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 PP_1769 PP_1769 chorismate mutase/Prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >FitnessBrowser__Putida:PP_1769 Length = 367 Score = 173 bits (438), Expect = 1e-47 Identities = 120/369 (32%), Positives = 199/369 (53%), Gaps = 24/369 (6%) Query: 259 ATKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIK---MERGE-PIELKDVEEEK 314 A + ++ LR I S+D IL LI R A ++AR+K ++ GE P+ + E Sbjct: 2 ADMSEQELKALRVRIDSLDEKILELISDRARCAEEVARVKTASLKEGEKPVFYRPEREAA 61 Query: 315 LWEVMSKTTLNPV---KLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMAL 369 + + + + P+ ++ +F IMS LA EE K IA LGP+G+F++ A+ Sbjct: 62 VLKRVMERNKGPLGNEEMARLFREIMSSCLALEEPLK-------IAYLGPEGTFTQAAAM 114 Query: 370 KLVGSRVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEA 429 K G V R + DE+ + V +G V++G+VP+ENS G V +D+ L HD+ + GE Sbjct: 115 KHFGHAVISRPMAAIDEVFREVAAGAVNFGVVPVENSTEGAVSHTLDSFLEHDMVICGEV 174 Query: 430 KLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML-- 487 +L ++H L+ + I IYSH Q++AQC +++ + P+V +S ++AA+ + Sbjct: 175 ELRIHHHLLVGENTKTDSITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNAEAAKRVKG 234 Query: 488 DDYSAAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEG-KITSLFFGVED 546 + SAAI + AA Y L L + I+D + N TRF +I + G TS+ + + Sbjct: 235 EWNSAAIAGDMAANLYGLTRLAEKIED-RPDNSTRFLMIGNQEVPPTGDDKTSIIVSMSN 293 Query: 547 KPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEV----EAPLREEDLLDLKQVT 602 KPGAL ++L F++ G +L ++E+RP+ +G YVFF++ PL + L + Q Sbjct: 294 KPGALHELLVPFYQNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLIKAVLEQISQEA 353 Query: 603 TFYKVVGVF 611 KV+G + Sbjct: 354 VALKVLGSY 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: 459 Number of extensions: 26 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: 367 Length adjustment: 33 Effective length of query: 587 Effective length of database: 334 Effective search space: 196058 Effective search space used: 196058 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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