Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate GFF3829 PGA1_262p02330 putative aspartate aminotransferase
Query= curated2:O67781 (394 letters) >FitnessBrowser__Phaeo:GFF3829 Length = 395 Score = 179 bits (454), Expect = 1e-49 Identities = 114/369 (30%), Positives = 186/369 (50%), Gaps = 14/369 (3%) Query: 24 AKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTKYAPSAGIPELREAIAEKLL 83 A+E+ A G D+I GEPD TP+ + + A+ G+T Y+ G LR+ +AE+ Sbjct: 24 AREMIAAGADIIEMTIGEPDVPTPEALMQTAGAAMMAGRTGYSDGRGEANLRQTLAERYS 83 Query: 84 KENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFFGGVPVEV 143 P ++ G + L+ + M + + GDEVL+ P + TY IR G V V Sbjct: 84 ASTGRAIGPDNVLCFPGTQTALYAVLMGVAEHGDEVLVGDPMYATYEGVIRASGADMVPV 143 Query: 144 PLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVERGIFIIS 203 PL+ E GF++ D+ EK+T R++AI++ +P+NPTG++ E+L I ++IIS Sbjct: 144 PLRPEHGFRMQANDIAEKITPRSRAILLTTPHNPTGSILTVEDLDAIGRLADVHDLWIIS 203 Query: 204 DECYEYFVYGDAKFVSP---ASFSDEVKNITFTVNAFSKSYSMTGWRIGYVACPEEYAKV 260 DE YE V+ A+FVSP A+F+D V V++ SKS++ G+R G+ + + Sbjct: 204 DEVYEQLVFDAAEFVSPLARAAFADRV----IVVSSISKSHAAPGFRSGWCIASKAFCDG 259 Query: 261 IASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRRDTAVEELSKIPGMDVV 320 + L+ + F +A++ + MR F R E L + + V Sbjct: 260 LLPLSETMLFGNQPFIADMTEQAVR--EGSPVAEGMRARFAARAAKLAERLHRDTALRVH 317 Query: 321 KPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFGAP--GFLRLSYALSEE 378 PE +F + A L GD ++ LL A VAV+PGS+FG G++R++ + ++ Sbjct: 318 SPEAG--MFAMINVAATGLDGDA-YAQDLLHSAGVAVMPGSSFGESLRGWVRVALTIEDD 374 Query: 379 RLVEGIRRI 387 + RI Sbjct: 375 AFDRALTRI 383 Lambda K H 0.317 0.135 0.383 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: 362 Number of extensions: 15 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: 394 Length of database: 395 Length adjustment: 31 Effective length of query: 363 Effective length of database: 364 Effective search space: 132132 Effective search space used: 132132 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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