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_013722033.1 ALIDE2_RS09890 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000204645.1:WP_013722033.1 Length = 366 Score = 173 bits (438), Expect = 1e-47 Identities = 123/369 (33%), Positives = 190/369 (51%), Gaps = 38/369 (10%) Query: 265 SIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTTL 324 ++ +LR I S+D +L+L+ +R A Q+ +K G P D + + ++ Sbjct: 10 ALADLRVQIDSLDHQLLQLVNQRARVAEQVGELKKREGTPFFRPDRVAQVIEKIQGA--- 66 Query: 325 NPVKLKE-----IFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVP 377 NP LK I+ IMS LA E +VA VLGP+G+F E+ A++ G Sbjct: 67 NPGPLKNAHVAAIWREIMSACLALESPQRVA-------VLGPEGTFCEQAAIEYFGGAAD 119 Query: 378 LRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCL 437 L YC++ DE+ +G YG+V +ENS G V +D L+ V GE L + H L Sbjct: 120 LMYCNSFDEVFHATAAGSAQYGVVGVENSNEGVVTRSLDMFLHTPCHVVGEVSLLIRHNL 179 Query: 438 VAKRKIELKE-IKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARM--LDDYSAAI 494 + R + E I+ + +HPQA+AQC ++ +LP R +S ++ AR+ + A I Sbjct: 180 L--RSVNSAEGIEAVLAHPQALAQCHAWLAKHLPHAERRPVSSNAEGARLAATNPAWAGI 237 Query: 495 MSENAARFYRLHVLRKGIQDLKGRNITRFYLI--------RRRSGRSEGKITSLFFGVED 546 SE AA+ Y LHV+ IQD N TRF +I +GR TSL V + Sbjct: 238 SSERAAQQYGLHVVAHAIQD-DAYNRTRFAIICLPHTLATPAPTGRD---CTSLIISVPN 293 Query: 547 KPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVT 602 +PGA+ D+L K G ++ + ESRPA TG +Y F++++E E + L +L+Q+ Sbjct: 294 RPGAVHDLLVPLKKHGVSMTRFESRPARTGQWEYYFYIDLEGHPAEANVAAALAELQQLC 353 Query: 603 TFYKVVGVF 611 FYK++G + Sbjct: 354 AFYKLLGTY 362 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: 391 Number of extensions: 21 Number of successful extensions: 5 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: 366 Length adjustment: 33 Effective length of query: 587 Effective length of database: 333 Effective search space: 195471 Effective search space used: 195471 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