Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_007507028.1 LRK54_RS04150 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_021560695.1:WP_007507028.1 Length = 454 Score = 176 bits (446), Expect = 1e-48 Identities = 139/432 (32%), Positives = 212/432 (49%), Gaps = 63/432 (14%) Query: 3 ARELIDKYH----MNTYSRFP-VTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAV 57 AR+L +H M+ + P V +V GEGA + D +G Y+D ++ N+ GH +P + Sbjct: 13 ARDLRHVWHPCTQMHDHESVPMVPIVRGEGAWLIDADGRRYLDGISSWWTNLFGHANPRL 72 Query: 58 VEAVKEQVERLIHCSNL-YYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLAR 116 A+ EQ L H + +EP E A L P L++VF+ ++G+ ++E A+K++ Sbjct: 73 AAALAEQARTLEHVIFAGFTHEPAIELAEELVRITPPGLDRVFYADNGSAAIEVALKMSF 132 Query: 117 KFT------GCTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLV---------PEFEHV 161 + T+FIA G +HG T+GALS + +R+ + PL+ +E Sbjct: 133 HYWLNQGHGEKTRFIALTGSYHGETLGALSVSDVALYRKTYAPLLLTPFLAPSPDAYEGE 192 Query: 162 P-----------YGDVNAVEKAIDDDTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEH 209 P G++ + + +T AVIVEP VQ G+R+ G+L LR LCDE Sbjct: 193 PGESPEQTAKRRLGELRTLLERHAHETCAVIVEPLVQCAGGMRMYHPGYLSGLRALCDEF 252 Query: 210 GLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGL-GGGVPVGATIAREEVAEAF-- 266 + I DE+ G GRTG FA E V PD +CL+KGL GG +P+ A + R+ V +AF Sbjct: 253 AVHFIADEIAVGFGRTGTLFACEQAAVTPDFMCLSKGLTGGTLPLSAVLTRDVVYQAFYA 312 Query: 267 -----EPGDHGSTFGGNPLACAAVCAAVS-----TVLEENLPEAAERKGKLAMRILS-EA 315 + H ++ GNPLAC ++ VLE N AA LA R+ A Sbjct: 313 EYNAGKAFLHSHSYTGNPLACRVALETLAIFRDEPVLEHNRQLAAH----LARRLQPLRA 368 Query: 316 EDVVEEVRGRGLMMGVEVGDDE-----------RAKDVAREMLDRGALVNVTSGDVIRLV 364 V +VR GL+ +E+ D+ R V L GAL+ G+V+ + Sbjct: 369 HPHVADVRQTGLIAAIELVADKASRRPYPAAERRGLRVYLHGLQHGALLR-PLGNVVYFM 427 Query: 365 PPLVIGEDELEK 376 PP V+ E E+++ Sbjct: 428 PPYVVSEAEIDQ 439 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: 420 Number of extensions: 31 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: 454 Length adjustment: 32 Effective length of query: 357 Effective length of database: 422 Effective search space: 150654 Effective search space used: 150654 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