Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_049778231.1 MVAN_RS16610 acetylornithine transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000015305.1:WP_049778231.1 Length = 379 Score = 611 bits (1576), Expect = e-180 Identities = 300/378 (79%), Positives = 336/378 (88%), Gaps = 2/378 (0%) Query: 19 MMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGH 78 MMNNYGTPP+ALA GDGAVVTDVDG+ Y+DLLGGIAVNVLGHRHPAVIEAVTRQM+TLGH Sbjct: 1 MMNNYGTPPLALAGGDGAVVTDVDGKAYLDLLGGIAVNVLGHRHPAVIEAVTRQMNTLGH 60 Query: 79 TSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRLTGRTKLVAAHDA 138 TSNLYATEPG+ALAE LV LLGA + FFCNSG EANEAAFK++RLTGRTK+VAA A Sbjct: 61 TSNLYATEPGVALAESLVGLLGAP--AKAFFCNSGTEANEAAFKITRLTGRTKVVAAEGA 118 Query: 139 FHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHTAAVFLEPIMGESG 198 FHGRTMGSLALTGQP+K+ PF PLPG VTHV YGD+D L VDD TAAVFLEPIMGE G Sbjct: 119 FHGRTMGSLALTGQPSKRAPFEPLPGGVTHVPYGDIDELRRVVDDQTAAVFLEPIMGEGG 178 Query: 199 VVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITPDVVTLAKGLGGG 258 VVVPPAGYL AAR+ITA GALLVLDEVQTG+GRTGAF+AHQHDGITPD+VTLAKGLGGG Sbjct: 179 VVVPPAGYLVAAREITAAHGALLVLDEVQTGVGRTGAFYAHQHDGITPDIVTLAKGLGGG 238 Query: 259 LPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGLVRRAEVLGKSLRH 318 LPIGACLA+G A+LLTPGLHGSTFGGNPVC AAALAVL+VLA +GLV RA+VLGK++ H Sbjct: 239 LPIGACLAIGDTADLLTPGLHGSTFGGNPVCTAAALAVLKVLADEGLVERADVLGKTIAH 298 Query: 319 GIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAAAPDVIRLAPPLIIA 378 G+E+LGHPL+DHVRGRGLL GI LTA AK E AR+AG+LVNAAAP ++RLAPPL+I Sbjct: 299 GVESLGHPLVDHVRGRGLLRGIVLTADAAKPVETAAREAGFLVNAAAPAIVRLAPPLVIT 358 Query: 379 EAQLDGFVAALPAILDRA 396 EAQ++ F++ALPAILD+A Sbjct: 359 EAQVETFLSALPAILDKA 376 Lambda K H 0.320 0.136 0.399 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: 610 Number of extensions: 25 Number of successful extensions: 2 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: 400 Length of database: 379 Length adjustment: 30 Effective length of query: 370 Effective length of database: 349 Effective search space: 129130 Effective search space used: 129130 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 Jul 25 2024. The underlying query database was built on Jul 25 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