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 WP_041098943.1 SUTH_RS09880 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000828635.1:WP_041098943.1 Length = 360 Score = 161 bits (407), Expect = 5e-44 Identities = 117/361 (32%), Positives = 183/361 (50%), Gaps = 22/361 (6%) Query: 263 AESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKT 322 + + +LR I +ID +LRLI R AR+I IK I + E + L V + Sbjct: 5 SHELGQLRDGIDAIDGDLLRLINERAKLARRIGEIKQGN---IYRPEREAQVLRRVAERN 61 Query: 323 T--LNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRY 380 L+ + I +MS E + TIA LGP G++SE A K G L Sbjct: 62 PGPLSAAAAQRIVREVMSACLALEQPL-----TIAYLGPAGTYSESAARKHFGGAPTLLP 116 Query: 381 CSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAK 440 C D++ +++ESG YG+VPIENS G + +D LL+ +++ GE L ++H L+ Sbjct: 117 CPAIDDVFRVIESGNAHYGVVPIENSTEGAIGRSLDLLLSSPLQICGEINLPIHHNLMT- 175 Query: 441 RKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSEN 498 R L ++ IYSH Q++AQC ++N LP V S ++AAR+ + +AA+ + Sbjct: 176 RCATLADVTRIYSHAQSLAQCHEWLNRNLPLVPRVPVASNAEAARLAAGEAGAAAVAGDA 235 Query: 499 AARFYRLHVLRKGIQDLKGRNITRFYLIRRR-SGRSEGKITSLFFGVEDKPGALKDVLEV 557 AA Y L ++ I+D N TRF ++ +G S TSL +++PGA+ +L Sbjct: 236 AAELYALPIIAASIED-DPNNTTRFVIVAEHDAGVSGSDRTSLVCSAQNRPGAVYQLLAP 294 Query: 558 FHKKGFNLRKLESRPA---GTGLGDYVFFVEVEA----PLREEDLLDLKQVTTFYKVVGV 610 F G ++ +LESRPA G +YVF++++E P L +L+ F K +G Sbjct: 295 FADNGVSMSRLESRPARGFGGSRWEYVFYIDIEGHRSEPAVARALEELRHRAGFVKELGS 354 Query: 611 F 611 + Sbjct: 355 Y 355 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: 416 Number of extensions: 22 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: 620 Length of database: 360 Length adjustment: 33 Effective length of query: 587 Effective length of database: 327 Effective search space: 191949 Effective search space used: 191949 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