Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_092991511.1 BLP65_RS00430 prephenate dehydratase
Query= BRENDA::O22241 (424 letters) >NCBI__GCF_900102855.1:WP_092991511.1 Length = 360 Score = 150 bits (378), Expect = 8e-41 Identities = 104/291 (35%), Positives = 151/291 (51%), Gaps = 30/291 (10%) Query: 125 LRVAYQGVPGAYSEAAAGKAYPNC-DAIPCDQFDVAFQAVELWIADRAVLPVENSLGGSI 183 + +A+ G G +S+ A K + + P D F+ VE AD V+PVENS G++ Sbjct: 91 MTIAFLGPEGTFSQEAVLKHFGHAIKGAPQAAIDEVFREVEAGSADYGVVPVENSTEGAV 150 Query: 184 HRNYDLLLRHRLHIVGEVQIPVHHCLL----ALPGVRTDCVSRVISHPQALAQTEHSLDV 239 + DLLLR L I GEV++ +H L+ +L G+RT + SH Q+ AQ LD Sbjct: 151 NITLDLLLRTSLKICGEVELRIHDHLMSRERSLEGIRT-----IYSHAQSFAQCREWLDS 205 Query: 240 LTPHAAREAFHDTAAAAEYISANDLHDTAAVASARAAELYNLQILADGIQDDPGNVTRFL 299 P+ R A + AA +A + AAVA A AAEL+ L LA+ I+D P N TRFL Sbjct: 206 HLPNVRRVAVSSNSEAARMAAAE--NGAAAVAGATAAELFGLNRLAENIEDIPDNTTRFL 263 Query: 300 MLAREPIIPRTDRPFKTSIVFAAQEHKGTSVLFKVLSAFAFRDISLTKIESRPHHNRPLR 359 +L RE P + KTS++ +++ G LF++L A +S+T+IESRP Sbjct: 264 ILGREDTPPSGED--KTSLLVSSRNESG--ALFQLLKPLADNGVSMTRIESRP------- 312 Query: 360 VVGDGSFGTSKNFEYMFYVDFEASMAEPRAQNALAEVQEYTSFLRVLGSYP 410 +EY+F+VD E P +AL E++ S +VLGS+P Sbjct: 313 -------SRQGMWEYVFFVDLEGHREMPAVASALVELERNASLFKVLGSFP 356 Lambda K H 0.318 0.131 0.387 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: 316 Number of extensions: 17 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: 424 Length of database: 360 Length adjustment: 31 Effective length of query: 393 Effective length of database: 329 Effective search space: 129297 Effective search space used: 129297 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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