Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012591140.1 MSIL_RS10885 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000021745.1:WP_012591140.1 Length = 424 Score = 174 bits (441), Expect = 4e-48 Identities = 133/383 (34%), Positives = 197/383 (51%), Gaps = 28/383 (7%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCS-NLYYN 77 P+ + +G+R+ +G E ID +A G+ HP + +AV+ Q++++ H + Sbjct: 27 PLPVASTKGSRITLADGRELIDGIASWWTACHGYNHPHIAQAVRGQLDKMPHVMFGGLAH 86 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLA------RKFTGCTKFIAFEGGF 131 EP AR LA P L +VFFC+SG+ +VE A+K++ + FTG TKF++F GG+ Sbjct: 87 EPALTLARRLAALLPDPLERVFFCDSGSVAVEVAMKMSVQFWLNQGFTGRTKFLSFRGGY 146 Query: 132 HGRTMGALSATWKPE-FREPFEPLVPEFEHVPYGDVNAVEKAID-------DDTAAVIVE 183 HG T +S E F + + A E A D ++ AA++VE Sbjct: 147 HGDTFACMSVCDPEEGMHSLFAGALAKQIIADLPVDEASEAAFDRLLAAHAEELAAIVVE 206 Query: 184 PV-QGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVC 242 P+ QG G+ L++LR D HG+LLI DEV +G GRTG FA E V+PDIV Sbjct: 207 PLAQGAGGMIFHGAEVLQKLRRAADRHGILLIFDEVFTGFGRTGTMFACESAGVVPDIVA 266 Query: 243 LAKGL-GGGVPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAAVSTVLEE 295 L+K L GG + + ATIA ++ E F D HG TF NPLACAA A++ +E Sbjct: 267 LSKALTGGTMGLAATIASRKIFEGFLSDDPLHALMHGPTFMANPLACAAANASLDLFEQE 326 Query: 296 -NLPEAAERKGKLAMRILSEAEDV--VEEVRGRGLMMGVEVGDDERAKDVAREMLDRGAL 352 L +AA L + L+ D V++VR G + VE+ + + R ++ G Sbjct: 327 PRLAQAAAISEALKLG-LAPCRDFPRVKDVRVLGAIGVVELDRIDDMNGLKRRFVEAGVW 385 Query: 353 VNVTSGDVIRLVPPLVIGEDELE 375 V +++ L P L IGE EL+ Sbjct: 386 VR-PFRNIVYLTPALTIGEGELK 407 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: 431 Number of extensions: 31 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: 389 Length of database: 424 Length adjustment: 31 Effective length of query: 358 Effective length of database: 393 Effective search space: 140694 Effective search space used: 140694 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