204 LVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLFAMQAAGVEPD 263 Query: 240 IVCLAKGL-GGGVPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAAVSTV 292 IV L+K L GG +P+ A +AR V EAF D HG T+ NPLACAA A++ Sbjct: 264 IVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAALMHGPTYMANPLACAAANASLDLF 323 Query: 293 LEENLPEAAERKGKLAMRILS--EAEDVVEEVRGRGLMMGVEVGDDERAKDVAREMLDRG 350 + R L A + V +VR G + VE D+ G Sbjct: 324 EDGAWARDVARVSAALAEGLEPCRAGEGVVDVRTLGAIGVVEFEAPVPVSDLCARFAALG 383 Query: 351 ALVNVTSGDVIRLVPPLVIGEDELEK 376 + G V+ L P +++L + Sbjct: 384 VWIR-PMGKVVYLTPAFTTPDEDLSR 408 Lambda K H 0.318 0.137 0.405 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: 417 Number of extensions: 29 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: 389 Length of database: 420 Length adjustment: 31 Effective length of query: 358 Effective length of database: 389 Effective search space: 139262 Effective search space used: 139262 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 09 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