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_089323438.1 CHB58_RS07210 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_900188395.1:WP_089323438.1 Length = 360 Score = 306 bits (784), Expect = 6e-88 Identities = 164/359 (45%), Positives = 234/359 (65%), Gaps = 9/359 (2%) Query: 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66 L+ LR ID +D +I+DL+S RA+ A EV VK + + FY PEREA +L + E Sbjct: 4 LEELRKEIDGIDRQIIDLLSRRAKLASEVGEVK-----RKKGLPFYVPEREAEILTKLEE 58 Query: 67 LNK--GPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 LNK G L E + +FREI+S+C ALE+P +V++LGP TF+ AALKHFG S +PM Sbjct: 59 LNKNYGVLPPESIRAIFREIISACRALEEPTKVSFLGPYATFTHLAALKHFGTSSDLRPM 118 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 +I +VF EV G V++GVVPVENS EG VN+T+D FL+ ++ ICGE+ + ++ HLL E Sbjct: 119 TSITDVFEEVDKGRVDYGVVPVENSIEGIVNYTVDMFLDTELKICGEIFVPVNLHLLSRE 178 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244 T+ + I ++YSH ++AQ +KWL + P+ E + VSS A AA+ E AAIA + A Sbjct: 179 TS-LENIEKVYSHRHAIAQAKKWLAENLPDAEVIEVSSTAKAAELASKEKGVAAIASEAA 237 Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQE-VPPTGDDKTSIIVSMRNKPGALHELLMPF 303 A LY L+ L I++ N TRF ++G ++ PTG+DKTSI+ S ++ GAL L PF Sbjct: 238 ALLYDLNILERNIQEISKNFTRFFVVGKKDSETPTGNDKTSIMFSTKHVAGALFHALKPF 297 Query: 304 HSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPK 362 ++LT+IE+RP++ W YVFF+D GH +P +K LE++ + +K+LGSYPK Sbjct: 298 ALYDVNLTKIESRPTKKRPWEYVFFVDIDGHKTEPRVKKALEEVAKDTSFMKILGSYPK 356 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: 315 Number of extensions: 15 Number of successful extensions: 5 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: 360 Length adjustment: 29 Effective length of query: 336 Effective length of database: 331 Effective search space: 111216 Effective search space used: 111216 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: 49 (23.5 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