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_013460777.1 SULKU_RS09630 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000183725.1:WP_013460777.1 Length = 360 Score = 128 bits (322), Expect = 4e-34 Identities = 102/349 (29%), Positives = 172/349 (49%), Gaps = 19/349 (5%) Query: 264 ESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEE---EKLWEVMS 320 +S+EE R I ID+ ++ L+ RR++ R++ IK E I + E+ ++L ++ Sbjct: 2 KSLEECRARIDEIDNEVVDLLNRRMEVVRRVGEIKHESNSAIYRPEREKAIIDRLTKISE 61 Query: 321 KT--TLNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPL 378 + LN ++ +F I ++A+ E + IA LGP+GSF+ + A G+ Sbjct: 62 SSGGLLNSQAIEAVFLEIFAVARNLE-----LPERIAYLGPEGSFTHQAAESRFGAMSDY 116 Query: 379 RYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLV 438 + + + K +E+ +G+VPIENS +G V +D L V++ E + + H Sbjct: 117 LSLGSIEAVFKTLEASRAKFGVVPIENSRDGVVGETLDLLGKSSVKIVAELYMPI-HMAF 175 Query: 439 AKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML---DDYSAAIM 495 A + ++ IK IYS + QC F+ + V ++ A +L D +AAI Sbjct: 176 ATKAEKIHHIKRIYSKDKGFGQCREFLTEHGLDVVEHIPVESTAKAAILAAKDPEAAAIC 235 Query: 496 SENAARFYRLHVLRKGIQDLKGRNITRFYLIRR-RSGRSEGKITSLFFGVED--KPGALK 552 S AA+ Y + L + I+D N TRF+++ ++G S TS+ ++D K GAL Sbjct: 236 SHIAAKLYGVPTLFENIEDTH-NNATRFFILSDFKNGISGEDKTSILVRLKDAQKAGALV 294 Query: 553 DVLEVFHKKGFNLRKLESRPAGTGLG-DYVFFVEVEAPLREEDLLDLKQ 600 LE F+ NL K+ESRP+ G Y FF++ + E + L Q Sbjct: 295 HFLEDFNNADINLSKIESRPSRDNDGFGYWFFIDFFGHIDEPKIQSLIQ 343 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: 423 Number of extensions: 22 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: 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