Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_029001755.1 H537_RS0136130 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_000430725.1:WP_029001755.1 Length = 442 Score = 206 bits (523), Expect = 1e-57 Identities = 145/416 (34%), Positives = 210/416 (50%), Gaps = 56/416 (13%) Query: 18 YTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSNI 77 + + P +L+ +G W EG +D AG+ + GHA P++ AI QA L ++ Sbjct: 25 FKQAPRLLARAEGMHYWTPEGRQVLDGVAGLWCVNAGHARPRIVQAIAQQASVLDYAPPF 84 Query: 78 YYTREQV-ELAKLLTAISPH--DRVFFANSGAEANEGAIKLARKFT------GKSEIIAA 128 Q ELA+ L ++P DRVFF NSG+E+ E A+K+A + ++ +I Sbjct: 85 QMGHPQAFELAEELVKLTPPGLDRVFFTNSGSESVETALKMALAYHRVRGEGSRTRLIGR 144 Query: 129 ENSFHGRTLATVTATGQKKYSEPFRPLPEGFKHV-----------PYGDIGAMADAVGD- 176 E +HG ++ G + F L G H+ +G A+ D Sbjct: 145 ERGYHGVNFGGISVGGIVGNRKLFGTLLTGVDHLRHTHDPARNAYSFGQPAHGAELADDL 204 Query: 177 ----------ETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRT 226 AA+I+EPV G GV++PP GYL+ ++E+ ++ +LLI DEV TGFGRT Sbjct: 205 ERLCALHDPSTIAAVIVEPVAGSTGVLLPPVGYLQRLREICDRHGILLIFDEVITGFGRT 264 Query: 227 GAMFASQLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPG-------DHGSTFGG 278 G F +Q FGV PD+ TVAK + G P+GAV A + AF G HG T+ Sbjct: 265 GQPFGAQTFGVTPDLMTVAKGLTNGCVPMGAVFARRSIHDAFMHGPEQLIEFPHGYTYSA 324 Query: 279 NPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEID 338 +P CAAA+AT++ +E+L RA ++ YF G+ L G V D+R +GL+ G+E+ Sbjct: 325 HPLACAAALATLQTYEEEQLLTRAGELHDYF-GQALHSLKGLPHVVDVRNIGLVGGVEL- 382 Query: 339 GECAGVVDAAR-----------EMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVL 383 A + DA E GVLI T G I + PPL+I+K ID VDVL Sbjct: 383 ---APLPDAPAKRAFNVFLDCWEQGVLIR-TTGDTIALSPPLIIEKSHIDRIVDVL 434 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: 497 Number of extensions: 27 Number of successful extensions: 6 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: 442 Length adjustment: 31 Effective length of query: 359 Effective length of database: 411 Effective search space: 147549 Effective search space used: 147549 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