Align Arogenate dehydratase 2; PhADT2; Prephenate dehydratase ADT3; EC 4.2.1.91; EC 4.2.1.51 (characterized)
to candidate WP_012991967.1 THAL_RS04735 prephenate dehydratase
Query= SwissProt::D3U716 (394 letters) >NCBI__GCF_000025605.1:WP_012991967.1 Length = 363 Score = 154 bits (389), Expect = 4e-42 Identities = 102/288 (35%), Positives = 163/288 (56%), Gaps = 28/288 (9%) Query: 107 LRVAYQGVRGAYSESAAEKAYP-NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSI 165 ++VAY G + ++ AA + + + + +P F+ VE D V+P+EN+ G + Sbjct: 91 IKVAYLGPKATFTHQAASEYFGLSAQYIPAPSIRDVFQEVETDRADYGVVPVENTTEGVV 150 Query: 166 HRNYDLLLRHRLHIVGEVKLAIRHCLLANNGVKIEDLKRVLSHPQALAQC----ENNLTK 221 + D+ L L IVGE+ + IR LL+ I +K+V SH QALAQC E N+ Sbjct: 151 NYTLDMFLESDLRIVGEIVIPIRLHLLSTC-TDISQIKKVFSHRQALAQCRMWLEKNMPW 209 Query: 222 LGLVREAVDDTAGAAKYIAFQQLKDAGAVASLAAARIYGLNVLAQDIQDDSDNVTRFLML 281 + L+ + TA A + IA ++ + + A+AS AA Y L+VLA++IQD+ +N TRFL++ Sbjct: 210 VDLIE--TESTARACE-IALEE-EASSAIASEVAAYTYHLHVLAENIQDNPNNYTRFLVI 265 Query: 282 AREPIIP-GTDKPFKTSVVFSLDEGPGVLFKALAVFAMRNINLTKIESRPLQKQALRVLD 340 + + G DK TS++F++ + PG L++AL F + N+NLTKIESRP +K+A Sbjct: 266 GKRSMKKTGKDK---TSLIFAVKDEPGALYRALESFYLYNVNLTKIESRPSKKKA----- 317 Query: 341 DSADGFPKYFPYLFYVDFEASMADQRAQNALGHLKEFATFLRVLGSYP 388 + Y+F+VD E D+ + A+ LK +++LGSYP Sbjct: 318 ---------WDYVFFVDLEGHTEDEHVREAIELLKSRTQMVKLLGSYP 356 Lambda K H 0.318 0.133 0.382 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: 300 Number of extensions: 13 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: 394 Length of database: 363 Length adjustment: 30 Effective length of query: 364 Effective length of database: 333 Effective search space: 121212 Effective search space used: 121212 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 (21.7 bits) S2: 50 (23.9 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