Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate 8501012 DvMF_1749 prephenate dehydratase (RefSeq)
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__Miya:8501012 Length = 418 Score = 259 bits (663), Expect = 7e-74 Identities = 150/361 (41%), Positives = 212/361 (58%), Gaps = 12/361 (3%) Query: 4 ADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKH 63 A +L +R ID LD +L+L++ RA + EV R+K + + ++P RE VL++ Sbjct: 57 AGRLGQIRHEIDGLDSDLLNLLNRRASLSLEVGRIKAD-----DAGIVFKPFREREVLEN 111 Query: 64 IMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKP 123 +M N GPL NE + ++REI+SS +L++P +VAYLGPEGTFS A ++ G +V P Sbjct: 112 LMAANGGPLPNEHLRSIWREILSSSRSLQRPQKVAYLGPEGTFSYFAGVEFLGKAVEYMP 171 Query: 124 MAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVG 183 +D VFR V GVVP+ENS G V +LD FL H++ I E+ RI H LL Sbjct: 172 QKDLDGVFRAVHDRQCELGVVPLENSLHGTVGQSLDLFLSHEVFIQSELFCRISHCLLTT 231 Query: 184 ETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDM 243 ET+ D +T +YSH Q LAQC WL P + S A AA+RV E +AAI Sbjct: 232 ETSLAD-VTTVYSHPQPLAQCGGWLRQALPGARIIPADSTASAARRVGGEKGAAAIGHRS 290 Query: 244 AAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPF 303 A L GL+ LA IED+P N TRF++IG G DKTS++ S+ ++PGAL E+L Sbjct: 291 LAALLGLNILARGIEDQPDNWTRFVVIGPAPAGQPGTDKTSMLFSVPDRPGALAEVLNLL 350 Query: 304 HSNGIDLTRIETRPSRSGKWTYVFFIDC---MGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 GI++ ++E+RP R KW YVFF+D +G+ + + L ++ H L++LGSY Sbjct: 351 AREGINMKKLESRPLRGEKWKYVFFVDVECDLGNEDYGRVVHELRRLCH---TLRILGSY 407 Query: 361 P 361 P Sbjct: 408 P 408 Lambda K H 0.319 0.133 0.390 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: 343 Number of extensions: 11 Number of successful extensions: 2 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: 365 Length of database: 418 Length adjustment: 31 Effective length of query: 334 Effective length of database: 387 Effective search space: 129258 Effective search space used: 129258 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