Align Prephenate dehydratase; PDT; EC 4.2.1.51 (uncharacterized)
to candidate Synpcc7942_0881 Synpcc7942_0881 prephenate dehydratase
Query= curated2:Q44104 (304 letters) >FitnessBrowser__SynE:Synpcc7942_0881 Length = 291 Score = 167 bits (422), Expect = 4e-46 Identities = 111/288 (38%), Positives = 155/288 (53%), Gaps = 14/288 (4%) Query: 4 IAYFGPVGTFTEQAARTFMA-------AGDELVAAETIPKALDAVRRGEADAACVPVENS 56 IA+ GPVGT+ E AA F A L+A +IP L + G D A VPVENS Sbjct: 6 IAHLGPVGTYAEMAALRFQAWLTQQDQQPSRLLACRSIPATLQTLADGAVDYAVVPVENS 65 Query: 57 VEGAVPATLDSLAVGEPLIGVAEAL-LPV-HFSVLTRDDVGEIRTVASHPHALAQVRKWL 114 VEG+V ATLDSL P + + AL LP+ H + D IR V SHP ALAQ ++WL Sbjct: 66 VEGSVAATLDSLWQ-LPQLSIQRALILPIAHALISFESDRTAIRQVLSHPQALAQCQQWL 124 Query: 115 EDNLPGARVVAAGSTAAAAVAVQAGEFDAAVTAPVAVEHYPLKVLATEVADVRDARTRFL 174 + +LP A ++ A ST A ++ A + + A E Y + + + + D D RTRF Sbjct: 125 QRHLPQAELIPANSTTEALQDLERHPQRAVIASTRAAELYQMPIQSFPINDSPDNRTRFW 184 Query: 175 LMRRPPVVLPEPTGADRTSIVAAAANRTGTLAELLTELATRGINLTRLDARPHKQNFGEY 234 ++ R P P GA + + AN G L + L LA R INL+R+++RP K++ GEY Sbjct: 185 VISRSPT----PGGACTSLNFSLDANVPGALVKPLQILADRRINLSRIESRPTKRSLGEY 240 Query: 235 RFFIDFEGHVAEPRIADALAALRRRCRDVRFLGSFARADGVAATIEPA 282 FF+D E + +P IA A+ A+ +R LGS+ D + + PA Sbjct: 241 LFFLDLEADLRDPAIAAAVQAVADCTEQLRVLGSYDSLDFTQSVLVPA 288 Lambda K H 0.320 0.133 0.381 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: 204 Number of extensions: 11 Number of successful extensions: 4 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: 304 Length of database: 291 Length adjustment: 26 Effective length of query: 278 Effective length of database: 265 Effective search space: 73670 Effective search space used: 73670 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: 48 (23.1 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