Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate GFF2973 PGA1_c30200 prephenate dehydratase
Query= BRENDA::Q9SA96 (392 letters) >FitnessBrowser__Phaeo:GFF2973 Length = 277 Score = 166 bits (419), Expect = 1e-45 Identities = 107/282 (37%), Positives = 146/282 (51%), Gaps = 15/282 (5%) Query: 107 RISFQGIPGAYSETAALKAFPNCETVPCEQFEAAFQAVELWLVDKAVLPIENSVGGSIHR 166 RI+ QG G+YS A K P+ + +PC FE A AV + A+LP+ENS G + Sbjct: 4 RIAIQGELGSYSHEACRKERPDMDVLPCRNFEDAINAVRSGAAELAMLPVENSTYGRVAD 63 Query: 167 NYDLLLRHRLHIVQEVHLPVNHCLLGVPGVKKEDIKCVLSHPQALDQCVNSLNNLGIQRI 226 + LL LHI+ E + V+ LLGVPG + EDIK SH L QC L+ I Sbjct: 64 IHRLLPHSGLHIIDEAFVRVHINLLGVPGAQLEDIKEAHSHLVLLPQCARFLSENNIHGR 123 Query: 227 SAKDTATAAQTVSSSGKIDVGAIASVRAANIYGLDILAENIQDDVNNVTRFLILAREPMI 286 + D A AA+ V+ G A+AS A IYGL++LA +I+D NN TRFL ++R+P Sbjct: 124 VSPDNARAARDVAEQGDKSHAALASELAGEIYGLEVLARHIEDHGNNTTRFLTMSRDPNT 183 Query: 287 PRT-DRPYKTSIVFSLEEGPGVLFKALAVFALRSINLSKIESRPQRRRPLRVVDGSNNGS 345 R + TS VF + P L+KA+ FA IN++K+ES +VDGS + Sbjct: 184 ERRGNHGMITSFVFQVRNIPAALYKAMGGFATNGINMTKLES--------YMVDGSFTAT 235 Query: 346 AKYFDYLFYIDFEASMADTRAQHALGHLQEFASFIRILGCYP 387 FY D + D + A+ L F + I ILG YP Sbjct: 236 Q------FYADIDGHPDDPNVRLAMDELAYFTTNIEILGVYP 271 Lambda K H 0.321 0.135 0.402 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: 250 Number of extensions: 18 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: 277 Length adjustment: 28 Effective length of query: 364 Effective length of database: 249 Effective search space: 90636 Effective search space used: 90636 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: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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