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_038205557.1 Q392_RS09585 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000745855.1:WP_038205557.1 Length = 373 Score = 171 bits (433), Expect = 5e-47 Identities = 116/367 (31%), Positives = 184/367 (50%), Gaps = 24/367 (6%) Query: 260 TKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVM 319 + ++ + ELR I ++D +L+L+ R A + +K G P D + + +V Sbjct: 12 SSSSDPLAELRQRIDTLDDQLLKLLNERARVAELVGEVKKREGTPFFRPDRVAQVIEKVK 71 Query: 320 SKTT--LNPVKLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSR 375 T L + I+ IMS LA E +VA VLGP+G+F E+ A++ G Sbjct: 72 RNNTGPLREAHVAAIWREIMSACLALESPQRVA-------VLGPEGTFCEQAAIEYFGGA 124 Query: 376 VPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNH 435 L +C++ DE+ SG YG+V +ENS G V +D L V GE L V H Sbjct: 125 ADLIHCASFDEVFHATASGSAQYGVVGVENSNEGVVTRSLDMFLQSPTHVVGEVSLLVRH 184 Query: 436 CLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAA 493 L+ +R+ L+ I+ + +HPQA+AQC ++ +LP R +S ++ AR+ + A Sbjct: 185 NLL-RRENSLEGIEAVLAHPQALAQCQAWLAKHLPGAERRAVSSNAEGARLAASNPAWAG 243 Query: 494 IMSENAARFYRLHVLRKGIQDLKGRNITRFYLIR-----RRSGRSEGKITSLFFGVEDKP 548 + SE AA Y LH++ IQD N TRF +I S TSL V ++P Sbjct: 244 LASERAAAQYGLHIVAHAIQD-DAYNRTRFAVITLPATLAMPPASGHDCTSLVVSVPNRP 302 Query: 549 GALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTF 604 GA+ D+L K ++ + ESRPA TG +Y F+++++ + L +L+ + F Sbjct: 303 GAVHDLLVPLKKHNVSMTRFESRPARTGQWEYYFYIDLDGHPSQAHVAAALAELRALCAF 362 Query: 605 YKVVGVF 611 YKV+G + Sbjct: 363 YKVIGAY 369 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: 401 Number of extensions: 19 Number of successful extensions: 6 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: 373 Length adjustment: 34 Effective length of query: 586 Effective length of database: 339 Effective search space: 198654 Effective search space used: 198654 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