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 H281DRAFT_03925 H281DRAFT_03925 chorismate mutase
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__Burk376:H281DRAFT_03925 Length = 360 Score = 325 bits (833), Expect = 1e-93 Identities = 170/359 (47%), Positives = 242/359 (67%), Gaps = 6/359 (1%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 ++LK LR RID+LD +++ L+++RA A EV VK K A +RPERE V+ + Sbjct: 7 NRLKPLRERIDALDAQLIALLNQRAAVALEVGEVK-----KHFNAPVFRPEREQQVIARL 61 Query: 65 MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 ++++GPL +E ++ ++REIM++ ALE+ ++ AYLGP GT+S+ A ++FG S+ P Sbjct: 62 QDMSEGPLASEHISAIWREIMAASRALEKTIKAAYLGPVGTYSEQAMHEYFGQSIEGLPC 121 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 +IDEVFR V AGA FGVVPVENSTEGAV+ TLD L+ + I GE+ L IHH+LL Sbjct: 122 PSIDEVFRSVEAGAAEFGVVPVENSTEGAVSRTLDLLLQTQLAIGGELALPIHHNLLTLN 181 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244 +TR+ +HAQ+LAQC++WL + P++ER AVSSNA+AA+ + AAIAGD A Sbjct: 182 GGLAG-VTRVCAHAQALAQCQRWLATNAPHLERQAVSSNAEAARMAAEDPTVAAIAGDRA 240 Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304 A YGL I+D P N TRF++IG + +G D+TS+IVS+ N+PGA+ +LL P Sbjct: 241 ATHYGLQVAYALIQDDPHNRTRFVMIGKERTGVSGHDQTSLIVSVANEPGAVFKLLEPLA 300 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363 + + +TR E+RP+R G W Y F+ID GH DP + LE++G +A LK+LGSYP+A Sbjct: 301 RHSVSMTRFESRPARVGTWEYYFYIDVEGHRDDPAVAAALEELGQKAAFLKILGSYPRA 359 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: 334 Number of extensions: 10 Number of successful extensions: 3 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 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