Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 8501786 DvMF_2502 glutamate-1-semialdehyde aminotransferase (RefSeq)
Query= curated2:Q9CNT1 (398 letters) >FitnessBrowser__Miya:8501786 Length = 425 Score = 123 bits (309), Expect = 9e-33 Identities = 91/276 (32%), Positives = 132/276 (47%), Gaps = 23/276 (8%) Query: 28 KGSHVWDQQGKDYIDFTSGIAVNSLGHCADEIVDVLKQQSEKLWHSSNWFTSEPTLALAT 87 KGSH+ G ++D+ LGH + + ++ +S E + LA Sbjct: 41 KGSHLTTVDGTSFVDYVQSWGPMLLGHAHPVVASAIHAAVDR--GTSYGAPCEDEVVLAE 98 Query: 88 KLVEKT-FAERVMFVNSGAEANEAALKLARRYAVDHFGYQKSKIIAFKQSFHGRT-LFTV 145 +++ E V VNSG EA +AL+LAR ++K++ F +HG F Sbjct: 99 AVIDALPGVEMVRMVNSGTEATMSALRLARGVT------GRNKVVKFVGCYHGHADAFLA 152 Query: 146 SVG-GQAKYSDGFGP-----KPADIVHVPFNDLAAVQAVMD---ENTCAVIVEPIQGESG 196 S G G A S P D + P+NDL AV + ++ A+IVEP+ G G Sbjct: 153 SAGSGVATLSIPGTPGVPEATVRDTLLAPYNDLTAVAELFTLHGKDIAAIIVEPVAGNMG 212 Query: 197 ILPASQDFLQGLRELCDQHNALLIFDEVQTGVGRTGYLYAYMKYEVVPDILTSAKALGNG 256 ++ FLQGLR+LC +H ALLIFDEV TG R Y A ++++ PD+ T K +G G Sbjct: 213 LVLPMNGFLQGLRDLCTEHGALLIFDEVITGF-RVNYGGAQKRFDITPDLTTLGKIIGGG 271 Query: 257 FPIGAMLTTHEIAKSFAP---GVHGTTFGGNPLACA 289 P+GA ++ + AP T GNPLA A Sbjct: 272 LPVGAYGGRADLMRRIAPCGEVYQAGTLSGNPLAMA 307 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: 344 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: 398 Length of database: 425 Length adjustment: 31 Effective length of query: 367 Effective length of database: 394 Effective search space: 144598 Effective search space used: 144598 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 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