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_086508931.1 BZY95_RS05310 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_002151265.1:WP_086508931.1 Length = 363 Score = 181 bits (460), Expect = 4e-50 Identities = 113/342 (33%), Positives = 195/342 (57%), Gaps = 17/342 (4%) Query: 260 TKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKM--ERGEPIELKDVEEEKLWE 317 T +++ LR I ID+ ILRLI R + A+Q+A +K ++G + E + L Sbjct: 2 TDSPNNLDTLRQRIDEIDNDILRLISARAECAKQVAEVKTKSDKGAVFYRPEREAQVLRR 61 Query: 318 VM--SKTTLNPVKLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVG 373 +M ++ LN ++ +F IMS LA E+ KVA LGP+G+F+++ ALK G Sbjct: 62 IMELNQGPLNSEEMARLFREIMSACLALEQPTKVA-------YLGPEGTFTQQAALKHFG 114 Query: 374 SRVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEV 433 + DE+ + VE+G V+YG+VP+ENS G V +D+ ++ + + GE L + Sbjct: 115 QSAVSMPMAAIDEVFREVEAGAVNYGVVPVENSTEGVVSHTLDSFMDSSIRICGEVVLRI 174 Query: 434 NHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYS 491 +H L+ ++ +YSHPQ++AQC +++ + P +S ++AA+M+ + +S Sbjct: 175 HHHLLVADTTLRDKVSRVYSHPQSLAQCRKWLDAHYPRAERVPVSSNAEAAKMIKGEWHS 234 Query: 492 AAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGA 550 AAI + AA+ Y L + + I+D + N TRF +I + G+ TS+ + ++PGA Sbjct: 235 AAIAGDMAAKLYGLEKVAEKIED-RPDNSTRFLIIGSQHVPMSGEDKTSIVVAMRNQPGA 293 Query: 551 LKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLRE 592 L ++LE FH+ +L +LE+RP+ TG+ +YVFF++ + + E Sbjct: 294 LHELLEPFHRHSIDLTRLETRPSRTGVWNYVFFIDFKGHVDE 335 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: 444 Number of extensions: 27 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: 363 Length adjustment: 33 Effective length of query: 587 Effective length of database: 330 Effective search space: 193710 Effective search space used: 193710 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