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_012473995.1 CPHAMN1_RS02740 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000020545.1:WP_012473995.1 Length = 279 Score = 155 bits (392), Expect = 1e-42 Identities = 97/275 (35%), Positives = 143/275 (52%), Gaps = 16/275 (5%) Query: 97 VAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNH 156 VAY G G +S+ AAL+ FG P + DE F V +V+ V+P+ENS G+++H Sbjct: 6 VAYQGEPGAYSEIAALR-FGDPA---PFESFDEAFYAVEHRSVSCAVIPIENSLGGSIHH 61 Query: 157 TLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVE 216 D L+H + I E + + H LL ++ ++ SH Q+L+QCRK+ +H N++ Sbjct: 62 NYDLLLQHPVRIVAETFVSVEHCLLGLPGASEEKKGKVLSHPQALSQCRKFFASHN-NLK 120 Query: 217 RVAVSSNADAAKRVKSEWNSA--AIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQE 274 A +AK + E N A AIA A +LYGL E + D N TRF I ++ Sbjct: 121 PEVAYDTAGSAKVIAEERNPAHFAIASKRAGELYGLKIFRENLADEEWNITRFFCITHED 180 Query: 275 ---------VPPTGDDKTSIIVSMRNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTY 325 P T KTSI+ ++ N+PG+L + IDLT+IE+RPS+ + Y Sbjct: 181 HTTELELRTAPDTARQKTSIVFTLPNEPGSLFRAMATLALRDIDLTKIESRPSKLKAFEY 240 Query: 326 VFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 F++D +G D I N L + A +KVLGSY Sbjct: 241 FFYVDFIGSQSDATIHNALTHLREFATMVKVLGSY 275 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: 234 Number of extensions: 16 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: 279 Length adjustment: 28 Effective length of query: 337 Effective length of database: 251 Effective search space: 84587 Effective search space used: 84587 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