Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate 200542 SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file)
Query= BRENDA::P39912 (358 letters) >FitnessBrowser__MR1:200542 Length = 671 Score = 94.7 bits (234), Expect = 6e-24 Identities = 62/203 (30%), Positives = 106/203 (52%), Gaps = 20/203 (9%) Query: 128 VESYEQVAEVAAAAKKQGIKILRGGAFKPRTSPYDFQGLGVEGLQIL----------KRV 177 +ES A +A +A + IK L+ FQ + +EG Q L ++ Sbjct: 453 LESSHAAAHIALSAFEHKIKQLK---------EVGFQAVILEGCQQLASKEAIIPKLRQT 503 Query: 178 ADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGLAAT 237 ++DL + I A + A ++ D++ + + M N LL AG + P+ L+R A+ Sbjct: 504 LHQYDLLCVIAIEQAADMPLATEHADMLFLTGKQMFNQALLTQAGTLPIPLFLERNDMAS 563 Query: 238 ISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDVTHS 297 EF+ A E I+SQGN Q+ILC+ GIRTY A TLD++++ ++K +HLP+ ++ ++ Sbjct: 564 YEEFLAATETILSQGNQQLILCDSGIRTYNNANLPTLDLASLILIKANSHLPIVINPCYA 623 Query: 298 TGRRDLLLPTAKAALAIGADGVM 320 L+L T + + ADG++ Sbjct: 624 INEDALVLQT-QGIKQLKADGIV 645 Score = 25.8 bits (55), Expect = 0.004 Identities = 13/50 (26%), Positives = 27/50 (54%) Query: 10 RQKADELNLQILKLINERGNVVKEIGKAKEAQGVNRFDPVRERTMLNNII 59 R++ +L+ +L L+ ER + E+ ++KE D RE+ +L ++ Sbjct: 11 REQITQLDNDLLSLLAERRRLSLEVARSKEVDVRPIRDTQREKELLARLV 60 Lambda K H 0.316 0.134 0.369 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: 432 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 358 Length of database: 671 Length adjustment: 34 Effective length of query: 324 Effective length of database: 637 Effective search space: 206388 Effective search space used: 206388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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