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 209398 DVU0462 chorismate mutase/prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >MicrobesOnline__882:209398 Length = 391 Score = 162 bits (410), Expect = 2e-44 Identities = 111/338 (32%), Positives = 182/338 (53%), Gaps = 16/338 (4%) Query: 263 AESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEP-IELKDVEEEKLWEVMSK 321 A+ ++ +R I +D +L L+ RR + ++ RIK +P I + E ++++ + Sbjct: 15 AQRLQAIRVTIDGLDRDLLALLNRRAALSLEVGRIKAT--DPGIVFRPFREREVFDNLEA 72 Query: 322 TTLNPVK---LKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPL 378 P+ L+ I+ I+S ++ + +A LGP+G+FS ++ +G + Sbjct: 73 ANEGPLPDEHLRAIWREIISSSRSLQRP-----QRVAYLGPEGTFSYFAGMEFLGRAMDY 127 Query: 379 RYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLV 438 R ++ + V + + G+VP+ENS+ GTV +D L H+V + E ++HCL+ Sbjct: 128 RPQPGLPDVFRAVHDRQCELGIVPLENSLQGTVGQSLDLFLQHEVFIQAELFCRISHCLL 187 Query: 439 AKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMS 496 L +I T+YSHPQ +AQC G++ +LP+ I T ST+ AAR + +AAI Sbjct: 188 G-TAAALADIDTVYSHPQPLAQCGGWLRAHLPNARIIPTESTAAAARRAAGEAGAAAIGH 246 Query: 497 ENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGALKDVL 555 + A L+VL +GI+D + N TRF +I +G+ TS+ F + DK GAL VL Sbjct: 247 RSLADLLGLNVLERGIED-QPDNWTRFVVIAPAPADQQGREKTSMLFSLPDKAGALAGVL 305 Query: 556 EVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREE 593 E+ ++G N++KLESRP YVFFV+VE L E Sbjct: 306 ELLAREGINMKKLESRPLRGEKWQYVFFVDVECDLGTE 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: 415 Number of extensions: 15 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: 391 Length adjustment: 34 Effective length of query: 586 Effective length of database: 357 Effective search space: 209202 Effective search space used: 209202 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: 52 (24.6 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