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_078715825.1 B5D49_RS01230 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_900167125.1:WP_078715825.1 Length = 372 Score = 147 bits (370), Expect = 1e-39 Identities = 105/330 (31%), Positives = 168/330 (50%), Gaps = 13/330 (3%) Query: 269 LRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLW--EVMSKTTLNP 326 +R I ++D IL L+ +R + + ++ R K EPI E+E + +V++ L Sbjct: 18 MRERIDALDEAILDLLNQRAEVSLEVGRHKAGSAEPIFKPRREKEVITRLQVLNPGPLPD 77 Query: 327 VKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYCSTTDE 386 L I+ IMS ++ + + LGP+G+FS ++ +G L S E Sbjct: 78 RHLYSIYREIMSSSRRLQRPER-----VVYLGPEGTFSYFAGIEFMGHMAELTPKSNLGE 132 Query: 387 IIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKRKIELK 446 + + V G + G+VP+ENS+ GTV +D + + V V E ++H L+A L Sbjct: 133 VFRAVAEGGAELGIVPLENSLQGTVGQTVDLFMRYPVFVQAELYSRISHALLAAVP-GLG 191 Query: 447 EIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARM---LDDYSAAIMSENAARFY 503 + +YSH +A+ QC ++ LP +ST+ AAR+ D SA + A + Sbjct: 192 HVTRVYSHSKALGQCGEWLEANLPEAPRLPMSSTAAAARLARDAGDGSAVVGHVRLAELF 251 Query: 504 RLHVLRKGIQDLKGRNITRFYLIRRRSGR-SEGKITSLFFGVEDKPGALKDVLEVFHKKG 562 L+VL + ++DL N TRF +I G+ E +S+ F D+PGAL VLE+F ++G Sbjct: 252 GLNVLAEHLEDLPD-NWTRFLVIAPAPGQEKERDKSSILFTTPDRPGALGTVLEIFSRRG 310 Query: 563 FNLRKLESRPAGTGLGDYVFFVEVEAPLRE 592 NL KLESRP+ YVFF ++E L + Sbjct: 311 VNLSKLESRPSRGERWKYVFFADLECDLAD 340 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: 424 Number of extensions: 18 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: 372 Length adjustment: 34 Effective length of query: 586 Effective length of database: 338 Effective search space: 198068 Effective search space used: 198068 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