Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Synpcc7942_0881 Synpcc7942_0881 prephenate dehydratase
Query= BRENDA::O22241 (424 letters) >FitnessBrowser__SynE:Synpcc7942_0881 Length = 291 Score = 116 bits (290), Expect = 1e-30 Identities = 97/296 (32%), Positives = 141/296 (47%), Gaps = 31/296 (10%) Query: 123 SSLRVAYQGVPGAYSEAAA--------GKAYPNCDAIPCDQFDVAFQAVELWIADRAVLP 174 S +A+ G G Y+E AA + + C Q + D AV+P Sbjct: 2 SERAIAHLGPVGTYAEMAALRFQAWLTQQDQQPSRLLACRSIPATLQTLADGAVDYAVVP 61 Query: 175 VENSLGGSIHRNYDLLLR-HRLHIVGEVQIPVHHCLLALPGVRTDCVSRVISHPQALAQT 233 VENS+ GS+ D L + +L I + +P+ H L++ RT + +V+SHPQALAQ Sbjct: 62 VENSVEGSVAATLDSLWQLPQLSIQRALILPIAHALISFESDRT-AIRQVLSHPQALAQC 120 Query: 234 EHSLDVLTPHAAREAFHDTAAAAEYISANDLHDTAAVASARAAELYNLQILADGIQDDPG 293 + L P A + T A + + + A +AS RAAELY + I + I D P Sbjct: 121 QQWLQRHLPQAELIPANSTTEALQDLERHP--QRAVIASTRAAELYQMPIQSFPINDSPD 178 Query: 294 NVTRFLMLAREPIIPRTDRPFKTSIVFAAQEHKGTSVLFKVLSAFAFRDISLTKIESRPH 353 N TRF +++R P T TS+ F+ + L K L A R I+L++IESRP Sbjct: 179 NRTRFWVISRSP----TPGGACTSLNFSLDANV-PGALVKPLQILADRRINLSRIESRP- 232 Query: 354 HNRPLRVVGDGSFGTSKNFEYMFYVDFEASMAEPRAQNALAEVQEYTSFLRVLGSY 409 R +G EY+F++D EA + +P A+ V + T LRVLGSY Sbjct: 233 ---TKRSLG----------EYLFFLDLEADLRDPAIAAAVQAVADCTEQLRVLGSY 275 Lambda K H 0.318 0.131 0.387 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: 281 Number of extensions: 17 Number of successful extensions: 5 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: 424 Length of database: 291 Length adjustment: 29 Effective length of query: 395 Effective length of database: 262 Effective search space: 103490 Effective search space used: 103490 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 (21.8 bits) S2: 49 (23.5 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