Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012114906.1 XAUT_RS14705 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000017645.1:WP_012114906.1 Length = 421 Score = 176 bits (447), Expect = 8e-49 Identities = 128/395 (32%), Positives = 194/395 (49%), Gaps = 30/395 (7%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P +V G GA + G +D ++ V GHCHP +V A+ EQ +L + Sbjct: 21 PPVVVRGNGAWLETASGGRILDAISSWWVITHGHCHPRIVAAIAEQAGQLDQVIFAGHTH 80 Query: 79 PQAEA-ARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF---TG--CTKFIAFEGGFH 132 P AEA AR L P+ L+ VFF +SG+ +VE A+K+A + TG T+ +A E G+H Sbjct: 81 PAAEALARGLVAMTPEGLDHVFFSDSGSTAVEVALKMAAGYWRHTGEQRTRILALEHGYH 140 Query: 133 GRTMGALSATWKPEFREPFEPLVPEFEHVPYGD-------VNAVEKAIDDDTAAVIVEP- 184 G T+G +S + + +EP + E +P+ + ++A+E A + AA++VEP Sbjct: 141 GDTIGTMSVGARGVYNAAYEPFLFEVTRLPFPEKGREQATLDALEAACREAPAALLVEPL 200 Query: 185 VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFAFEHEDVLPDIVCLA 244 + G G+ I G L E+ +C HG+L I DEV +G GRTG FA E V+PDI C A Sbjct: 201 ILGAGGMYIYGPGVLAEMAAICARHGVLFIADEVMTGFGRTGTLFACEQAGVVPDIACYA 260 Query: 245 KGL-GGGVPVGATIAREEVAEAFEPGD------HGSTFGGNPLACAAVCAAVSTVLEENL 297 KGL GG +P+ T+ R + +A D H S+F NP+ACAA A + EE + Sbjct: 261 KGLTGGSLPLAVTLCRSAIFDAHYSTDRARTFFHSSSFTANPIACAAAVANLKIWAEEPV 320 Query: 298 PEAAERKGKLAMRILSEAED--VVEEVRGRGLMMGVEV--GDDERAKDVAREML----DR 349 G L+ D VR G + +++ D DV + D Sbjct: 321 RGRITALGDAQEERLANFRDDRRFANVRRIGTIAALDLVAPDPGYLADVGPRLAAFFRDE 380 Query: 350 GALVNVTSGDVIRLVPPLVIGEDELEKALAELADA 384 G L+ G+ + ++PP ++L+ +A A Sbjct: 381 GLLIR-PLGNTLYVMPPYCTTAEDLDLVYGAIATA 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: 424 Number of extensions: 22 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: 421 Length adjustment: 31 Effective length of query: 358 Effective length of database: 390 Effective search space: 139620 Effective search space used: 139620 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