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 WP_012282983.1 HM1_RS08655 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000019165.1:WP_012282983.1 Length = 293 Score = 199 bits (507), Expect = 6e-56 Identities = 107/270 (39%), Positives = 157/270 (58%), Gaps = 6/270 (2%) Query: 97 VAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNH 156 V YLGPEGTFS+ AA F +P ++I V+ + + ++P+ENS EG +N Sbjct: 21 VGYLGPEGTFSEEAARAFFLPDTTLRPFSSISAVYEALSLWEIEAAILPLENSIEGTINQ 80 Query: 157 TLDSFLEHD-IVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNV 215 TLD +E+ + I GE+ L +H+HLLV R+ +YSH Q LAQCR++L+A PN Sbjct: 81 TLDELVENPGLFIFGELILPVHNHLLVPPGVDWTRVVEVYSHPQPLAQCRRFLEAKLPNA 140 Query: 216 ERVAVSSNADAAKRVKS----EWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIG 271 +A +S + AK+ E AA+ AA+ GL I+ RP N TRF+++G Sbjct: 141 RLIATASTVEGAKKALELTVPEAPRAAVGSAFAARRLGLQIAQSDIQSRPNNKTRFVVVG 200 Query: 272 SQEVPPTGDDKTSIIVSM-RNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYVFFID 330 Q PTG+DKTS++ S+ +++PG L+ +L F I+LTRIE+RP++ Y+FFID Sbjct: 201 RQLTEPTGNDKTSLVCSLPQDRPGGLYAILKEFAEREINLTRIESRPTKHELGQYLFFID 260 Query: 331 CMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 +GH +D + L IG +VLGSY Sbjct: 261 FVGHQRDRTVAEALNAIGQFTTLTRVLGSY 290 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: 280 Number of extensions: 13 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: 365 Length of database: 293 Length adjustment: 28 Effective length of query: 337 Effective length of database: 265 Effective search space: 89305 Effective search space used: 89305 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 Apr 10 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