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_012400150.1 BPHY_RS03735 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000020045.1:WP_012400150.1 Length = 360 Score = 158 bits (399), Expect = 4e-43 Identities = 109/359 (30%), Positives = 186/359 (51%), Gaps = 16/359 (4%) Query: 266 IEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEV--MSKTT 323 ++ LR I +ID+ ++ L+ +R A ++ +K P+ + E++ + + MS+ Sbjct: 9 LKPLRERIDAIDAQLIALLNQRAAVALEVGEVKKHFNAPVFRPEREQQVIARLQEMSEGP 68 Query: 324 LNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYCST 383 L + I+ IM+ ++ E + T A LGP G++SE+ + G + CS+ Sbjct: 69 LAGEHISAIWREIMAASRALEKNI-----TAAYLGPAGTYSEQAMHEYFGQSIEGLPCSS 123 Query: 384 TDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKRKI 443 DE+ + VE+G ++G+VPIENS G V +D LL + + GE L ++H L+ Sbjct: 124 IDEVFRSVEAGGAEFGVVPIENSTEGAVSRTLDLLLQTQLLIGGELALPIHHNLLTLNG- 182 Query: 444 ELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSENAAR 501 L + + +H QA+AQC ++ + P + + +S ++AARM D AAI + AA Sbjct: 183 GLTGVTRVCAHAQALAQCQRWLATHAPHIERQAVSSNAEAARMAADDPTIAAIAGDRAAT 242 Query: 502 FYRLHVLRKGIQDLKGRNITRFYLI-RRRSGRSEGKITSLFFGVEDKPGALKDVLEVFHK 560 Y L V IQD N TRF +I ++ +G S TSL V ++PGA+ +LE K Sbjct: 243 QYGLQVAHALIQD-DPHNRTRFVMIGKQPTGASGYDKTSLIVSVANEPGAMFKLLEPLAK 301 Query: 561 KGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKVVGVFDEVK 615 G ++ + ESRPA G +Y F++++E + L +L Q F K++G + + Sbjct: 302 HGVSMTRFESRPARVGTWEYYFYIDLEGHRDDASVSAALAELGQKADFLKILGSYPRAR 360 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: 342 Number of extensions: 20 Number of successful extensions: 3 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