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_073036353.1 BUB04_RS01735 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_900129305.1:WP_073036353.1 Length = 374 Score = 152 bits (384), Expect = 2e-41 Identities = 115/358 (32%), Positives = 184/358 (51%), Gaps = 20/358 (5%) Query: 265 SIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDV-EEEKLWEVMSKTT 323 S+E+LR I ++D IL + RR+ QI RIK E+G ++ D EE + + + Sbjct: 6 SLEKLRRGIDALDQEILDRLNRRMRLVEQIGRIKAEKG--LDTFDPGREEAVCRRLVEAN 63 Query: 324 LNPV---KLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRY 380 P+ ++ I+ I++ +++ + + + LGP+ ++S AL + G Sbjct: 64 PGPLPAESVRAIYREILAASRKLQQPLK-----VTFLGPEWTYSHLAALSVFGHTARYVP 118 Query: 381 CSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAK 440 + ++ + G +VPIENS+ G + +D L V V GE LEV HCL + Sbjct: 119 QAALVDVFDSLCKGLSHVAVVPIENSLEGGIGQTMDLLYERPVRVVGECYLEVAHCLCS- 177 Query: 441 RKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAAR--MLDDYSAAIMSEN 498 R + I +Y+HP A+ QC +I+ +L I ST+ AAR D SAA+ + Sbjct: 178 RAADFGSIGKLYAHPHALGQCRKWISEHLRHAEIFECASTAKAAREAAADPASAALCNVK 237 Query: 499 AARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGKI-TSLFFGVEDKPGALKDVLEV 557 AA Y L VL + ++D G N TRF ++ + G TS+ F V DKPGAL VL+V Sbjct: 238 AAEHYGLSVLAERVEDHPG-NTTRFIVLGLKENTPTGDDKTSILFAVADKPGALYQVLDV 296 Query: 558 FHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREEDLLD-LKQV---TTFYKVVGVF 611 F G N+ ++ESRP Y+FF ++ +++ + D LK+ TTF+KV+G + Sbjct: 297 FTLHGLNMTRIESRPNRLHPWQYLFFADIGGHEKDKHVEDALKEAASRTTFFKVLGSY 354 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: 484 Number of extensions: 23 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: 374 Length adjustment: 34 Effective length of query: 586 Effective length of database: 340 Effective search space: 199240 Effective search space used: 199240 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 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