Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate CA265_RS11630 CA265_RS11630 prephenate dehydratase
Query= BRENDA::Q9FNJ8 (425 letters) >FitnessBrowser__Pedo557:CA265_RS11630 Length = 277 Score = 145 bits (367), Expect = 1e-39 Identities = 108/291 (37%), Positives = 152/291 (52%), Gaps = 26/291 (8%) Query: 124 STLRVAYQGVPGAYSEAAAGKAYPNS-EAIPCDQFDVAFQAVELWIADRAVLPVENSLGG 182 +T RVA QG+ ++ E AA K + E + C+ F +E AD V+ +ENS+ G Sbjct: 3 TTKRVAIQGIKASFHEEAAYKFFGKDIETVECNSFKETCDKLEKNDADFVVMAIENSIAG 62 Query: 183 SIHRNYDLLLRHRLHIVGEVQIPVHHCLLALPGVRTDCITRVISHPQALAQTEGSLNKLT 242 S+ NY L+ +VGEV +P+ L+ALPGV+ + I V SHP A+ Q Sbjct: 63 SLLPNYTLIRDFGFSVVGEVYLPIQLHLMALPGVKFEDIKVVTSHPIAIRQCIDFFYDY- 121 Query: 243 PKAAIEAFHDTAAAAEYIAANNLHDTAAVASARAAELYGLQILADGIQDDAGNVTRFLML 302 P I +DTAA A+ I L DT A+A++ AAELY L IL ++ + N TRFL+L Sbjct: 122 PHIKIVESNDTAACAKRIQEEQLTDTMAIANSLAAELYSLNILERRVESNKKNYTRFLIL 181 Query: 303 ARDPIIPRTD---RPFKTSIVFAAQEHKGTSVLFKVLSAFAFRNISLTKIESRPHQNCPV 359 +D +TD + K SI F G+ L VL+ FA +++SLTKI+S P Sbjct: 182 KKD----KTDEGKKINKASICFQVGHKAGS--LATVLNIFAEQDVSLTKIQSMP------ 229 Query: 360 RVVGDENVGTSKHFEYTFYVDFEASMAEARAQNALAEVQEYTSFLRVLGSY 410 V+G N EY FYVD E E + A+ + +YTS +LG Y Sbjct: 230 -VLGKRN-------EYYFYVDLEWPSTE-KYDKAIRKALKYTSNFNILGEY 271 Lambda K H 0.317 0.130 0.380 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: 218 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: 425 Length of database: 277 Length adjustment: 29 Effective length of query: 396 Effective length of database: 248 Effective search space: 98208 Effective search space used: 98208 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 (21.7 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