Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012590678.1 MSIL_RS08460 ornithine--oxo-acid transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000021745.1:WP_012590678.1 Length = 410 Score = 295 bits (754), Expect = 2e-84 Identities = 164/399 (41%), Positives = 241/399 (60%), Gaps = 16/399 (4%) Query: 1 MDARELIDKYHM---NTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAV 57 M ++ I++ H+ Y+ PV L G GA V+D +G+ YID+++ + GH HP + Sbjct: 1 MSGQQAINREHVFGAQNYAPLPVVLSHGRGAHVFDVDGHRYIDMMSAYSAASFGHLHPRL 60 Query: 58 VEAVKEQVERLIHCSNLYYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARK 117 V+A+++Q+ERL S ++++ + LA+ A L+ N+G E+VE AIK AR+ Sbjct: 61 VKAMRDQLERLDIVSRAFHSDNLGGFCQELAQFA--GLDSCLVMNTGAEAVETAIKAARR 118 Query: 118 FT--------GCTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDVNAV 169 + + I G FHGRT + + P + F P P F VP+GD +A+ Sbjct: 119 YAYDELAIPADKAEIIVAYGNFHGRTTTIVGFSDDPNSKRGFGPFAPGFASVPFGDADAI 178 Query: 170 EKAIDDDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFF 229 E AI+ TAAV+VEP+QGE GV +PPEG+L LR +CD HG+LL+ DEVQSG GRTG+ F Sbjct: 179 ELAINRCTAAVLVEPIQGEGGVIVPPEGYLANLRRICDRHGILLLFDEVQSGFGRTGRNF 238 Query: 230 AFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGDHGSTFGGNPLACAAVCAA 288 F+HED +PD + + K LGGG +PV A IAR + + F PG HGSTFGGNPLA A AA Sbjct: 239 CFQHEDAVPDGLIVGKALGGGLMPVSAFIARRALMDVFTPGSHGSTFGGNPLAAAVGRAA 298 Query: 289 VSTVLEENLPEAAERKGKLAMRILSE-AEDVVEEVRGRGLMMGVEVGDDE-RAKDVAREM 346 ++ + EE L E + G++ + L + +RG+GL G+E+ + +AK+V M Sbjct: 299 IALMQEEQLAERSRALGEVLLDALHRIRHPAIIALRGKGLWAGIELDPAQAKAKEVCLAM 358 Query: 347 LDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADAL 385 + RG L T V+RL PPLVI E ++ +A++ L++AL Sbjct: 359 MRRGVLAKETHESVLRLAPPLVIEERDMLQAVSVLSEAL 397 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: 398 Number of extensions: 18 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: 410 Length adjustment: 31 Effective length of query: 358 Effective length of database: 379 Effective search space: 135682 Effective search space used: 135682 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