Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate Ac3H11_3828 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62)
Query= curated2:Q9AAL3 (392 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3828 Length = 445 Score = 162 bits (410), Expect = 2e-44 Identities = 126/406 (31%), Positives = 177/406 (43%), Gaps = 61/406 (15%) Query: 9 ARANIDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHA--SN 66 A+ + I R +G WL D DG+ YLD + VN GH P + AL Q L H + Sbjct: 32 AQPPVAIARAQGPWLIDTDGKRYLDGISSWWVNLFGHSHPHIQAALVDQLGKLDHVMLAG 91 Query: 67 LYRLPAQEALATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGN 126 P E L+ +L T F+ + GA A E A+K + + GRP + + Sbjct: 92 FTHAPVVE-LSERLAALTGLGHAFYGSDGAAATEIALKMSAHYWRNTGRPAKSHFVGLAG 150 Query: 127 AFHGRTLATISATDQMKVREGFTPLYDAFDTTPFNDIEGAARAITPQ------------- 173 +HG T+ ++ TD RE + PL DT P D AA Q Sbjct: 151 GYHGETVGALAVTDIAIFREAYAPLVRLADTVPSPDARSAAPGEAAQDVARRAAAALEAW 210 Query: 174 -------TAAILVEP-IQGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHL 225 TAA +VEP +Q G+ P +L RALC+++++ L++DE+ G GRTG + Sbjct: 211 LQEHHTTTAAFIVEPLVQCAAGMAMHDPEYLRLARALCNRYEVHLVVDEIAVGFGRTGTM 270 Query: 226 FAHELYGVRPDIIAVAKGL-GGGFPIGACLAT---------EDAASGMTPGSHGSTYGGN 275 FAH+ G+RPD I ++KGL GG P+ A L T +D A G H +Y GN Sbjct: 271 FAHQQAGIRPDFICLSKGLTGGTLPLSAVLTTDAVYAAFYDDDVARGFL---HSHSYTGN 327 Query: 276 PLACAVASAVLDAVLAPGFLETVRERAALVDALLERLLR----RHS-------------- 317 PLAC A A L+ L R A +D L + RH+ Sbjct: 328 PLACRAALATLELFDQLDALNANRALAQHIDTACAPLTQHPRVRHARRLGMIWAWDVDTT 387 Query: 318 --DLFVRAQGHGLMRGLQVRASARDVVAH----LRDFGVMTVAAGA 357 D R H + RGL +R + + A L + V +A GA Sbjct: 388 LPDFSRRYHQHAMARGLVLRPIGKTLYAMPPYVLDNEAVQCLAGGA 433 Lambda K H 0.322 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: 428 Number of extensions: 19 Number of successful extensions: 3 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: 392 Length of database: 445 Length adjustment: 32 Effective length of query: 360 Effective length of database: 413 Effective search space: 148680 Effective search space used: 148680 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 (21.9 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