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_013012193.1 DACET_RS14930 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000025725.1:WP_013012193.1 Length = 356 Score = 172 bits (436), Expect = 2e-47 Identities = 122/351 (34%), Positives = 183/351 (52%), Gaps = 22/351 (6%) Query: 273 IKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTTLNPVK---L 329 I +ID IL L+ +R A I IK G P+ + E+K++E ++ P L Sbjct: 11 IDTIDKEILELLNKRAKEAMSIGEIKKAEGAPLYVPS-REKKIFERLTSINSGPFPNDAL 69 Query: 330 KEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYCSTTDEI 387 K +F I+S L+ EE KV LGP+G+F+ ALK G L T E+ Sbjct: 70 KAVFREIISASLSLEEVQKVG-------YLGPEGTFTNLAALKQFGLSAELVPVRTIPEV 122 Query: 388 IKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKRKIELKE 447 VE G + +G+VP+ENS+ G V +D + +++ GE LEV H L+ R ++ + Sbjct: 123 FDNVERGRMGFGIVPVENSLEGVVNHTLDTFVTSHLKISGEIFLEVTHNLM-NRSGDIGD 181 Query: 448 IKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSENAARFYRL 505 IK IYSH QA+ QC ++ P++ ++ ST+ AA M DD +AAI SE A Y L Sbjct: 182 IKHIYSHIQAIGQCRKWLAENCPNIPVQEVESTAKAAEMASRDDSTAAIASEMAVLKYSL 241 Query: 506 HVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGALKDVLEVFHKKGFN 564 + + I+D N TRF +I G TS+ F K G+L +VL +F +K N Sbjct: 242 RFVERSIED-NSSNYTRFLIIGDFEPLPTGNDKTSIVFAAAHKAGSLYEVLSIFARKNIN 300 Query: 565 LRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKVVGVF 611 + K+ESRP+ +YVFFV+++ +E L +L + T F KV+G + Sbjct: 301 MTKIESRPSRQKAWEYVFFVDLDGHKDDEPIAEALNELIEHTAFVKVLGSY 351 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: 406 Number of extensions: 14 Number of successful extensions: 5 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: 356 Length adjustment: 33 Effective length of query: 587 Effective length of database: 323 Effective search space: 189601 Effective search space used: 189601 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