Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012334877.1 M446_RS24880 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000019365.1:WP_012334877.1 Length = 415 Score = 192 bits (488), Expect = 1e-53 Identities = 144/401 (35%), Positives = 201/401 (50%), Gaps = 40/401 (9%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P+ +G+R+ ++G +D +A G+ HP + AV Q++ + H Sbjct: 22 PLRAARTQGSRILLEDGRSLVDGIASWWTACHGYNHPEIARAVAAQLDAMPHVMFGGLTH 81 Query: 79 PQAEA-ARLLAEAAPKDLNKVFFCNSGTESVECAIKLA------RKFTGCTKFIAFEGGF 131 AE AR LA P DL+ VFF +SG+ +VE A+K A R G ++F AF GG+ Sbjct: 82 APAETLARRLAGLLPGDLDHVFFSDSGSVAVEVALKAAAQVWLNRGVAGRSRFAAFRGGY 141 Query: 132 HGRTMGALSATWKPE-FREPFEPLVPEFEHVPYGDVNAVEKAID-------DDTAAVIVE 183 HG TMGA+S E F +PE D A E A+D D A VIVE Sbjct: 142 HGDTMGAMSVCDPEEGMHRRFGRYLPEQVFFDLPDTRAREAALDAGLARHRDGLAGVIVE 201 Query: 184 P-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVC 242 P VQG G+R+ P L + L HGL+LI+DEV +G GRTG FA E V+PD++C Sbjct: 202 PLVQGAGGMRMHPPEVLARIARLARRHGLILILDEVFTGFGRTGSLFACEQAGVVPDLIC 261 Query: 243 LAKGL-GGGVPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAAVSTVLEE 295 L+K L GG +P+ AT+A E+ AF D HG TF NPLACAA A++ E Sbjct: 262 LSKALTGGTMPLAATVATTEIFSAFWSDDPAAALMHGPTFMANPLACAAANASLDLFARE 321 Query: 296 NLPEAAERKGKLAMRILSEAEDVVEEVRGR---------GLMMGVEVGDDERAKDVAREM 346 P A+ + LA R+ E+ + +RGR G + V++ + Sbjct: 322 --PRLAQARA-LAARL----EEGLAPLRGRPGIVDVRVLGAIGAVQLAPPLDLAGLKAAF 374 Query: 347 LDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387 L+RG V GD++ L P L IGE++L LA + + L A Sbjct: 375 LERGVWVR-PFGDIVYLTPCLTIGEEDLGLLLAAMREVLGA 414 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: 453 Number of extensions: 29 Number of successful extensions: 7 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: 415 Length adjustment: 31 Effective length of query: 358 Effective length of database: 384 Effective search space: 137472 Effective search space used: 137472 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