Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate HSERO_RS18430 HSERO_RS18430 chorismate mutase
Query= BRENDA::O30012 (620 letters) >FitnessBrowser__HerbieS:HSERO_RS18430 Length = 357 Score = 167 bits (423), Expect = 7e-46 Identities = 113/352 (32%), Positives = 185/352 (52%), Gaps = 16/352 (4%) Query: 269 LRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTT--LNP 326 LR I +ID+ IL L+ +R A+++ +K E P+ + E + L + L Sbjct: 9 LRQKIDAIDAQILDLLNQRARVAQEVGHVKAETNAPVFRPEREAQVLRRAADRNPGPLLG 68 Query: 327 VKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYCSTTDE 386 ++ IF +MS + E +V +A LGP+G+FSE+ + G + C + DE Sbjct: 69 ADIQTIFREVMSACRALEKRVV-----VAYLGPEGTFSEQAVYQQFGHAIEGLSCVSIDE 123 Query: 387 IIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKRKIELK 446 + + E+G D+G+VPIENS G + +D LL + + GE + V+H L+ +++ Sbjct: 124 VFRDAEAGTADFGVVPIENSSEGVINRTLDLLLQTTLTISGEVSIPVHHSLMTASG-KME 182 Query: 447 EIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSENAARFYR 504 I I +H QA+AQC ++N PS+ + S ++AARM D AAI E A + Y Sbjct: 183 GITRICAHSQALAQCNAWLNQNYPSIERQAVASNAEAARMAGEDQSVAAIAGEIAGQKYN 242 Query: 505 LHVLRKGIQDLKGRNITRFYLI-RRRSGRSEGKITSLFFGVEDKPGALKDVLEVFHKKGF 563 L + IQD N TRF +I R R+ S TS+ V +K GA+ ++L + G Sbjct: 243 LQTVNAHIQD-DPHNRTRFAVIGRLRTAPSGRDQTSIVLSVPNKAGAVYNLLAPLARHGV 301 Query: 564 NLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKVVGVF 611 ++ + ESRPA G +Y F+V++E ++E L +L+Q F+K++G + Sbjct: 302 SMTRFESRPARMGAWEYYFYVDLEGHEQDEKVAQALEELRQNAAFFKLLGSY 353 Lambda K H 0.320 0.137 0.380 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: 397 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 620 Length of database: 357 Length adjustment: 33 Effective length of query: 587 Effective length of database: 324 Effective search space: 190188 Effective search space used: 190188 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: 51 (24.3 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