Align aromatic-amino-acid aminotransferase (EC 2.6.1.1) (characterized)
to candidate Dsui_1904 Dsui_1904 aspartate/tyrosine/aromatic aminotransferase
Query= metacyc::PHETRANTHAUERA-MONOMER (404 letters) >FitnessBrowser__PS:Dsui_1904 Length = 398 Score = 648 bits (1671), Expect = 0.0 Identities = 318/397 (80%), Positives = 348/397 (87%) Query: 1 MFEHVDAYPGDPILSLVETFHHDPRPRKVNLGIGLYYDEEGRIPLLGSVEKAEAALAANP 60 MFEHVDAY GDPIL+LVETFH D R KVNLGIGLYYDE+GRIPLLGSV +AEAA+AA P Sbjct: 1 MFEHVDAYAGDPILTLVETFHKDSRTTKVNLGIGLYYDEQGRIPLLGSVRQAEAAIAAAP 60 Query: 61 GPRPYLPMEGAADYRAAVQKLLFGPDSAALRAGRIATIQTIGGSGALKVGADLLKRYFPA 120 PR YLPMEGAADYRA VQKLLFG DSAAL+AGRIATIQT+GGSGALKVGADLLKRYFP Sbjct: 61 APRSYLPMEGAADYRAVVQKLLFGADSAALKAGRIATIQTLGGSGALKVGADLLKRYFPK 120 Query: 121 SEVWVSDPTWDNHRSIFEGAGIEVHDYPYYDAASGGVRFDEMIETLQSLPAQSIVLLHPC 180 SE WVS+PTWDNHRSIFEGAGI VHDYPYYDA +GGV F M+ L+ LP QSIVLLHPC Sbjct: 121 SEAWVSNPTWDNHRSIFEGAGIAVHDYPYYDANTGGVDFTGMVACLKGLPEQSIVLLHPC 180 Query: 181 CHNPTGVDLSTAQWQEVIAVVASRGLIPFLDIAYQGFGDNLDDDAYAARAMADAGVSFFV 240 CHNPTGVDLS QWQ+VIA+VA R LIPFLDIAYQGFGD LD+DAYA RA+AD+G+ F V Sbjct: 181 CHNPTGVDLSREQWQQVIAIVAERKLIPFLDIAYQGFGDGLDEDAYAIRALADSGLPFLV 240 Query: 241 SNSFSKNLSFYGERCGGLSVVCQDADEAERVLGQLKFTVRRNYSSPPVHGGRVAAAVMND 300 SNSFSKNLSFYGER GGLSVVC+DA+EA RVLGQLKFTVRRNYSSPP+HG V VMND Sbjct: 241 SNSFSKNLSFYGERVGGLSVVCKDAEEAGRVLGQLKFTVRRNYSSPPIHGELVTTIVMND 300 Query: 301 AGLHEEWVGEVRGMRERIKAMREKLHEVLSSTLPGRDFSYFVKQRGMFSYTGLTPEQVDR 360 A LH EWV EV MR RI+AMR+KL+EVL++ +PG+DFSYF KQRGMFSYTGL+P QVDR Sbjct: 301 AALHAEWVKEVTEMRTRIQAMRQKLYEVLTARVPGKDFSYFTKQRGMFSYTGLSPAQVDR 360 Query: 361 LREEFAVYVVQSGRMCVAGLNRGNVDYVAKAMAAVLQ 397 LREEF VY+V+SGRMCVAGLN GNV YVA+AMAAVLQ Sbjct: 361 LREEFGVYLVRSGRMCVAGLNTGNVAYVAEAMAAVLQ 397 Lambda K H 0.320 0.136 0.409 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: 556 Number of extensions: 12 Number of successful extensions: 1 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: 404 Length of database: 398 Length adjustment: 31 Effective length of query: 373 Effective length of database: 367 Effective search space: 136891 Effective search space used: 136891 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