Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_092345303.1 BLU87_RS04965 ornithine--oxo-acid transaminase
Query= curated2:O27392 (390 letters) >NCBI__GCF_900107645.1:WP_092345303.1 Length = 400 Score = 311 bits (798), Expect = 2e-89 Identities = 163/400 (40%), Positives = 238/400 (59%), Gaps = 14/400 (3%) Query: 1 MDSEEIIELERKFIMQTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKV 60 M E I LE ++ Y +VL+ GKG VWD++GN Y+DC A + + GH HPK+ Sbjct: 1 MQQSEFIGLEDQYGAHNYKPLDVVLTRGKGVWVWDVDGNKYLDCLAAYSAVNQGHCHPKI 60 Query: 61 ALAICHQAQRLIHSSNIYYTREQVELAKLLTAISPHDRVFFANSGAEANEGAIKLARKF- 119 A+ QA++L +S + + + L ++ +V NSGAEA E AIK RK+ Sbjct: 61 MQAMVTQAEKLTLTSRAFRNDQLGPFYQELCELTHSHKVLPMNSGAEAVETAIKTVRKWG 120 Query: 120 -------TGKSEIIAAENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHVPYGDIGAMAD 172 K+EII N+FHGRT++ V+ + + F P GFK +P+GD A Sbjct: 121 YLVKGVPQDKAEIIVCANNFHGRTISIVSFSTDENARAGFGPFTPGFKCIPFGDAAAFET 180 Query: 173 AVGDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMFAS 232 A+ T A ++EP+QGE GVIIPP+ YLK V+E++ +++V+LILDE+QTG GRTG + Sbjct: 181 AITANTVAFLVEPIQGEAGVIIPPDDYLKQVREISDRHNVVLILDEIQTGLGRTGKLLTE 240 Query: 233 QLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGDHGSTFGGNPWGCAAAIATIE 291 + G+E D+T + KA+ GG YP+ AVL+N V +PG+HGSTFGGNP CA A A ++ Sbjct: 241 EYAGIEADLTLIGKALSGGFYPVSAVLSNTEVMDVLQPGEHGSTFGGNPLACAVARAALK 300 Query: 292 VLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEID---GECAGVVDAA 348 VL +E L E + + G YFL L+++ H ++++RG GLM+ IE G G Sbjct: 301 VLFEENLIENSYEQGEYFLNELKKISH--PHIKEVRGRGLMLAIEFHPEVGGARGYCYKL 358 Query: 349 REMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGHVIS 388 +E G+L T +IR PPLVIK+EE+D ++ + V+S Sbjct: 359 KEQGILAKDTHENIIRFAPPLVIKREEVDLILEAINQVLS 398 Lambda K H 0.320 0.138 0.404 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: 403 Number of extensions: 21 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: 390 Length of database: 400 Length adjustment: 31 Effective length of query: 359 Effective length of database: 369 Effective search space: 132471 Effective search space used: 132471 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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