Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_017599949.1 D471_RS0118255 acetylornithine transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000341125.1:WP_017599949.1 Length = 403 Score = 403 bits (1035), Expect = e-117 Identities = 214/397 (53%), Positives = 264/397 (66%), Gaps = 5/397 (1%) Query: 6 TTTATMRQRWQAVMMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAV 65 T+ A +R+R+ A +M NYG PPIAL+ G G + DVDGR Y+DL+ GIAV+ LGH HPA+ Sbjct: 2 TSGADLRERFSAALMPNYGVPPIALSLGRGCEIYDVDGRQYLDLIAGIAVSGLGHGHPAL 61 Query: 66 IEAVTRQMSTLGHTSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSR 125 ++AV Q +TL HTSNL+ E + LAE LVALLG D +VFF NSG EANEAA KL + Sbjct: 62 VKAVAHQAATLAHTSNLFVHEREVELAERLVALLGGD--AKVFFANSGTEANEAALKLVK 119 Query: 126 LT---GRTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVD 182 GR VAA FHGRT GSLALTG+ + + PF P DV V +GD+DAL AVD Sbjct: 120 RAAGPGRHYFVAATRGFHGRTSGSLALTGKDSIREPFGPYGMDVRFVPHGDIDALTEAVD 179 Query: 183 DHTAAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHD 242 AVF EP GE+GVV P GYLA R + GA VLDE+Q+G+GRTG +FAHQ Sbjct: 180 TGCVAVFTEPTQGEAGVVPAPEGYLAGVRAVCDETGAAFVLDEIQSGVGRTGQWFAHQDA 239 Query: 243 GITPDVVTLAKGLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLAS 302 G+ PDV+TLAKGLGGGLPIGAC+ G A+ G HGSTFGGNPV AAALAVL + S Sbjct: 240 GVRPDVLTLAKGLGGGLPIGACVGFGDYADAFQKGDHGSTFGGNPVACAAALAVLDTIES 299 Query: 303 DGLVRRAEVLGKSLRHGIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVN 362 +GL+ V+G L ++A+ HPL++ RG GL + LTAP A + A G+LVN Sbjct: 300 EGLLAHTAVMGDLLAEQLDAIDHPLLEGQRGSGLWRALTLTAPVAAHVQDQAAVRGFLVN 359 Query: 363 AAAPDVIRLAPPLIIAEAQLDGFVAALPAILDRAVGA 399 A P+ IRLAPPL+I Q+ F+ ALP +LD A A Sbjct: 360 AVGPETIRLAPPLVITPEQIGVFIEALPTVLDAAEAA 396 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: 505 Number of extensions: 19 Number of successful extensions: 4 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: 403 Length adjustment: 31 Effective length of query: 369 Effective length of database: 372 Effective search space: 137268 Effective search space used: 137268 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